Fri Jul 31 12:09:00 CDT 2015 References

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1750 entries

The LASER database: Formalizing design rules for metabolic engineering
Winkler, James D. and Halweg-Edwards, Andrea L. and Gill, Ryan T.
Metabolic Engineering Communications
2015-12-
doi:10.1016/j.meteno.2015.06.003
Toward a standard in structural genome annotation for prokaryotes
Tripp, H. James and Sutton, Granger and White, Owen and Wortman, Jennifer and Pati, Amrita and Mikhailova, Natalia and Ovchinnikova, Galina and Payne, Samuel H. and Kyrpides, Nikos C. and Ivanova, Natalia
Standards in Genomic Sciences
2015-07-25
doi:10.1186/s40793-015-0034-9
A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
Siretskiy, Alexey and Sundqvist, Tore and Voznesenskiy, Mikhail and Spjuth, Ola
GigaScience
2015-06-04
doi:10.1186/s13742-015-0058-5
Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study
Walker, Timothy M. and Kohl, Thomas A. and Omar, Shaheed V. and Hedge, Jessica and Del Ojo Elias, Carlos and Bradley, Phelim and Iqbal, Zamin and Feuerriegel, Silke and Niehaus, Katherine E. and Wilson, Daniel J. and Clifton, David A. and Kapatai, Georgia and Ip, Camilla L. C. and Bowden, Rory and Drobniewski, Francis A. and Allix-Béguec, Caroline and Gaudin, Cyril and Parkhill, Julian and Diel, Roland and Supply, Philip and Crook, Derrick W. and Smith, E. Grace and Walker, A. Sarah and Ismail, Nazir and Niemann, Stefan and Peto, Tim E. A.
The Lancet Infectious Diseases
2015-06-
doi:10.1016/s1473-3099(15)00062-6
Exascale Computing and Big Data
Reed, Daniel A. and Dongarra, Jack
Commun. ACM
2015-06-
doi:10.1145/2699414
A Bronchial Genomic Classifier for the Diagnostic Evaluation of Lung Cancer
Silvestri, Gerard A. and Vachani, Anil and Whitney, Duncan and Elashoff, Michael and Porta Smith, Kate and Ferguson, J. Scott and Parsons, Ed and Mitra, Nandita and Brody, Jerome and Lenburg, Marc E. and Spira, Avrum
N Engl J Med
2015-05-17
doi:10.1056/nejmoa1504601
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Li, Dinghua and Liu, Chi-Man M. and Luo, Ruibang and Sadakane, Kunihiko and Lam, Tak-Wah W.
Bioinformatics (Oxford, England)
2015-05-15
doi:10.1093/bioinformatics/btv033
Making Sense of Performance in Data Analytics Frameworks
Ousterhout, Kay and Rasti, Ryan and Ratnasamy, Sylvia and Shenker, Scott and Chun, Byung-Gon
12th USENIX Symposium on Networked Systems Design and Implementation (NSDI 15)
2015-05-
https://www.usenix.org/conference/nsdi15/technical-sessions/presentation/ousterhout
Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.
Bradley, Phelim and Gordon, N. Claire and Walker, Timothy M. and Dunn, Laura and Heys, Simon and Huang, Bill and Earle, Sarah and Pankhurst, Louise J. and Anson, Luke and de Cesare, Mariateresa and Piazza, Paolo and Votintseva, Antonina A. and Golubchik, Tanya and Wilson, Daniel J. and Wyllie, David H. and Diel, Roland and Niemann, Stefan and Feuerriegel, Silke and Kohl, Thomas A. and Ismail, Nazir and Omar, Shaheed V. and Smith, E. Grace and Buck, David and McVean, Gil and Walker, A. Sarah and Peto, Tim and Crook, Derrick and Iqbal, Zamin
bioRxiv
2015-04-26
doi:10.1101/018564
Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage
Merker, Matthias and Blin, Camille and Mona, Stefano and Duforet-Frebourg, Nicolas and Lecher, Sophie and Willery, Eve and Blum, Michael G. B. and Rusch-Gerdes, Sabine and Mokrousov, Igor and Aleksic, Eman and Allix-Beguec, Caroline and Antierens, Annick and Augustynowicz-Kopec, Ewa and Ballif, Marie and Barletta, Francesca and Beck, Hans P. and Barry, Clifton E. and Bonnet, Maryline and Borroni, Emanuele and Campos-Herrero, Isolina and Cirillo, Daniela and Cox, Helen and Crowe, Suzanne and Crudu, Valeriu and Diel, Roland and Drobniewski, Francis and Fauville-Dufaux, Maryse and Gagneux, Sebastien and Ghebremichael, Solomon and Hanekom, Madeleine and Hoffner, Sven and Jiao, Wei-wei and Kalon, Stobdan and Kohl, Thomas A. and Kontsevaya, Irina and Lillebaek, Troels and Maeda, Shinji and Nikolayevskyy, Vladyslav and Rasmussen, Michael and Rastogi, Nalin and Samper, Sofia and Sanchez-Padilla, Elisabeth and Savic, Branislava and Shamputa, Isdore C. and Shen, Adong and Sng, Li-Hwei and Stakenas, Petras and Toit, Kadri and Varaine, Francis and Vukovic, Dragana and Wahl, Celine and Warren, Robin and Supply, Philip and Niemann, Stefan and Wirth, Thierry
Nat Genet
2015-03-19
doi:10.1038/ng.3195
Massively parallel single-amino-acid mutagenesis
Kitzman, Jacob O. and Starita, Lea M. and Lo, Russell S. and Fields, Stanley and Shendure, Jay
Nat Meth
2015-03-05
doi:10.1038/nmeth.3223
Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs
Younsi, Reda and MacLean, Dan
Bioinformatics
2015-03-01
doi:10.1093/bioinformatics/btu706
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
Brettin, Thomas and Davis, James J. and Disz, Terry and Edwards, Robert A. and Gerdes, Svetlana and Olsen, Gary J. and Olson, Robert and Overbeek, Ross and Parrello, Bruce and Pusch, Gordon D. and Shukla, Maulik and Thomason, James A. and Stevens, Rick and Vonstein, Veronika and Wattam, Alice R. and Xia, Fangfang
Scientific Reports
2015-02-10
doi:10.1038/srep08365
Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling
Suzuki, Yo and Assad-Garcia, Nacyra and Kostylev, Maxim and Noskov, Vladimir N. and Wise, Kim S. and Karas, Bogumil J. and Stam, Jason and Montague, Michael G. and Hanly, Timothy J. and Enriquez, Nico J. and Ramon, Adi and Goldgof, Gregory M. and Richter, R. Alexander and Vashee, Sanjay and Chuang, Ray-Yuan and Winzeler, Elizabeth A. and Hutchison, Clyde A. and Gibson, Daniel G. and Smith, Hamilton O. and Glass, John I. and Venter, J. Craig
Genome Research
2015-02-05
doi:10.1101/gr.182477.114
Parente2: a fast and accurate method for detecting identity by descent
Rodriguez, Jesse M. and Bercovici, Sivan and Huang, Lin and Frostig, Roy and Batzoglou, Serafim
Genome Research
2015-02-01
doi:10.1101/gr.173641.114
DIME: A Novel Framework for De Novo Metagenomic Sequence Assembly.
Guo, Xuan and Yu, Ning and Ding, Xiaojun and Wang, Jianxin and Pan, Yi
Journal of computational biology : a journal of computational molecular cell biology
2015-02-
http://view.ncbi.nlm.nih.gov/pubmed/25684202
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
Koren, Sergey and Phillippy, Adam M.
Current Opinion in Microbiology
2015-02-
doi:10.1016/j.mib.2014.11.014
Reference-free detection of isolated SNPs
Uricaru, Raluca and Rizk, Guillaume and Lacroix, Vincent and Quillery, Elsa and Plantard, Olivier and Chikhi, Rayan and Lemaitre, Claire and Peterlongo, Pierre
Nucleic Acids Research
2015-01-30
doi:10.1093/nar/gku1187
Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach
Broin, Pilib \~A. and Smith, Terry J. and Golden, Aaron A. J.
BMC Bioinformatics
2015-01-28
doi:10.1186/s12859-015-0450-2
Fast inexact mapping using advanced tree exploration on backward search methods
Torres, Jos\~A\copyright S. and Dom\~A­nguez, Andr\~A\copyrights T. and Gim\~A\copyrightnez, Joaqu\~A­n T. and Castell\~A³, Ignacio M. and Bl\~A!`zquez, Joaqu\~A­n D. and Espert, Ignacio B.
BMC Bioinformatics
2015-01-28
doi:10.1186/s12859-014-0438-3
Extending reference assembly models
Church, Deanna M. and Schneider, Valerie A. and Steinberg, Karyn M. and Schatz, Michael C. and Quinlan, Aaron R. and Chin, Chen-Shan and Kitts, Paul A. and Aken, Bronwen and Marth, Gabor T. and Hoffman, Michael M. and Herrero, Javier and Lisandra and Durbin, Richard and Flicek, Paul
Genome Biology
2015-01-24
doi:10.1186/s13059-015-0587-3
Application of metagenomics in the human gut microbiome.
Wang, Wei-Lin L. and Xu, Shao-Yan Y. and Ren, Zhi-Gang G. and Tao, Liang and Jiang, Jian-Wen W. and Zheng, Shu-Sen S.
World journal of gastroenterology : WJG
2015-01-21
doi:10.3748/wjg.v21.i3.803
Curation, integration and visualization of bacterial virulence factors in PATRIC
Mao, Chunhong and Abraham, David and Wattam, Alice R. and Wilson, Meredith J. C. and Shukla, Maulik and Yoo, Hyun S. and Sobral, Bruno W.
Bioinformatics
2015-01-15
doi:10.1093/bioinformatics/btu631
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
McMurdie, Paul J. and Holmes, Susan
Bioinformatics
2015-01-15
doi:10.1093/bioinformatics/btu616
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
Ahn, Tae-Hyuk and Chai, Juanjuan and Pan, Chongle
Bioinformatics
2015-01-15
doi:10.1093/bioinformatics/btu641
scrm: efficiently simulating long sequences using the approximated coalescent with recombination
Staab, Paul R. and Zhu, Sha and Metzler, Dirk and Lunter, Gerton
Bioinformatics
2015-01-08
doi:10.1093/bioinformatics/btu861
Searching for repetitions in biological networks: methods, resources and tools
Panni, Simona and Rombo, Simona E.
Briefings in Bioinformatics
2015-01-01
doi:10.1093/bib/bbt084
Comparison of software packages for detecting differential expression in RNA-seq studies
Seyednasrollah, Fatemeh and Laiho, Asta and Elo, Laura L.
Briefings in Bioinformatics
2015-01-01
doi:10.1093/bib/bbt086
High-throughput DNA sequence data compression
Zhu, Zexuan and Zhang, Yongpeng and Ji, Zhen and He, Shan and Yang, Xiao
Briefings in Bioinformatics
2015-01-01
doi:10.1093/bib/bbt087
BigDataScript: a scripting language for data pipelines
Cingolani, Pablo and Sladek, Rob and Blanchette, Mathieu
Bioinformatics
2015-01-01
doi:10.1093/bioinformatics/btu595
Rational design of antibiotic treatment plans: a treatment strategy for managing evolution and reversing resistance.
Mira, Portia M. and Crona, Kristina and Greene, Devin and Meza, Juan C. and Sturmfels, Bernd and Barlow, Miriam
PloS one
2015-xx-
http://view.ncbi.nlm.nih.gov/pubmed/25946134
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Li, Dinghua and Liu, Chi-Man and Luo, Ruibang and Sadakane, Kunihiko and Lam, Tak-Wah
2014-12-23
http://arxiv.org/abs/1409.7208
Determining the quality and complexity of next-generation sequencing data without a reference genome
Anvar, Seyed Y. and Khachatryan, Lusine and Vermaat, Martijn and van Galen, Michiel and Pulyakhina, Irina and Ariyurek, Yavuz and Kraaijeveld, Ken and den Dunnen, Johan T. and de Knijff, Peter and \^a€™t Hoen, Peter A. C. and Laros, Jeroen F. J.
Genome Biology
2014-12-17
doi:10.1186/preaccept-1559595347144548
Life in a World without Microbes
Gilbert, Jack A. and Neufeld, Josh D.
PLoS Biol
2014-12-16
doi:10.1371/journal.pbio.1002020
LoRDEC: accurate and efficient long read error correction
Salmela, Leena and Rivals, Eric
Bioinformatics
2014-12-15
doi:10.1093/bioinformatics/btu538
KmerStream: streaming algorithms for k-mer abundance estimation
Melsted, P\'all and Halld\'orsson, Bjarni V.
Bioinformatics
2014-12-15
doi:10.1093/bioinformatics/btu713
Journaled string tree—a scalable data structure for analyzing thousands of similar genomes on your laptop
Rahn, René and Weese, David and Reinert, Knut
Bioinformatics
2014-12-15
doi:10.1093/bioinformatics/btu438
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
Green, Richard E. and Braun, Edward L. and Armstrong, Joel and Earl, Dent and Nguyen, Ngan and Hickey, Glenn and Vandewege, Michael W. and St. John, John A. and Capella-Gutiérrez, Salvador and Castoe, Todd A. and Kern, Colin and Fujita, Matthew K. and Opazo, Juan C. and Jurka, Jerzy and Kojima, Kenji K. and Caballero, Juan and Hubley, Robert M. and Smit, Arian F. and Platt, Roy N. and Lavoie, Christine A. and Ramakodi, Meganathan P. and Finger, John W. and Suh, Alexander and Isberg, Sally R. and Miles, Lee and Chong, Amanda Y. and Jaratlerdsiri, Weerachai and Gongora, Jaime and Moran, Christopher and Iriarte, Andrés and McCormack, John and Burgess, Shane C. and Edwards, Scott V. and Lyons, Eric and Williams, Christina and Breen, Matthew and Howard, Jason T. and Gresham, Cathy R. and Peterson, Daniel G. and Schmitz, J\"urgen and Pollock, David D. and Haussler, David and Triplett, Eric W. and Zhang, Guojie and Irie, Naoki and Jarvis, Erich D. and Brochu, Christopher A. and Schmidt, Carl J. and McCarthy, Fiona M. and Faircloth, Brant C. and Hoffmann, Federico G. and Glenn, Travis C. and Gabald\'on, Toni and Paten, Benedict and Ray, David A.
Science
2014-12-12
doi:10.1126/science.1254449
Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies
Denton, James F. and Lugo-Martinez, Jose and Tucker, Abraham E. and Schrider, Daniel R. and Warren, Wesley C. and Hahn, Matthew W.
PLoS Comput Biol
2014-12-04
doi:10.1371/journal.pcbi.1003998
Poretools: a toolkit for analyzing nanopore sequence data.
Loman, Nicholas J. and Quinlan, Aaron R.
Bioinformatics (Oxford, England)
2014-12-01
doi:10.1093/bioinformatics/btu555
Simple Parallel Biconnectivity Algorithms for Multicore Platforms
Slota, G. M. and Madduri, K.
Proc.\\ 20th IEEE Int'l. Conf.\\ on High Performance Computing (HiPC)
2014-12-
http://www.google.com/search?hl=en&site=&q=Simple Parallel Biconnectivity Algorithms for Multicore Platforms&btnG=Search
Metagenomes from two microbial consortia associated with Santa Barbara seep oil
Hawley, Erik R. and Malfatti, Stephanie A. and Pagani, Ioanna and Huntemann, Marcel and Chen, Amy and Foster, Brian and Copeland, Alexander and del Rio, Tijana G. and Pati, Amrita and Jansson, Janet R. and Gilbert, Jack A. and Tringe, Susannah G. and Lorenson, Thomas D. and Hess, Matthias
Marine Genomics
2014-12-
doi:10.1016/j.margen.2014.06.003
MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
Afiahayati and Sato, Kengo and Sakakibara, Yasubumi
DNA Research
2014-11-27
doi:10.1093/dnares/dsu041
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Inouye, Michael and Dashnow, Harriet and Raven, Lesley-Ann and Schultz, Mark B. and Pope, Bernard J. and Tomita, Takehiro and Zobel, Justin and Holt, Kathryn E.
Genome Medicine
2014-11-20
doi:10.1186/s13073-014-0090-6
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Treangen, Todd J. and Ondov, Brian D. and Koren, Sergey and Phillippy, Adam M.
Genome Biology
2014-11-19
doi:10.1186/s13059-014-0524-x
Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples
Matranga, Christian B. and Andersen, Kristian G. and Winnicki, Sarah and Busby, Michele and Gladden, Adrianne D. and Tewhey, Ryan and Stremlau, Matthew and Berlin, Aaron and Gire, Stephen K. and England, Eleina and Moses, Lina M. and Mikkelsen, Tarjei S. and Odia, Ikponmwonsa and Ehiane, Philomena E. and Folarin, Onikepe and Goba, Augustine and Kahn, S. H. and Grant, Donald S. and Honko, Anna and Hensley, Lisa and Happi, Christian and Garry, Robert F. and Malboeuf, Christine M. and Birren, Bruce W. and Gnirke, Andreas and Levin, Joshua Z. and Sabeti, Pardis C.
Genome Biology
2014-11-18
doi:10.1186/s13059-014-0519-7
EPGA: de novo assembly using the distributions of reads and insert size
Luo, Junwei and Wang, Jianxin and Zhang, Zhen and Wu, Fang-Xiang and Li, Min and Pan, Yi
Bioinformatics
2014-11-17
doi:10.1093/bioinformatics/btu762
Variable-Order de Bruijn Graphs
Boucher, Christina and Bowe, Alex and Gagie, Travis and Puglisi, Simon J. and Sadakane, Kunihiko
2014-11-17
http://arxiv.org/abs/1411.2718
SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips
Marcus, Shoshana and Lee, Hayan and Schatz, Michael C.
Bioinformatics
2014-11-13
doi:10.1093/bioinformatics/btu756
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Salter, Susannah J. and Cox, Michael J. and Turek, Elena M. and Calus, Szymon T. and Cookson, William O. and Moffatt, Miriam F. and Turner, Paul and Parkhill, Julian and Loman, Nicholas J. and Walker, Alan W.
BMC Biology
2014-11-12
doi:10.1186/s12915-014-0087-z
A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing
Schwartz, Rachel S. and Harkins, Kelly and Stone, Anne C. and Cartwright, Reed A.
2014-11-12
http://arxiv.org/abs/1305.3665
Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
Salipante, Stephen J. and Roach, David J. and Kitzman, Jacob O. and Snyder, Matthew W. and Stackhouse, Bethany and Butler-Wu, Susan M. and Lee, Choilee and Cookson, Brad T. and Shendure, Jay
Genome Research
2014-11-04
doi:10.1101/gr.180190.114
Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network
Rustad, Tige R. and Minch, Kyle J. and Ma, Shuyi and Winkler, Jessica K. and Hobbs, Samuel and Hickey, Mark and Brabant, William and Turkarslan, Serdar and Price, Nathan D. and Baliga, Nitin S. and Sherman, David R.
Genome Biology
2014-11-03
doi:10.1186/s13059-014-0502-3
Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph
Vandervalk, Benjamin P. and Jackman, Shaun D. and Raymond, Anthony and Mohamadi, Hamid and Yang, Chen and Attali, Dean A. and Chu, Justin and Warren, Rene L. and Birol, Inanc
Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on
2014-11-
doi:10.1109/bibm.2014.6999126
Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly
Georganas, E. and Buluc, A. and Chapman, J. and Oliker, L. and Rokhsar, D. and Yelick, K.
High Performance Computing, Networking, Storage and Analysis, SC14: International Conference for
2014-11-
doi:10.1109/sc.2014.41
Slim Fly: A Cost Effective Low-Diameter Network Topology
Besta, M. and Hoefler, T.
2014-11-
http://www.google.com/search?hl=en&site=&q=Slim Fly: A Cost Effective Low-Diameter Network Topology&btnG=Search
The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility.
Kos, Veronica N. and Déraspe, Maxime and McLaughlin, Robert E. and Whiteaker, James D. and Roy, Paul H. and Alm, Richard A. and Corbeil, Jacques and Gardner, Humphrey
Antimicrobial agents and chemotherapy
2014-11-
doi:10.1128/AAC.03954-14
Fast and sensitive protein alignment using DIAMOND.
Buchfink, Benjamin and Xie, Chao and Huson, Daniel H.
Nature methods
2014-11-
doi:10.1038/nmeth.3176
SketchBio: a scientist\^a€™s 3D interface for molecular modeling and animation
Waldon, Shawn M. and Thompson, Peter M. and Hahn, Patrick J. and Russell, M.
BMC Bioinformatics
2014-10-30
doi:10.1186/1471-2105-15-334
Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads
Moncunill, Valenti and Gonzalez, Santi and Bea, Silvia and Andrieux, Lise O. and Salaverria, Itziar and Royo, Cristina and Martinez, Laura and Puiggros, Montserrat and Segura-Wang, Maia and Stutz, Adrian M. and Navarro, Alba and Royo, Romina and Gelpi, Josep L. and Gut, Ivo G. and Lopez-Otin, Carlos and Orozco, Modesto and Korbel, Jan O. and Campo, Elias and Puente, Xose S. and Torrents, David
Nature Biotechnology
2014-10-26
doi:10.1038/nbt.3027
GATB: Genome Assembly & Analysis Tool Box
Drezen, Erwan and Rizk, Guillaume and Chikhi, Rayan and Deltel, Charles and Lemaitre, Claire and Peterlongo, Pierre and Lavenier, Dominique
Bioinformatics
2014-10-15
doi:10.1093/bioinformatics/btu406
Science is innate!
Gilbert, Jack A.
Genome Biology
2014-10-02
doi:10.1186/s13059-014-0477-0
Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs
Scholz, Matthew and Lo, Chien-Chi and Chain, Patrick S. G.
Scientific Reports
2014-10-01
doi:10.1038/srep06480
Workload characterization for MG-RAST metagenomic data analytics service in the cloud
Tang, Wei and Bischof, Jared and Desai, Narayan and Mahadik, Kanak and Gerlach, Wolfgang and Harrison, Travis and Wilke, Andreas and Meyer, Folker
Big Data (Big Data), 2014 IEEE International Conference on
2014-10-
doi:10.1109/bigdata.2014.7004394
PULP: Scalable Multi-Objective Multi-Constraint Partitioning for Small-World Networks
Slota, G. M. and Madduri, K. and Rajamanickam, S.
Proc.\\ 2nd IEEE Int'l. Conf. on Big Data (BigData)
2014-10-
http://www.google.com/search?hl=en&site=&q=PULP: Scalable Multi-Objective Multi-Constraint Partitioning for Small-World Networks&btnG=Search
A massively parallel algorithm for constructing the BWT of large string sets
Pantaleoni, Jacopo
2014-10-
http://arxiv.org/abs/1410.0562
Does evolutionary theory need a rethink?
Laland, Kevin and Uller, Tobias and Feldman, Marc and Sterelny, Kim and M\"uller, Gerd B. and Moczek, Armin and Jablonka, Eva and Odling-Smee, John and Wray, Gregory A. and Hoekstra, Hopi E. and Futuyma, Douglas J. and Lenski, Richard E. and Mackay, Trudy F. C. and Schluter, Dolph and Strassmann, Joan E.
Nature
2014-10-
doi:10.1038/514161a
Alignathon: A competitive assessment of whole genome alignment methods
Earl, D. and Nguyen, N. K. and Hickey, G. and Harris, R. S. and Fitzgerald, S. and Beal, K. and Seledtsov, I. and Molodtsov, V. and Raney, B. and Clawson, H. and Kim, J. and Kemena, C. and Chang, J. M. and Erb, I. and Poliakov, A. and Hou, M. and Herrero, J. and Solovyev, V. and Darling, A. E. and Ma, J. and Notredame, C. and Brudno, M. and Dubchak, I. and Haussler, D. and Paten, B.
Genome Research
2014-10-
doi:10.1101/gr.174920.114
SAGE: String-overlap Assembly of GEnomes
Ilie, Lucian and Haider, Bahlul and Molnar, Michael and Solis-Oba, Roberto
BMC Bioinformatics
2014-09-15
doi:10.1186/1471-2105-15-302
String graph construction using incremental hashing.
Ben-Bassat, Ilan and Chor, Benny
Bioinformatics (Oxford, England)
2014-09-02
doi:10.1093/bioinformatics/btu578
TRAM: Optimizing Fine-grained Communication with Topological Routing and Aggregation of Messages
Wesolowski, Lukasz and Venkataraman, Ramprasad and Gupta, Abhishek and Yeom, Jae-Seung and Bisset, Keith and Sun, Yanhua and Jetley, Pritish and Quinn, Thomas R. and Kale, Laxmikant V.
Proceedings of the International Conference on Parallel Processing
2014-09-
http://www.google.com/search?hl=en&site=&q=TRAM: Optimizing Fine-grained Communication with Topological Routing and Aggregation of Messages&btnG=Search
Binning metagenomic contigs by coverage and composition
Alneberg, Johannes and Bjarnason, Brynjar S. and de Bruijn, Ino and Schirmer, Melanie and Quick, Joshua and Ijaz, Umer Z. and Lahti, Leo and Loman, Nicholas J. and Andersson, Anders F. and Quince, Christopher
Nature Methods
2014-09-
doi:10.1038/nmeth.3103
Cancer genomics: one cell at a time
Navin, Nicholas E.
Genome Biology
2014-08-30
doi:10.1186/s13059-014-0452-9
Which is more important for classifying microbial communities: who's there or what they can do?
Xu, Zhenjiang and Malmer, Daniel and Langille, Morgan G. I. and Way, Samuel F. and Knight, Rob
The ISME Journal
2014-08-29
doi:10.1038/ismej.2014.157
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters
Chu, Justin and Sadeghi, Sara and Raymond, Anthony and Jackman, Shaun D. and Nip, Ka M. and Mar, Richard and Mohamadi, Hamid and Butterfield, Yaron S. and Robertson, A. Gordon and Birol, Inan\cc
Bioinformatics
2014-08-20
doi:10.1093/bioinformatics/btu558
Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes
Chewapreecha, Claire and Marttinen, Pekka and Croucher, Nicholas J. and Salter, Susannah J. and Harris, Simon R. and Mather, Alison E. and Hanage, William P. and Goldblatt, David and Nosten, Francois H. and Turner, Claudia and Turner, Paul and Bentley, Stephen D. and Parkhill, Julian
PLoS Genet
2014-08-07
doi:10.1371/journal.pgen.1004547
Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions.
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Genome Biology
2014-07-30
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Satellite remote sensing data can be used to model marine microbial metabolite turnover
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Genome Biology
2014-07-25
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DBSecSys: a database of Burkholderia mallei secretion systems
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BMC Bioinformatics
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BMC Bioinformatics
2014-07-16
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Bioinformatics (Oxford, England)
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Biocellion: accelerating computer simulation of multicellular biological system models.
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Bioinformatics (Oxford, England)
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Bioinformatics (Oxford, England)
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A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
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Nature Communications
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KMC 2: Fast and resource-frugal \$k\$-mer counting
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A statistical approach for inferring the 3D structure of the genome
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Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.
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2014-06-
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Bioinformatics (Oxford, England)
2014-06-
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A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
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Bioinformatics (Oxford, England)
2014-06-
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Ragout—a reference-assisted assembly tool for bacterial genomes
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Omega: an Overlap-graph de novo Assembler for Metagenomics.
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Bioinformatics (Oxford, England)
2014-06-
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Nonhuman genetics. Genomic basis for the convergent evolution of electric organs.
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Science (New York, N.Y.)
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Horizontal genome transfer as an asexual path to the formation of new species.
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Bioinformatics (Oxford, England)
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AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
Bao, Ergude and Jiang, Tao and Girke, Thomas
Bioinformatics
2014-06-
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Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
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Genome Research
2014-06-
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A Performance Model for the Communication in Fast Multipole Methods on HPC Platforms
Ibeid, Huda and Yokota, Rio and Keyes, David
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Reference-free SNP detection: dealing with the data deluge
Leggett, Richard M. and MacLean, Dan
BMC Genomics
2014-05-20
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SparkSeq: fast, scalable, cloud-ready tool for the interactive genomic data analysis with nucleotide precision
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HiPGA: A High Performance Genome Assembler for Short Read Sequence Data
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PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
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Bioinformatics
2014-05-
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New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing
Song, Kai and Ren, Jie and Reinert, Gesine and Deng, Minghua and Waterman, Michael S. and Sun, Fengzhu
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2014-05-
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Exploring genome characteristics and sequence quality without a reference
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Silverbush, Dana and Sharan, Roded
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Neurobiology: To care or not to care
Rodriguez, Ivan
Nature
2014-05-
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Fecal transplantation poses dilemma for FDA
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Nature Biotechnology
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Victim Selection and Distributed Work Stealing Performance: A Case Study
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Bio Simulators: a web UI for biological simulation.
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The ctenophore genome and the evolutionary origins of neural systems
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Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models
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2014-05-
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A semi-synthetic organism with an expanded genetic alphabet
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2014 IEEE 28th International Parallel and Distributed Processing Symposium
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Sensory biology: Radio waves zap the biomagnetic compass
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How Well Do Graph-Processing Platforms Perform? An Empirical Performance Evaluation and Analysis
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2014 IEEE 28th International Parallel and Distributed Processing Symposium
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Nat Meth
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Traversing Trillions of Edges in Real Time: Graph Exploration on Large-Scale Parallel Machines
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2014-05-
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Genome Biology
2014-04-28
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2014-04-07
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bioRxiv
2014-04-
doi:10.1101/004507
Restless Legs Syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon
Spieler, Derek and Kaffe, Maria and Knauf, Franziska and Bessa, José and Tena, Juan J. and Giesert, Florian and Schormair, Barbara and Tilch, Erik and Lee, Heekyoung and Horsch, Marion and Czamara, Darina and Karbalai, Nazanin and von Toerne, Christine and Waldenberger, Melanie and Gieger, Christian and Lichtner, Peter and Claussnitzer, Melina and Naumann, Ronald and M\"uller-Myhsok, Bertram and Torres, Miguel and Garrett, Lillian and Rozman, Jan and Klingenspor, Martin and Gailus-Durner, Valérie and Fuchs, Helmut and de Angelis, Martin H. and Beckers, Johannes and H\"olter, Sabine M. and Meitinger, Thomas and Hauck, Stefanie M. and Laumen, Helmut and Wurst, Wolfgang and Casares, Fernando and G\'omez-Skarmeta, Jose L. and Winkelmann, Juliane
Genome Research
2014-04-
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Turtle: Identifying frequent k-mers with cache-efficient algorithms.
Roy, Rajat S. and Bhattacharya, Debashish and Schliep, Alexander
Bioinformatics (Oxford, England)
2014-04-
doi:10.1093/bioinformatics/btu132
On the middle ground between open source and commercial software - the case of the Newbler program
Nederbragt, Alexander
Genome Biology
2014-04-
doi:10.1186/gb4173
KmerStream: Streaming algorithms for k-mer abundance estimation
Melsted, P\'all and Halld\'orsson, Bjarni V.
bioRxiv
2014-04-
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SplitMEM: Graphical pan-genome analysis with suffix skips
Marcus, Shoshana and Lee, Hayan and Schatz, Michael
bioRxiv
2014-04-
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Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples
Li, Heng
2014-04-
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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Yang and Smyth, Gordon K. and Shi, Wei
Bioinformatics
2014-04-
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Fast alignment-free sequence comparison using spaced-word frequencies.
Leimeister, Chris-Andre and Boden, Marcus and Horwege, Sebastian and Lindner, Sebastian and Morgenstern, Burkhard
Bioinformatics (Oxford, England)
2014-04-
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Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
Kajitani, Rei and Toshimoto, Kouta and Noguchi, Hideki and Toyoda, Atsushi and Ogura, Yoshitoshi and Okuno, Miki and Yabana, Mitsuru and Harada, Masahira and Nagayasu, Eiji and Maruyama, Haruhiko and Kohara, Yuji and Fujiyama, Asao and Hayashi, Tetsuya and Itoh, Takehiko
Genome Research
2014-04-
doi:10.1101/gr.170720.113
Oseltamivir for influenza in adults and children: systematic review of clinical study reports and summary of regulatory comments
Jefferson, Tom and Jones, Mark and Doshi, Peter and Spencer, Elizabeth A. and Onakpoya, Igho and Heneghan, Carl J.
BMJ : British Medical Journal
2014-04-
doi:10.1136/bmj.g2545
Reconstructing complex regions of genomes using long-read sequencing technology
Huddleston, John and Ranade, Swati and Malig, Maika and Antonacci, Francesca and Chaisson, Mark and Hon, Lawrence and Sudmant, Peter H. and Graves, Tina A. and Alkan, Can and Dennis, Megan Y. and Wilson, Richard K. and Turner, Stephen W. and Korlach, Jonas and Eichler, Evan E.
Genome Research
2014-04-
doi:10.1101/gr.168450.113
Tackling soil diversity with the assembly of large, complex metagenomes
Howe, Adina C. and Jansson, Janet K. and Malfatti, Stephanie A. and Tringe, Susannah G. and Tiedje, James M. and Brown, C. Titus
Proceedings of the National Academy of Sciences
2014-04-
doi:10.1073/pnas.1402564111
Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction
Laczny, Cedric C. and Pinel, Nicol\'as and Vlassis, Nikos and Wilmes, Paul
Scientific Reports
2014-03-31
doi:10.1038/srep04516
KAnalyze: A Fast Versatile Pipelined K-mer Toolkit
Audano, Peter and Vannberg, Fredrik
Bioinformatics
2014-03-18
doi:10.1093/bioinformatics/btu152
DIAMUND: Direct Comparison of Genomes to Detect Mutations
Salzberg, Steven L. and Pertea, Mihaela and Fahrner, Jill A. and Sobreira, Nara
Human Mutation
2014-03-01
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A CPU-GPU Hybrid Implementation and Model-Driven Scheduling of the Fast Multipole Method
Choi, J. and Chandramowlishwaran, A. and Madduri, K. and Vuduc, R.
Proc.\\ 7th Workshop on General Purpose Processing using GPUs (GPGPU)
2014-03-
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DIAMUND: direct comparison of genomes to detect mutations.
Salzberg, Steven L. and Pertea, Mihaela and Fahrner, Jill A. and Sobreira, Nara
Human mutation
2014-03-
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Harnessing Microbiota to Kill a Pathogen: Fixing the microbiota to treat Clostridium difficile infections
Taur, Ying and Pamer, Eric G.
Nature Medicine
2014-03-
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A bioinformatician's guide to the forefront of suffix array construction algorithms
Shrestha, Anish M. and Frith, Martin C. and Horton, Paul
Briefings in Bioinformatics
2014-03-
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A biochemical landscape of A-to-I RNA editing in the human brain transcriptome
Sakurai, Masayuki and Ueda, Hiroki and Yano, Takanori and Okada, Shunpei and Terajima, Hideki and Mitsuyama, Toutai and Toyoda, Atsushi and Fujiyama, Asao and Kawabata, Hitomi and Suzuki, Tsutomu
Genome Research
2014-03-
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The present and future role of microfluidics in biomedical research
Sackmann, Eric K. and Fulton, Anna L. and Beebe, David J.
Nature
2014-03-
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A survey of tools for variant analysis of next-generation genome sequencing data.
Pabinger, Stephan and Dander, Andreas and Fischer, Maria and Snajder, Rene and Sperk, Michael and Efremova, Mirjana and Krabichler, Birgit and Speicher, Michael R. and Zschocke, Johannes and Trajanoski, Zlatko
Briefings in bioinformatics
2014-03-
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The CAVE artists
Lewis, Dyani
Nature Medicine
2014-03-
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A comprehensive evaluation of assembly scaffolding tools.
Hunt, Martin and Newbold, Chris and Berriman, Matthew and Otto, Thomas D.
Genome biology
2014-03-
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Ecosystem services expand the biodiversity conservation toolbox – A response to Deli\`ege and Neuteleers
Cimon-Morin, Jér\^ome and Darveau, Marcel and Poulin, Monique
Biological Conservation
2014-03-
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Dense genomic sampling identifies highways of pneumococcal recombination
Chewapreecha, Claire and Harris, Simon R. and Croucher, Nicholas J. and Turner, Claudia and Marttinen, Pekka and Cheng, Lu and Pessia, Alberto and Aanensen, David M. and Mather, Alison E. and Page, Andrew J. and Salter, Susannah J. and Harris, David and Nosten, Francois and Goldblatt, David and Corander, Jukka and Parkhill, Julian and Turner, Paul and Bentley, Stephen D.
Nature Genetics
2014-02-9
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Characterizing Biological Networks using Subgraph counting and Enumeration
Slota, G. and Madduri, K.
2014-02-
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Illuminating the future of DNA sequencing
Watson, Mick
Genome Biology
2014-02-
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Variation Ontology for annotation of variation effects and mechanisms.
Vihinen, Mauno
Genome research
2014-02-
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Strain/species identification in metagenomes using genome-specific markers
Tu, Qichao and He, Zhili and Zhou, Jizhong
Nucleic Acids Research
2014-02-
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Phylogeny-based classification of microbial communities.
Tanaseichuk, Olga and Borneman, James and Jiang, Tao
Bioinformatics (Oxford, England)
2014-02-
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The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed
Sexton, Brittany S. and Avey, Denis and Druliner, Brooke R. and Fincher, Justin A. and Vera, Daniel L. and Grau, Daniel J. and Borowsky, Mark L. and Gupta, Shobhit and Girimurugan, Senthil B. and Chicken, Eric and Zhang, Jinfeng and Noble, William S. and Zhu, Fanxiu and Kingston, Robert E. and Dennis, Jonathan H.
Genome Research
2014-02-
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MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets
Reddy, Rachamalla M. and Mohammed, Monzoorul H. and Mande, Sharmila S.
Genomics
2014-02-
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Automated ensemble assembly and validation of microbial genomes
Koren, Sergey and Treangen, Todd J. and Hill, Christopher M. and Pop, Mihai and Phillippy, Adam M.
bioRxiv
2014-02-
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Comparative Genomics of Isolates of a Pseudomonas aeruginosa Epidemic Strain Associated with Chronic Lung Infections of Cystic Fibrosis Patients
Jeukens, Julie and Boyle, Brian and Kukavica-Ibrulj, Irena and Ouellet, Myriam M. and Aaron, Shawn D. and Charette, Steve J. and Fothergill, Joanne L. and Tucker, Nicholas P. and Winstanley, Craig and Levesque, Roger C.
PLoS ONE
2014-02-
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VAMPS: a website for visualization and analysis of microbial population structures
Huse, Susan and Welch, David M. and Voorhis, Andy and Shipunova, Anna and Morrison, Hilary and Eren, A. and Sogin, Mitchell
BMC Bioinformatics
2014-02-
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Fuel gain exceeding unity in an inertially confined fusion implosion
Hurricane, O. A. and Callahan, D. A. and Casey, D. T. and Celliers, P. M. and Cerjan, C. and Dewald, E. L. and Dittrich, T. R. and D\"oppner, T. and Hinkel, D. E. and Hopkins, L. F. Berzak and Kline, J. L. and Le Pape S. and Ma, T. and MacPhee, A. G. and Milovich, J. L. and Pak, A. and Park, H. S. and Patel, P. K. and Remington, B. A. and Salmonson, J. D. and Springer, P. T. and Tommasini, R.
Nature
2014-02-
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Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).
Durbin, Richard
Bioinformatics (Oxford, England)
2014-02-
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TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
Chen, Ken and Chen, Lei and Fan, Xian and Wallis, John and Ding, Li and Weinstock, George
Genome Research
2014-02-
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Inactivation of dairy bacteriophages by commercial sanitizers and disinfectants
Campagna, Céline and Villion, Manuela and Labrie, Simon J. and Duchaine, Caroline and Moineau, Sylvain
International Journal of Food Microbiology
2014-02-
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Scalable Parallel I/O on a Blue Gene/Q Supercomputer Using Compression, Topology-Aware Data Aggregation, and Subfiling
Bui, Huy and Finkel, Hal and Vishwanath, Venkatram and Habib, Salma and Heitmann, Katrin and Leigh, Jason and Papka, Michael and Harms, Kevin
2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing
2014-02-
doi:10.1109/PDP.2014.60
Dissemination of scientific software with Galaxy ToolShed
Blankenberg, Daniel and Von Kuster Gregory and Bouvier, Emil and Baker, Dannon and Afgan, Enis and Stoler, Nicholas and the Galaxy Team and Taylor, James and Nekrutenko, Anton
Genome Biology
2014-02-
doi:10.1186/gb4161
A Review of Hardware Acceleration for Computational Genomics
Aluru, S. and Jammula, N.
Design & Test, IEEE
2014-02-
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ITEP: An integrated toolkit for exploration of microbial pan-genomes
Benedict, Matthew N. and Henriksen, James R. and Metcalf, William W. and Whitaker, Rachel J. and Price, Nathan D.
BMC Genomics
2014-01-03
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EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.
Hunter, Sarah and Corbett, Matthew and Denise, Hubert and Fraser, Matthew and Gonzalez-Beltran, Alejandra and Hunter, Christopher and Jones, Philip and Leinonen, Rasko and McAnulla, Craig and Maguire, Eamonn and Maslen, John and Mitchell, Alex and Nuka, Gift and Oisel, Arnaud and Pesseat, Sebastien and Radhakrishnan, Rajesh and Rocca-Serra, Philippe and Scheremetjew, Maxim and Sterk, Peter and Vaughan, Daniel and Cochrane, Guy and Field, Dawn and Sansone, Susanna-Assunta A.
Nucleic acids research
2014-01-01
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Do We Need Hundreds of Classifiers to Solve Real World Classification Problems?
Delgado, Manuel F. and Cernadas, Eva and Barro, Senén and Amorim, Dinani
J. Mach. Learn. Res.
2014-01-
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PATRIC, the bacterial bioinformatics database and analysis resource.
Wattam, Alice R. and Abraham, David and Dalay, Oral and Disz, Terry L. and Driscoll, Timothy and Gabbard, Joseph L. and Gillespie, Joseph J. and Gough, Roger and Hix, Deborah and Kenyon, Ronald and Machi, Dustin and Mao, Chunhong and Nordberg, Eric K. and Olson, Robert and Overbeek, Ross and Pusch, Gordon D. and Shukla, Maulik and Schulman, Julie and Stevens, Rick L. and Sullivan, Daniel E. and Vonstein, Veronika and Warren, Andrew and Will, Rebecca and Wilson, Meredith J. and Yoo, Hyun Seung S. and Zhang, Chengdong and Zhang, Yan and Sobral, Bruno W.
Nucleic acids research
2014-01-
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An environmental bacterial taxon with a large and distinct metabolic repertoire
Wilson, Micheal C. and Mori, Tetsushi and R\"uckert, Christian and Uria, Agustinus R. and Helf, Maximilian J. and Takada, Kentaro and Gernert, Christine and Steffens, Ursula A. E. and Heycke, Nina and Schmitt, Susanne and Rinke, Christian and Helfrich, Eric J. N. and Brachmann, Alexander O. and Gurgui, Cristian and Wakimoto, Toshiyuki and Kracht, Matthias and Cr\"usemann, Max and Hentschel, Ute and Abe, Ikuro and Matsunaga, Shigeki and Kalinowski, J\"orn and Takeyama, Haruko and Piel, J\"orn
Nature
2014-01-
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A new method for modeling coalescent processes with recombination.
Wang, Ying and Zhou, Ying and Li, Linfeng and Chen, Xian and Liu, Yuting and Ma, Zhi-Ming and Xu, Shuhua
BMC bioinformatics
2014-01-
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The 3,000 rice genomes project.
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GigaScience
2014-01-
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A paleogenomic perspective on evolution and gene function: new insights from ancient DNA.
Shapiro, B. and Hofreiter, M.
Science (New York, N.Y.)
2014-01-
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Metavir 2: new tools for viral metagenome comparison and assembled virome analysis.
Roux, Simon and Tournayre, Jeremy and Mahul, Antoine and Debroas, Didier and Enault, Fran\ccois
BMC bioinformatics
2014-01-
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The role of replicates for error mitigation in next-generation sequencing
Robasky, Kimberly and Lewis, Nathan E. and Church, George M.
Nat Rev Genet
2014-01-
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Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline
Reid, Jeffrey and Carroll, Andrew and Veeraraghavan, Narayanan and Dahdouli, Mahmoud and Sundquist, Andreas and English, Adam and Bainbridge, Matthew and White, Simon and Salerno, William and Buhay, Christian and Yu, Fuli and Muzny, Donna and Daly, Richard and Duyk, Geoff and Gibbs, Richard and Boerwinkle, Eric
BMC Bioinformatics
2014-01-
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MoTeX-II: structured MoTif eXtraction from large-scale datasets.
Pissis, Solon P.
BMC bioinformatics
2014-01-
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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
Overbeek, Ross and Olson, Robert and Pusch, Gordon D. and Olsen, Gary J. and Davis, James J. and Disz, Terry and Edwards, Robert A. and Gerdes, Svetlana and Parrello, Bruce and Shukla, Maulik and Vonstein, Veronika and Wattam, Alice R. and Xia, Fangfang and Stevens, Rick
Nucleic Acids Research
2014-01-
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Efficient sequential and parallel algorithms for planted motif search
Nicolae, Marius and Rajasekaran, Sanguthevar
BMC Bioinformatics
2014-01-
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GPU-Accelerated BWT Construction for Large Collection of Short Reads
Liu, Chi-Man and Luo, Ruibang and Lam, Tak-Wah
2014-01-
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Using Genome Query Language to uncover genetic variation
Kozanitis, Christos and Heiberg, Andrew and Varghese, George and Bafna, Vineet
Bioinformatics
2014-01-
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A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA.
Huson, Daniel H. and Xie, Chao
Bioinformatics (Oxford, England)
2014-01-
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MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.
Glass, Elizabeth M. and Dribinsky, Yekaterina and Yilmaz, Pelin and Levin, Hal and Van Pelt Robert and Wendel, Doug and Wilke, Andreas and Eisen, Jonathan A. and Huse, Sue and Shipanova, Anna and Sogin, Mitch and Stajich, Jason and Knight, Rob and Meyer, Folker and Schriml, Lynn M.
The ISME journal
2014-01-
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Sequence alignment visualization in HTML5 without Java
Gille, Christoph and Birgit, Weyand and Gille, Andreas
Bioinformatics
2014-01-
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Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions
Fricke, W. Florian and Rasko, David A.
Nature Reviews Genetics
2014-01-
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Human Analysts at Superhuman Scales: What Has Friendly Software To Do?
Godzaridis, Elenie and Boisvert, Sébastien and Xia, Fangfang and Kandel, Mikhail and Behling, Steve and Long, Bill and Sosa, Carlos P. and Laviolette, Fran\ccois and Corbeil, Jacques
2014-01-
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A unified model for yeast transcript definition
de Boer, Carl G. and van Bakel, Harm and Tsui, Kyle and Li, Joyce and Morris, Quaid D. and Nislow, Corey and Greenblatt, Jack F. and Hughes, Timothy R.
Genome Research
2014-01-
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Low coverage sequencing of two Asian elephant (Elephas maximus) genomes.
Dastjerdi, Akbar and Robert, Christelle and Watson, Mick
GigaScience
2014-01-
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Informed and automated k-mer size selection for genome assembly
Chikhi, Rayan and Medvedev, Paul
Bioinformatics
2014-01-
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Frontiers in biology
Cesari, Francesca and Chou, I-han and Eggleston, Angela K. and Gray, Noah and Nath, Deepa and Shadan, Sadaf and Skipper, Magdalena
Nature
2014-01-
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Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
Battle, Alexis and Mostafavi, Sara and Zhu, Xiaowei and Potash, James B. and Weissman, Myrna M. and McCormick, Courtney and Haudenschild, Christian D. and Beckman, Kenneth B. and Shi, Jianxin and Mei, Rui and Urban, Alexander E. and Montgomery, Stephen B. and Levinson, Douglas F. and Koller, Daphne
Genome Research
2014-01-
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ISAAC - InterSpecies Analysing Application using Containers
Baier, Herbert and Schultz, Jorg
BMC Bioinformatics
2014-01-
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ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software.
Jacomy, Mathieu and Venturini, Tommaso and Heymann, Sebastien and Bastian, Mathieu
PloS one
2014-xx-
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Antimicrobial resistance determinants in Acinetobacter baumannii isolates taken from military treatment facilities.
Taitt, Chris Rowe R. and Leski, Tomasz A. and Stockelman, Michael G. and Craft, David W. and Zurawski, Daniel V. and Kirkup, Benjamin C. and Vora, Gary J.
Antimicrobial agents and chemotherapy
2014-xx-
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Surface micropattern limits bacterial contamination.
Mann, Ethan E. and Manna, Dipankar and Mettetal, Michael R. and May, Rhea M. and Dannemiller, Elisa M. and Chung, Kenneth K. and Brennan, Anthony B. and Reddy, Shravanthi T.
Antimicrobial resistance and infection control
2014-xx-
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BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.
Luo, Ruibang and Wong, Yiu-Lun L. and Law, Wai-Chun C. and Lee, Lap-Kei K. and Cheung, Jeanno and Liu, Chi-Man M. and Lam, Tak-Wah W.
PeerJ
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Demonstrating microbial co-occurrence pattern analyses within and between ecosystems.
Williams, Ryan J. and Howe, Adina and Hofmockel, Kirsten S.
Frontiers in microbiology
2014-xx-
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Genetic diagnosis of two dopa-responsive dystonia families by exome sequencing.
Sun, Zhan-fang F. and Zhang, Yu-han H. and Guo, Ji-feng F. and Sun, Qi-ying Y. and Mei, Jun-pu P. and Zhou, Han-lin L. and Guan, Li-ping P. and Tian, Jin-yong Y. and Hu, Zheng-mao M. and Li, Jia-da D. and Xia, Kun and Yan, Xin-xiang X. and Tang, Bei-sha S.
PloS one
2014-xx-
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A multi-step comparison of short-read full plastome sequence assembly methods in grasses
Wysocki, William P. and Clark, Lynn G. and Kelchner, Scot A. and Burke, Sean V. and Pires, J. Chris and Edger, Patrick P. and Mayfield, Dustin R. and Triplett, Jimmy K. and Columbus, J. Travis and Ingram, Amanda L. and Others
Taxon
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FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
Silva, Genivaldo Gueiros G. and Cuevas, Daniel A. and Dutilh, Bas E. and Edwards, Robert A.
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Focus: A New Multilayer Graph Model for Short Read Analysis and Extraction of Biologically Relevant Features
Warnke, Julia and Ali, Hesham
Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
2014-xx-
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Big Data Challenges for Estimating Genome Assembler Quality
Biswas, Abhishek and Gauthier, David and Ranjan, Desh and Zubair, Mohammad
Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
2014-xx-
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The Earth Microbiome project: successes and aspirations
Gilbert, Jack A. and Jansson, Janet K. and Knight, Rob
BMC Biology
2014-xx-
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Slim Fly: A Cost Effective Low-diameter Network Topology
Besta, Maciej and Hoefler, Torsten
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
2014-xx-
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Constructing Similarity Graphs from Large-Scale Biological Sequence Collections
Zola, Jaroslaw
Proceedings of the 2014 IEEE International Parallel & Distributed Processing Symposium Workshops
2014-xx-
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EgoNet: identification of human disease ego-network modules
Yang, Rendong and Bai, Yun and Qin, Zhaohui and Yu, Tianwei
BMC Genomics
2014-xx-
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Kraken: ultrafast metagenomic sequence classification using exact alignments
Wood, Derrick and Salzberg, Steven
Genome Biology
2014-xx-
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Three Transductive Set Covering Machines
Schmid, Florian and Lausser, Ludwig and Kestler, HansA
Data Analysis, Machine Learning and Knowledge Discovery
2014-xx-
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dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes
Safonova, Yana and Bankevich, Anton and Pevzner, PavelA
Research in Computational Molecular Biology
2014-xx-
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Fast lossless compression via cascading Bloom filters
Rozov, Roye and Shamir, Ron and Halperin, Eran
BMC Bioinformatics
2014-xx-
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Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
Neale, David and Wegrzyn, Jill and Stevens, Kristian and Zimin, Aleksey and Puiu, Daniela and Crepeau, Marc and Cardeno, Charis and Koriabine, Maxim and Morris, Ann H. and Liechty, John and Garcia, Pedro M. and Gross, Hans V. and Lin, Brian and Zieve, Jacob and Dougherty, William and Soriano, Sara F. and Wu, Le S. and Gilbert, Don and Marcais, Guillaume and Roberts, Michael and Holt, Carson and Yandell, Mark and Davis, John and Smith, Katherine and Dean, Jeffrey and Lorenz, W. and Whetten, Ross and Sederoff, Ronald and Wheeler, Nicholas and McGuire, Patrick and Main, Doreen and Loopstra, Carol and Mockaitis, Keithanne and DeJong, Pieter and Yorke, James and Salzberg, Steven and Langley, Charles
Genome Biology
2014-xx-
doi:10.1186/gb-2014-15-3-r59
SWAP-Assembler: Scalable and Efficient Genome Assembly towards Thousands of Cores
Meng, Jintao and Wang, Bingqiang and Wei, Yanjie and Feng, Shengzhong and Balaji, Pavan
4th annual RECOMB satellite workshop on massively parallel sequencing (RECOMB-seq 2014)
2014-xx-
http://www.google.com/search?hl=en&site=&q=SWAP-Assembler: Scalable and Efficient Genome Assembly towards Thousands of Cores&btnG=Search
Earth before life
Marzban, Caren and Viswanathan, Raju and Yurtsever, Ulvi
Biology Direct
2014-xx-
doi:doi:10.1186/1745-6150-9-1
What is the difference between the breakpoint graph and the de Bruijn graph?
Lin, Yu and Nurk, Sergey and Pevzner, Pavel A.
BMC Genomics
2014-xx-
doi:10.1186/1471-2164-15-S6-S6
AliGROOVE -- visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support
K\"uck, Patrick and Meid, Sandra A. and Christian, Gross and Waegele, Johann W. and Misof, Bernhard
BMC Bioinformatics
2014-xx-
doi:10.1186/1471-2105-15-294
Automated ensemble assembly and validation of microbial genomes
Koren, Sergey and Treangen, Todd J. and Hill, Christopher M. and Pop, Mihai and Phillippy, Adam M.
BMC Bioinformatics
2014-xx-
doi:10.1186/1471-2105-15-126
Genome alignment with graph data structures: a comparison
Kehr, Birte and Trappe, Kathrin and Holtgrewe, Manuel and Reinert, Knut
BMC Bioinformatics
2014-xx-
doi:10.1186/1471-2105-15-99
Next-Generation Sequence Assemblers
El-Metwally, Sara and Ouda, OsamaM and Helmy, Mohamed
Next Generation Sequencing Technologies and Challenges in Sequence Assembly
2014-xx-
doi:10.1007/978-1-4939-0715-1_11
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
Boetzer, Marten and Pirovano, Walter
BMC Bioinformatics
2014-xx-
doi:10.1186/1471-2105-15-211
Accelerating De Bruijn Graph-Based Genome Assembly for High-Throughput Short Read Data
Zhao, Kun and Liu, Weiguo and Voss, Gerrit and Mueller-Wittig, Wolfgang
Parallel and Distributed Systems (ICPADS), 2013 International Conference on
2013-12-
doi:10.1109/icpads.2013.68
Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa, Shinichi and Mende, Daniel R. and Zeller, Georg and Izquierdo-Carrasco, Fernando and Berger, Simon A. and Kultima, Jens R. and Coelho, Luis P. and Arumugam, Manimozhiyan and Tap, Julien and Nielsen, Henrik B. and Rasmussen, Simon and Brunak, S\o and Pedersen, Oluf and Guarner, Francisco and de Vos, Willem M. and Wang, Jun and Li, Junhua and Doré, Jo\"el and Ehrlich, S. Dusko and Stamatakis, Alexandros and Bork, Peer
Nature methods
2013-12-
doi:10.1038/nmeth.2693
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
Selvaraj, Siddarth and Dixon and Bansal, Vikas and Ren, Bing
Nat Biotech
2013-12-
doi:10.1038/nbt.2728
Fragment assignment in the cloud with eXpress-D
Roberts, Adam and Feng, Harvey and Pachter, Lior
BMC Bioinformatics
2013-12-
doi:10.1186/1471-2105-14-358
A comparison study of succinct data structures for use in GWAS
Putnam, Patrick and Zhang, Ge and Wilsey, Philip
BMC Bioinformatics
2013-12-
doi:10.1186/1471-2105-14-369
The altered landscape of the human skin microbiome in patients with primary immunodeficiencies
Oh, Julia and Freeman, Alexandra F. and Program, Nisc C. and Park, Morgan and Sokolic, Robert and Candotti, Fabio and Holland, Steven M. and Segre, Julia A. and Kong, Heidi H.
Genome Research
2013-12-
doi:10.1101/gr.159467.113
BioPig: a Hadoop-based analytic toolkit for large-scale sequence data
Nordberg, Henrik and Bhatia, Karan and Wang, Kai and Wang, Zhong
Bioinformatics
2013-12-
doi:10.1093/bioinformatics/btt528
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
Mortazavi, Ali and Pepke, Shirley and Jansen, Camden and Marinov, Georgi K. and Ernst, Jason and Kellis, Manolis and Hardison, Ross C. and Myers, Richard M. and Wold, Barbara J.
Genome Research
2013-12-
doi:10.1101/gr.158261.113
Metcalfe's Law after 40 Years of Ethernet
Metcalfe, Bob
Computer
2013-12-
doi:10.1109/mc.2013.374
Playing fast and loose with mutation
Mather, Alison E. and Harris, Simon R.
Nat Rev Micro
2013-12-
doi:10.1038/nrmicro3164
Processing genome scale tabular data with wormtable
Kelleher, Jerome and Ness, Rob and Halligan, Daniel
BMC Bioinformatics
2013-12-
doi:10.1186/1471-2105-14-356
Toward a statistically explicit understanding of de novo sequence assembly
Howison, Mark and Zapata, Felipe and Dunn, Casey W.
Bioinformatics
2013-12-
doi:10.1093/bioinformatics/btt525
When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes
Gardner, Shea N. and Hall, Barry G.
PLoS ONE
2013-12-
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Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.
Eren, A. Murat and Maignien, Lo"\is and Sul, Woo J. and Murphy, Leslie G. and Grim, Sharon L. and Morrison, Hilary G. and Sogin, Mitchell L.
Methods in ecology and evolution / British Ecological Society
2013-12-
doi:10.1111/2041-210X.12114
Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
El-Metwally, Sara and Hamza, Taher and Zakaria, Magdi and Helmy, Mohamed
PLoS Comput Biol
2013-12-
doi:10.1371/journal.pcbi.1003345
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
Burton, Joshua N. and Adey, Andrew and Patwardhan, Rupali P. and Qiu, Ruolan and Kitzman, Jacob O. and Shendure, Jay
Nat Biotech
2013-12-
doi:10.1038/nbt.2727
CONCOCT: Clustering cONtigs on COverage and ComposiTion
Alneberg, Johannes and Bjarnason, Brynjar S. and de Bruijn, Ino and Schirmer, Melanie and Quick, Joshua and Ijaz, Umer Z. and Loman, Nicholas J. and Andersson, Anders F. and Quince, Christopher
2013-12-
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The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity.
Hermann-Bank, Marie Louise L. and Skovgaard, Kerstin and Stockmarr, Anders and Larsen, Niels and M\olbak, Lars
BMC genomics
2013-11-14
doi:10.1186/1471-2164-14-788
Investigating biocomplexity through the agent-based paradigm
Kaul, H. and Ventikos, Y.
Briefings in Bioinformatics
2013-11-12
doi:10.1093/bib/bbt077
Kinetic Turbulence Simulations at Extreme Scale on Leadership-Class Systems
Wang, B. and Ethier, S. and Tang, W. and Williams, T. and Ibrahim, K. and Madduri, K. and Williams, S. and Oliker, L.
Proc.\\ ACM/IEEE Conf.\\ on Supercomputing (SC)
2013-11-
doi:http://dx.doi.org/10.1145/2503210.2503258
Slimming down via the microbiota
Nat Med
2013-11-
doi:10.1038/nm.3398
The MaSuRCA genome assembler
Zimin, Aleksey V. and Mar\ccais, Guillaume and Puiu, Daniela and Roberts, Michael and Salzberg, Steven L. and Yorke, James A.
Bioinformatics
2013-11-
doi:10.1093/bioinformatics/btt476
Assessment of transcript reconstruction methods for RNA-seq
Steijger, Tamara and Abril, Josep F. and Engstrom, Par G. and Kokocinski, Felix and Consortium, The RGASP and Hubbard, Tim J. and Guigo, Roderic and Harrow, Jennifer and Bertone, Paul
Nature Methods
2013-11-
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snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing
Shahib, Ali A. and Underwood, Anthony
BMC Bioinformatics
2013-11-
doi:10.1186/1471-2105-14-326
A widespread self-cleaving ribozyme class is revealed by bioinformatics
Roth, Adam and Weinberg, Zasha and Chen, Andy G. Y. and Kim, Peter B. and Ames, Tyler D. and Breaker, Ronald R.
Nature Chemical Biology
2013-11-
doi:10.1038/nchembio.1386
Facial Changes Caused by Smoking: A Comparison between Smoking and Nonsmoking Identical Twins.
Okada, Haruko C. and Alleyne, Brendan and Varghai, Kaveh and Kinder, Kimberly and Guyuron, Bahman
Plastic and reconstructive surgery
2013-11-
doi:10.1097/prs.0b013e3182a4c20a
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.
Nijkamp, Jurgen F. and Pop, Mihai and Reinders, Marcel J. T. and de Ridder, Dick
Bioinformatics (Oxford, England)
2013-11-
doi:10.1093/bioinformatics/btt502
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.
Nijkamp, Jurgen F. and Pop, Mihai and Reinders, Marcel J. and de Ridder, Dick
Bioinformatics (Oxford, England)
2013-11-
doi:10.1093/bioinformatics/btt502
Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis.
Low, Teck Y. and van Heesch, Sebastiaan and van den Toorn, Henk and Giansanti, Piero and Cristobal, Alba and Toonen, Pim and Schafer, Sebastian and H\"ubner, Norbert and van Breukelen, Bas and Mohammed, Shabaz and Cuppen, Edwin and Heck, Albert J. and Guryev, Victor
Cell reports
2013-11-
doi:10.1016/j.celrep.2013.10.041
So you want to be a computational biologist?
Loman, Nick and Watson, Mick
Nat Biotech
2013-11-
doi:10.1038/nbt.2740
China's Publication Bazaar
Hvistendahl, Mara
Science
2013-11-
doi:10.1126/science.342.6162.1035
Using HPX and LibGeoDecomp for scaling HPC applications on heterogeneous supercomputers
Heller, Thomas and Kaiser, Hartmut and Sch\"afer, Andreas and Fey, Dietmar
Proceedings of the Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems - ScalA '13
2013-11-
doi:10.1145/2530268.2530269
Programming for Exascale Computers
Gropp, William and Snir, Marc
Computing in Science & Engineering
2013-11-
doi:10.1109/MCSE.2013.96
Hybrid MPI
Friedley, Andrew and Bronevetsky, Greg and Hoefler, Torsten and Lumsdaine, Andrew
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13
2013-11-
doi:10.1145/2503210.2503294
Systematic evaluation of spliced alignment programs for RNA-seq data
Engstr\"om, P\"ar G. and Steijger, Tamara and Sipos, Botond and Grant, Gregory R. and Kahles, André and Alioto, Tyler and Behr, Jonas and Bertone, Paul and Bohnert, Regina and Campagna, Davide and Davis, Carrie A. and Dobin, Alexander and Gingeras, Thomas R. and Goldman, Nick and Guig\'o Roderic and Harrow, Jennifer and Hubbard, Tim J. and Jean, Géraldine and Kosarev, Peter and Li, Sheng and Liu, Jinze and Mason, Christopher E. and Molodtsov, Vladimir and Ning, Zemin and Ponstingl, Hannes and Prins, Jan F. and R\"atsch, Gunnar and Ribeca, Paolo and Seledtsov, Igor and Solovyev, Victor and Valle, Giorgio and Vitulo, Nicola and Wang, Kai and Wu, Thomas D. and Zeller, Georg
Nature Methods
2013-11-
doi:10.1038/nmeth.2722
Information Theory of DNA Shotgun Sequencing
Motahari, Abolfazl S. and Bresler, Guy and Tse, David N. C.
IEEE Trans. Inf. Theor.
2013-10-
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A scalable data analysis platform for metagenomics
Tang, Wei and Wilkening, J. and Desai, N. and Gerlach, W. and Wilke, A. and Meyer, F.
Big Data, 2013 IEEE International Conference on
2013-10-
doi:10.1109/bigdata.2013.6691723
Fast Approximate Subgraph Counting and Enumeration
Slota, G. and Madduri, K.
Proc.\\ 42nd Int'l.\\ Conf.\\ on Parallel Processing (ICPP)
2013-10-
doi:http://dx.doi.org/10.1109/ICPP.2013.30
Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data.
Stoesser, N. and Batty, E. M. and Eyre, D. W. and Morgan, M. and Wyllie, D. H. and Del Ojo Elias, C. and Johnson, J. R. and Walker, A. S. and Peto, T. E. and Crook, D. W.
The Journal of antimicrobial chemotherapy
2013-10-
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'Big data', Hadoop and cloud computing in genomics
O'Driscoll, Aisling and Daugelaite, Jurate and Sleator, Roy D.
Journal of Biomedical Informatics
2013-10-
doi:10.1016/j.jbi.2013.07.001
In need of an upgrade
Nature Biotechnology
2013-10-
doi:10.1038/nbt.2717
ExpressionBlast: mining large, unstructured expression databases
Zinman, Guy E. and Naiman, Shoshana and Kanfi, Yariv and Cohen, Haim and Bar-Joseph, Ziv
Nat Meth
2013-10-
doi:10.1038/nmeth.2630
A dynamic hashing approach to build the de bruijn graph for genome assembly
Zhao, Kun and Liu, Weiguo and Voss, G. and Muller-Wittig, W.
TENCON 2013 - 2013 IEEE Region 10 Conference (31194)
2013-10-
doi:10.1109/tencon.2013.6719008
An avian retrovirus uses canonical expression and processing mechanisms to generate viral microRNA
Yao, Yongxiu and Smith, Lorraine P. and Nair, Venugopal and Watson, Mick
Journal of Virology
2013-10-
doi:10.1128/jvi.02921-13
Quantifying long-term scientific impact.
Wang, Dashun and Song, Chaoming and Barab\'asi, Albert-L\'aszl\'o L.
Science (New York, N.Y.)
2013-10-
doi:10.1126/science.1237825
Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology
Ruan, Jue and Jiang, Lan and Chong, Zechen and Gong, Qiang and Li, Heng and Li, Chunyan and Tao, Yong and Zheng, Caihong and Zhai, Weiwei and Turissini, David and Cannon, Charles and Lu, Xuemei and Wu, Chung I.
BMC Genomics
2013-10-
doi:10.1186/1471-2164-14-711
Compact representation of k-mer de Bruijn graphs for genome read assembly
Rodland, Einar
BMC Bioinformatics
2013-10-
doi:10.1186/1471-2105-14-313
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products.
Nurk, Sergey and Bankevich, Anton and Antipov, Dmitry and Gurevich, Alexey A. and Korobeynikov, Anton and Lapidus, Alla and Prjibelski, Andrey D. and Pyshkin, Alexey and Sirotkin, Alexander and Sirotkin, Yakov and Stepanauskas, Ramunas and Clingenpeel, Scott R. and Woyke, Tanja and McLean, Jeffrey S. and Lasken, Roger and Tesler, Glenn and Alekseyev, Max A. and Pevzner, Pavel A.
Journal of computational biology : a journal of computational molecular cell biology
2013-10-
doi:10.1089/cmb.2013.0084
'Candidatus Competibacter'-lineage genomes retrieved from metagenomes reveal functional metabolic diversity
McIlroy, Simon J. and Albertsen, Mads and Andresen, Eva K. and Saunders, Aaron M. and Kristiansen, Rikke and Stokholm-Bjerregaard, Mikkel and Nielsen, Kare L. and Nielsen, Per H.
The ISME Journal
2013-10-
doi:10.1038/ismej.2013.162
A Turing test for artificial expression data.
Maier, Robert and Zimmer, Ralf and K\"uffner, Robert
Bioinformatics (Oxford, England)
2013-10-
doi:10.1093/bioinformatics/btt438
MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus
Liu, Wei-Ting and Lamsa, Anne and Wong, Weng R. and Boudreau, Paul D. and Kersten, Roland and Peng, Yao and Moree, Wilna J. and Duggan, Brendan M. and Moore, Bradley S. and Gerwick, William H. and Linington, Roger G. and Pogliano, Kit and Dorrestein, Pieter C.
The Journal of Antibiotics
2013-10-
doi:10.1038/ja.2013.99
Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota
Lee, Sunghee and Cantarel, Brandi and Henrissat, Bernard and Gevers, Dirk and Birren, Bruce W. and Huttenhower, Curtis and Ko, GwangPyo
The ISME Journal
2013-10-
doi:10.1038/ismej.2013.167
Bacterial evolution of antibiotic hypersensitivity
Lazar, Viktoria and Pal Singh Gajinder and Spohn, Reka and Nagy, Istvan and Horvath, Balazs and Hrtyan, Monika and Busa-Fekete, Robert and Bogos, Balazs and Mehi, Orsolya and Csorgo, Balint and Posfai, Gyorgy and Fekete, Gergely and Szappanos, Balazs and Kegl, Balazs and Papp, Balazs and Pal, Csaba
Molecular Systems Biology
2013-10-
doi:10.1038/msb.2013.57
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.
Kwak, Daniel and Kam, Alfred and Becerra, David and Zhou, Qikuan and Hops, Adam and Zarour, Eleyine and Kam, Arthur and Sarmenta, Luis and Blanchette, Mathieu and Waldisp\"uhl, Jér\^ome
Genome biology
2013-10-
doi:10.1186/gb-2013-14-10-r116
NeSSM: A Next-Generation Sequencing Simulator for Metagenomics
Jia, Ben and Xuan, Liming and Cai, Kaiye and Hu, Zhiqiang and Ma, Liangxiao and Wei, Chaochun
PLoS ONE
2013-10-
doi:10.1371/journal.pone.0075448
RACER: Rapid and accurate correction of errors in reads
Ilie, Lucian and Molnar, Michael
Bioinformatics
2013-10-
doi:10.1093/bioinformatics/btt407
The social structure of microbial community involved in colonization resistance
He, Xuesong and McLean, Jeffrey S. and Guo, Lihong and Lux, Renate and Shi, Wenyuan
The ISME Journal
2013-10-
doi:10.1038/ismej.2013.172
Sleep It Out
Herculano-Houzel, Suzana
Science
2013-10-
doi:10.1126/science.1245798
Pathoscope: Species identification and strain attribution with unassembled sequencing data
Francis, Owen E. and Bendall, Matthew and Manimaran, Solaiappan and Hong, Changjin and Clement, Nathan L. and Castro-Nallar, Eduardo and Snell, Quinn and Schaalje, G. Bruce and Clement, Mark J. and Crandall, Keith A. and Johnson, W. Evan
Genome Research
2013-10-
doi:10.1101/gr.150151.112
Improving the performance of actor model runtime environments on multicore and manycore platforms
Francesquini, Emilio and Goldman, Alfredo and Méhaut, Jean-Fran\ccois
Proceedings of the 2013 workshop on Programming based on actors, agents, and decentralized control - AGERE! '13
2013-10-
doi:10.1145/2541329.2541342
A NUMA-Aware Runtime Environment for the Actor Model
Francesquini, Emilio and Goldman, Alfredo and Mehaut, Jean-Francois
2013 42nd International Conference on Parallel Processing
2013-10-
doi:10.1109/ICPP.2013.34
An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome
Ferrarini, Marco and Moretto, Marco and Ward, Judson and Surbanovski, Nada and Stevanovic, Vladimir and Giongo, Lara and Viola, Roberto and Cavalieri, Duccio and Velasco, Riccardo and Cestaro, Alessandro and Sargent, Daniel
BMC Genomics
2013-10-
doi:10.1186/1471-2164-14-670
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Edgar, Robert C.
Nat Meth
2013-10-
doi:10.1038/nmeth.2604
Fostering synergies between ecosystem services and biodiversity in conservation planning: A review
Cimon-Morin, Jér\^ome and Darveau, Marcel and Poulin, Monique
Biological Conservation
2013-10-
doi:10.1016/j.biocon.2013.06.023
Semiconductor-based DNA sequencing of histone modification states.
Cheng, Christine S. and Rai, Kunal and Garber, Manuel and Hollinger, Andrew and Robbins, Dana and Anderson, Scott and Macbeth, Alyssa and Tzou, Austin and Carneiro, Mauricio O. and Raychowdhury, Raktima and Russ, Carsten and Hacohen, Nir and Gershenwald, Jeffrey E. and Lennon, Niall and Nusbaum, Chad and Chin, Lynda and Regev, Aviv and Amit, Ido
Nature communications
2013-10-
doi:10.1038/ncomms3672
Native actors
Charousset, Dominik and Schmidt, Thomas C. and Hiesgen, Raphael and W\"ahlisch, Matthias
Proceedings of the 2013 workshop on Programming based on actors, agents, and decentralized control - AGERE! '13
2013-10-
doi:10.1145/2541329.2541336
Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution
Carr, Rogan and Shen-Orr, Shai S. and Borenstein, Elhanan
PLoS Comput Biol
2013-10-
doi:10.1371/journal.pcbi.1003292
The anatomy of successful computational biology software
Altschul, Stephen and Demchak, Barry and Durbin, Richard and Gentleman, Robert and Krzywinski, Martin and Li, Heng and Nekrutenko, Anton and Robinson, James and Rasband, Wayne and Taylor, James and Trapnell, Cole
Nature Biotechnology
2013-10-
doi:10.1038/nbt.2721
Differential Debugging
Spinellis, Diomidis
IEEE Software
2013-09-
doi:10.1109/MS.2013.103
The mutational landscape of chromatin regulatory factors across 4623 tumor samples
Perez, Abel G. and Sanz, Alba J. and Bigas, Nuria L.
Genome Biology
2013-09-
doi:10.1186/gb-2013-14-9-r106
Multi-parallel prefiltering on the convey HC-1 for supporting homology detection
Nowak, Fabian and Bromberger, Michael and Schindewolf, Martin and Karl, Wolfgang
Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13
2013-09-
doi:10.1145/2488551.2488587
Accurate and universal delineation of prokaryotic species
Mende, Daniel R. and Sunagawa, Shinichi and Zeller, Georg and Bork, Peer
Nat Meth
2013-09-
doi:10.1038/nmeth.2575
Genomics in the clouds
Marx, Vivien
Nature Methods
2013-09-
doi:10.1038/nmeth.2654
Cas9 as a versatile tool for engineering biology
Mali, Prashant and Esvelt, Kevin M. and Church, George M.
Nature Methods
2013-09-
doi:10.1038/nmeth.2649
McMPI
Holmes, Daniel and Booth, Stephen
Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13
2013-09-
doi:10.1145/2488551.2488572
Optimizing SNP microarray probe design for high accuracy microbial genotyping
Gardner, Shea N. and Thissen, James B. and McLoughlin, Kevin S. and Slezak, Tom and Jaing, Crystal J.
Journal of Microbiological Methods
2013-09-
doi:10.1016/j.mimet.2013.07.006
Actor scheduling for multicore hierarchical memory platforms
Francesquini, Emilio and Goldman, Alfredo and Méhaut, Jean-Fran\ccois
Proceedings of the twelfth ACM SIGPLAN workshop on Erlang - Erlang '13
2013-09-
doi:10.1145/2505305.2505313
Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era
Edwards, Robert and Haggerty, John and Cassman, Noriko and Busch, Julia and Aguinaldo, Kristen and Chinta, Sowmya and Vaughn, Meredith and Morey, Robert and Harkins, Timothy and Teiling, Clotilde and Fredrikson, Karin and Dinsdale, Elizabeth
BMC Genomics
2013-09-
doi:10.1186/1471-2164-14-600
Enabling MPI interoperability through flexible communication endpoints
Dinan, James and Balaji, Pavan and Goodell, David and Miller, Douglas and Snir, Marc and Thakur, Rajeev
Proceedings of the 20th European MPI Users' Group Meeting on - EuroMPI '13
2013-09-
doi:10.1145/2488551.2488553
CLARITY for mapping the nervous system
Chung, Kwanghun and Deisseroth, Karl
Nature Methods
2013-09-
doi:10.1038/nmeth1013-1035a
Microbial production of short-chain alkanes
Choi, Yong J. and Lee, Sang Y.
Nature
2013-09-
doi:10.1038/nature12536
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
Chikhi, Rayan and Rizk, Guillaume
Algorithms for Molecular Biology
2013-09-
doi:10.1186/1748-7188-8-22
Scalable metagenomic taxonomy classification using a reference genome database.
Ames, Sasha K. and Hysom, David A. and Gardner, Shea N. and Lloyd, G. Scott and Gokhale, Maya B. and Allen, Jonathan E.
Bioinformatics (Oxford, England)
2013-09-
doi:10.1093/bioinformatics/btt389
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, Morgan G. I. and Zaneveld, Jesse and Caporaso, J. Gregory and McDonald, Daniel and Knights, Dan and Reyes, Joshua A. and Clemente, Jose C. and Burkepile, Deron E. and Vega Thurber, Rebecca L. and Knight, Rob and Beiko, Robert G. and Huttenhower, Curtis
Nature Biotechnology
2013-08-25
doi:10.1038/nbt.2676
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill
Rivers, Adam R. and Sharma, Shalabh and Tringe, Susannah G. and Martin, Jeffrey and Joye, Samantha B. and Moran, Mary A.
The ISME Journal
2013-08-01
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Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.
Williams, David and Trimble, William L. and Shilts, Meghan and Meyer, Folker and Ochman, Howard
BMC genomics
2013-08-
doi:10.1186/1471-2164-14-537
F1: A Distributed SQL Database That Scales
Shute, Jeff and Vingralek, Radek and Samwel, Bart and Handy, Ben and Whipkey, Chad and Rollins, Eric and Oancea, Mircea and Littlefield, Kyle and Menestrina, David and Ellner, Stephan and Cieslewicz, John and Rae, Ian and Stancescu, Traian and Apte, Himani
Proc. VLDB Endow.
2013-08-
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DeNovoGear: de novo indel and point mutation discovery and phasing
Ramu, Avinash and Noordam, Michiel J. and Schwartz, Rachel S. and Wuster, Arthur and Hurles, Matthew E. and Cartwright, Reed A. and Conrad, Donald F.
Nature Methods
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High-Throughput Compression of FASTQ Data with SeqDB
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Computational Biology and Bioinformatics, IEEE/ACM Transactions on
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MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data.
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Bioinformatics (Oxford, England)
2013-01-
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Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.
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BMC genomics
2013-01-
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MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
Treangen, ToddJ and Koren, Sergey and Sommer, DanielD and Liu, Bo and Astrovskaya, Irina and Ondov, Brian and Darling, AaronE and Phillippy, AdamM and Pop, Mihai
Genome Biology
2013-01-
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The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.
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PLoS biology
2013-01-
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Visualizing multidimensional cancer genomics data
Schroeder, Michael and Perez, Abel G. and Bigas, Nuria L.
Genome Medicine
2013-01-
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Streaming fragment assignment for real-time analysis of sequencing experiments
Roberts, Adam and Pachter, Lior
Nat Meth
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Nat Meth
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Computing: A vision for data science
Mattmann, Chris A.
Nature
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Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild
Martin, Christopher H. and Wainwright, Peter C.
Science
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The impact of free-ranging domestic cats on wildlife of the United States
Loss, Scott R. and Will, Tom and Marra, Peter P.
Nat Commun
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Binary Interval Search
Layer, Ryan M. and Skadron, Kevin and Robins, Gabriel and Hall, Ira M. and Quinlan, Aaron R.
Bioinformatics
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Studying the microbiology of the indoor environment.
Kelley, Scott T. and Gilbert, Jack A.
Genome biology
2013-01-
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Extending the BEAGLE library to a multi-FPGA platform.
Jin, Zheming and Bakos, Jason D.
BMC bioinformatics
2013-01-
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High-throughput microbial population genomics using the Cortex variation assembler
Iqbal, Zamin and Turner, Isaac and McVean, Gil
Bioinformatics
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Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, Woong Y. and Fu, Yanfang and Reyon, Deepak and Maeder, Morgan L. and Tsai, Shengdar Q. and Sander, Jeffry D. and Peterson, Randall T. and Yeh, J-R J. and Joung, J. Keith
Nature Biotechnology
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On the Immortality of Television Sets: ” Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE
Graur, Dan and Zheng, Yichen and Price, Nicholas and Azevedo, Ricardo B. R. and Zufall, Rebecca A. and Elhaik, Eran
Genome Biology and Evolution
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When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.
Gardner, Shea N. and Hall, Barry G.
PloS one
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Nature Biotechnology
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Optimal assembly for high throughput shotgun sequencing.
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BMC bioinformatics
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Graph Partitioning for Scalable Distributed Graph Computations
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Graph Partitioning and Graph Clustering
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Analysis and optimization of gyrokinetic toroidal simulations on homogenous and heterogenous platforms
Ibrahim, K. Z. and Madduri, K. and Williams, S. and Wang, B. and Ethier, S. and Oliker, L.
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Ugander, Johan and Backstrom, Lars
Proceedings of the Sixth ACM International Conference on Web Search and Data Mining
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Holzschuher, Florian and Peinl, René
Proceedings of the Joint EDBT/ICDT 2013 Workshops
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Communication and topology-aware load balancing in Charm++ with TreeMatch
Jeannot, E. and Meneses, E. and Mercier, G. and Tessier, F. and Zheng, Gengbin
Cluster Computing (CLUSTER), 2013 IEEE International Conference on
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Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes
Zhang, Quan and Rho, Mina and Tang, Haixu and Doak, Thomas and Ye, Yuzhen
Genome Biology
2013-xx-
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Improved Parallel Processing of Massive De Bruijn Graph for Genome Assembly
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Web Technologies and Applications
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Plant and Animal Genome XXI Conference
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GigaScience
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CGAL: computing genome assembly likelihoods
Rahman, Atif and Pachter, Lior
Genome Biology
2013-xx-
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Detecting Superbubbles in Assembly Graphs
Onodera, Taku and Sadakane, Kunihiko and Shibuya, Tetsuo
Algorithms in Bioinformatics
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Taming Biological Big Data with D4M
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Lincoln Laboratory Journal
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MPI + MPI: a new hybrid approach to parallel programming with MPI plus shared memory
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Programming for Exascale Computers
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Web-based visual analysis for high-throughput genomics
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BMC Genomics
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Poncho: Enabling Smart Administration of Full Private Clouds
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Robust Bloom Filters for Large MultiLabel Classification Tasks
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Hobbes: Composition and Virtualization As the Foundations of an Extreme-scale OS/R
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Proceedings of the 3rd International Workshop on Runtime and Operating Systems for Supercomputers
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BMC Genomics
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Pan-PCR, a computational method for designing bacterial-typing assays based on whole genome sequence data.
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Journal of clinical microbiology
2012-12-
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Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons
Vezzi, Francesco and Narzisi, Giuseppe and Mishra, Bud
PLoS ONE
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MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.
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Source code for biology and medicine
2012-12-
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Measuring community similarity with phylogenetic networks.
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Molecular biology and evolution
2012-12-
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Electrosynthesis of commodity chemicals by an autotrophic microbial community.
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Applied and environmental microbiology
2012-12-
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Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
Lewis, Steven and Csordas, Attila and Killcoyne, Sarah and Hermjakob, Henning and Hoopmann, Michael R. and Moritz, Robert L. and Deutsch, Eric W. and Boyle, John
BMC bioinformatics
2012-12-
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Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets
Howe, Adina C. and Pell, Jason and Canino-Koning, Rosangela and Mackelprang, Rachel and Tringe, Susannah and Jansson, Janet and Tiedje, James M. and Brown, C. Titus
arXiv
2012-12-
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Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.
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Proceedings of the National Academy of Sciences of the United States of America
2012-12-
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Bioinformatics (Oxford, England)
2012-12-
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Flexible and efficient genome tiling design with penalized uniqueness score
Du, Yang and Murani, Eduard and Ponsuksili, Siriluck and Wimmers, Klaus
BMC Bioinformatics
2012-12-
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Proceedings of the 2012 ACM conference on CoNEXT student workshop - CoNEXT Student '12
2012-12-
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A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences
Boulund, Fredrik and Johnning, Anna and Pereira, Mariana B. and Larsson, D. G. Joakim and Kristiansson, Erik
BMC Genomics
2012-12-
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Ray Meta: scalable de novo metagenome assembly and profiling
Boisvert, Sebastien and Raymond, Frederic and Godzaridis, Elenie and Laviolette, Francois and Corbeil, Jacques
Genome Biology
2012-12-
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CLEVER: clique-enumerating variant finder
Marschall, Tobias and Costa, Ivan G. and Canzar, Stefan and Bauer, Markus and Klau, Gunnar W. and Schliep, Alexander and Sch\"onhuth, Alexander
Bioinformatics
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NUMA-aware graph mining techniques for performance and energy efficiency
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Copy Number Variation detection from 1000 Genomes project exon capture sequencing data
Wu, Jiantao and Grzeda, Krzysztof and Stewart, Chip and Grubert, Fabian and Urban, Alexander and Snyder, Michael and Marth, Gabor
BMC Bioinformatics
2012-11-
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Varon, Andres and Wheeler, Ward
BMC Bioinformatics
2012-11-
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Capturing native long-range contiguity by in situ library construction and optical sequencing
Schwartz, Jerrod J. and Lee, Choli and Hiatt, Joseph B. and Adey, Andrew and Shendure, Jay
Proceedings of the National Academy of Sciences
2012-11-
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MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
Namiki, Toshiaki and Hachiya, Tsuyoshi and Tanaka, Hideaki and Sakakibara, Yasubumi
Nucleic Acids Research
2012-11-
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iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data
Mezlini, Aziz M. and Smith, Eric J. M. and Fiume, Marc and Buske, Orion and Savich, Gleb and Shah, Sohrab and Aparicion, Sam and Chiang, Derek and Goldenberg, Anna and Brudno, Michael
Genome Research
2012-11-
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Bioinformatics for the Human Microbiome Project
Gevers, Dirk and Pop, Mihai and Schloss, Patrick D. and Huttenhower, Curtis
PLoS Comput Biol
2012-11-
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A Large-Scale Model of the Functioning Brain
Eliasmith, Chris and Stewart, Terrence C. and Choo, Xuan and Bekolay, Trevor and DeWolf, Travis and Tang, Yichuan and Rasmussen, Daniel
Science
2012-11-
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Oculus: faster sequence alignment by streaming read compression
Chinnaiyan, Arul and Iyer, Matthew and Veeneman, Brendon
BMC Bioinformatics
2012-11-
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Next-generation sequencing in the clinic: are we ready?
Biesecker, Leslie G. and Burke, Wylie and Kohane, Isaac and Plon, Sharon E. and Zimmern, Ron
Nature Reviews Genetics
2012-11-
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Publishing: Handful of papers dominates citation
Barabasi, Albert-Laszlo and Song, Chaoming and Wang, Dashun
Nature
2012-11-
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CloudMan as a platform for tool, data, and analysis distribution
Afgan, Enis and Chapman, Brad and Taylor, James
BMC Bioinformatics
2012-11-
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pGraph: Efficient Parallel Construction of Large-Scale Protein Sequence Homology Graphs
Wu, Changjun and Kalyanaraman, A. and Cannon, W. R.
Parallel and Distributed Systems, IEEE Transactions on
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Denoising PCR-amplified metagenome data
Rosen, Michael and Callahan, Benjamin and Fisher, Daniel and Holmes, Susan
BMC Bioinformatics
2012-10-
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A metagenome-wide association study of gut microbiota in type 2 diabetes
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Actor-based runtime model of adaptable feedback control loops
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2012-10-
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STAR: ultrafast universal RNA-seq aligner
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Bioinformatics
2012-10-
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Provirophages and transpovirons as the diverse mobilome of giant viruses
Desnues, Christelle and La Scola Bernard and Yutin, Natalya and Fournous, Ghislain and Robert, Catherine and Azza, Sa\$backslash\$"id and Jardot, Priscilla and Monteil, Sonia and Campocasso, Angélique and Koonin, Eugene V. and Raoult, Didier
Proceedings of the National Academy of Sciences
2012-10-
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SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models
Aziz, Ramy K. and Devoid, Scott and Disz, Terrence and Edwards, Robert A. and Henry, Christopher S. and Olsen, Gary J. and Olson, Robert and Overbeek, Ross and Parrello, Bruce and Pusch, Gordon D. and Stevens, Rick L. and Vonstein, Veronika and Xia, Fangfang
PLoS ONE
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An efficient algorithm for DNA fragment assembly in MapReduce.
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2012-09-28
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Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
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Science
2012-09-28
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An integrated encyclopedia of DNA elements in the human genome
Nature
2012-09-
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Insights from Genomics into Bacterial Pathogen Populations
Wilson, Daniel J.
PLoS Pathog
2012-09-
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Efficient sequence assembly and variant calling using compressed data structures
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2012-09-
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Genomics' Big Talker
Pennisi, Elizabeth
Science
2012-09-
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Popularity versus similarity in growing networks
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Nature
2012-09-
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ALCF MPI Benchmarks: Understanding Machine-Specific Communication Behavior
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Diversity, stability and resilience of the human gut microbiota
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2012-09-
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High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.
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A graph-based approach for designing extensible pipelines
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BMC Genomics
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Comparative Genomics of Vancomycin-Resistant Staphylococcus aureus Strains and Their Positions within the Clade Most Commonly Associated with Methicillin-Resistant S. aureus Hospital-Acquired Infection in the United States
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mBio
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Improving neural networks by preventing co-adaptation of feature detectors
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Error-correcting properties of the SOLiD Exact Call Chemistry
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BMC Bioinformatics
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Analyses of the Microbial Diversity across the Human Microbiome
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PLoS ONE
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Nature biotechnology
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A Scalable Bootstrap for Massive Data
Kleiner, Ariel and Talwalkar, Ameet and Sarkar, Purnamrita and Jordan, Michael I.
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Keegan, Kevin P. and Trimble, William L. and Wilkening, Jared and Wilke, Andreas and Harrison, Travis and D'Souza, Mark and Meyer, Folker
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The phylogenetic Kantorovich–Rubinstein metric for environmental sequence samples
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Consortium, The Human Microbiome Project
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PAMI: A Parallel Active Message Interface for the Blue Gene/Q Supercomputer
Kumar, Sameer and Mamidala, Amith R. and Faraj, Daniel A. and Smith, Brian and Blocksome, Michael and Cernohous, Bob and Miller, Douglas and Parker, Jeff and Ratterman, Joseph and Heidelberger, Philip and Chen, Dong and Steinmacher-Burrow, Burkhard
2012 IEEE 26th International Parallel and Distributed Processing Symposium
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Readjoiner: a fast and memory efficient string graph-based sequence assembler
Gonnella, Giorgio and Kurtz, Stefan
BMC Bioinformatics
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Characterizing Load and Communication Imbalance in Large-Scale Parallel Applications
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Exploiting sparseness in de novo genome assembly
Ye, Chengxi and Ma, Zhanshan S. and Cannon, Charles H. and Pop, Mihai and Yu, Douglas W.
BMC Bioinformatics
2012-04-19
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The role of robustness in phenotypic adaptation and innovation
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Proceedings of the Royal Society B: Biological Sciences
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GenomeSpace: An environment for frictionless bioinformatics
Reich, Michael and Liefeld, John and Thorvaldsdottir, Helga and Ocana, Marco and Polk, Eliot and Jang, D. K. and Mesirov, Jill
Cancer Research
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Performance comparison of benchtop high-throughput sequencing platforms
Loman, Nicholas J. and Misra, Raju V. and Dallman, Timothy J. and Constantinidou, Chrystala and Gharbia, Saheer E. and Wain, John and Pallen, Mark J.
Nature Biotechnology
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Fast gapped-read alignment with Bowtie 2
Langmead, Ben and Salzberg, Steven L.
Nat Meth
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The human microbiome: at the interface of health and disease
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Nature Reviews Genetics
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A Bayesian Approach to Discovering Truth from Conflicting Sources for Data Integration
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Genome-wide metabolic network reconstruction of the picoalga Ostreococcus.
Krumholz, Elias W. and Yang, Hong and Weisenhorn, Pamela and Henry, Christopher S. and Libourel, Igor G.
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Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease
Young, Bernadette C. and Golubchik, Tanya and Batty, Elizabeth M. and Fung, Rowena and Larner-Svensson, Hanna and Votintseva, Antonina A. and Miller, Ruth R. and Godwin, Heather and Knox, Kyle and Everitt, Richard G. and Iqbal, Zamin and Rimmer, Andrew J. and Cule, Madeleine and Ip, Camilla L. C. and Didelot, Xavier and Harding, Rosalind M. and Donnelly, Peter and Peto, Tim E. and Crook, Derrick W. and Bowden, Rory and Wilson, Daniel J.
Proceedings of the National Academy of Sciences
2012-03-
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GAGE: A critical evaluation of genome assemblies and assembly algorithms
Salzberg, Steven L. and Phillippy, Adam M. and Zimin, Aleksey and Puiu, Daniela and Magoc, Tanja and Koren, Sergey and Treangen, Todd J. and Schatz, Michael C. and Delcher, Arthur L. and Roberts, Michael and Mar\ccais, Guillaume and Pop, Mihai and Yorke, James A.
Genome Research
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An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
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The ISME journal
2012-03-
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SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.
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Bioinformatics (Oxford, England)
2012-03-
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Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.
Krampis, Konstantinos and Booth, Tim and Chapman, Brad and Tiwari, Bela and Bicak, Mesude and Field, Dawn and Nelson, Karen E.
BMC bioinformatics
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Phylo: a citizen science approach for improving multiple sequence alignment.
Kawrykow, Alexander and Roumanis, Gary and Kam, Alfred and Kwak, Daniel and Leung, Clarence and Wu, Chu and Zarour, Eleyine and Players, Phylo and Sarmenta, Luis and Blanchette, Mathieu and Waldisp\"uhl, Jér\^ome
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Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species
Raymond, Frédéric and Boisvert, Sébastien and Roy, Gaétan and Ritt, Jean-Fran\ccois and Légaré, Danielle and Isnard, Amandine and Stanke, Mario and Olivier, Martin and Tremblay, Michel J. and Papadopoulou, Barbara and Ouellette, Marc and Corbeil, Jacques
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Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
Iverson, Vaughn and Morris, Robert M. and Frazar, Christian D. and Berthiaume, Chris T. and Morales, Rhonda L. and Armbrust, E. Virginia
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Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing
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Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic
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Applied and Environmental Microbiology
2012-01-
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Repetitive DNA and next-generation sequencing: computational challenges and solutions
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A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
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Learning from our GWAS mistakes: from experimental design to scientific method
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F1 - The Fault-Tolerant Distributed RDBMS Supporting Google's Ad Business
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The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
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Combining randomization and discrimination for fine-grained image categorization
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MPI ON MILLIONS OF CORES
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Parallel Processing Letters
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Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
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Nucleic Acids Research
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2011-xx-
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BMC Bioinformatics
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Multiplex De Novo Sequencing of Peptide Antibiotics
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EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
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Genome Biology
2011-xx-
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
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BMC Bioinformatics
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Constrained De Novo Sequencing of Peptides with Application to Conotoxins
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SciNet: Lessons Learned from Building a Power-efficient Top-20 System and Data Centre
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BMC Genomics
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Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme
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Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud
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Navigating the future of bacterial molecular epidemiology
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AM++: a generalized active message framework
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PLoS Genet
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Genome Biology
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Following the Motions of Water Molecules in Aqueous Solutions
Skinner, James L.
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Genome Biology
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Nature Photonics
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Virtual screening: an endless staircase?
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Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code
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Computational Biology and Chemistry
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Prediction of Co-Receptor Usage of HIV-1 from Genotype
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Computational Biology and Chemistry
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BEDTools: a flexible suite of utilities for comparing genomic features
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Li, Heng and Durbin, Richard
Bioinformatics
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Kronecker Graphs: An Approach to Modeling Networks
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Intestinal Bacteria and the Regulation of Immune Cell Homeostasis
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Annual Review of Immunology
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Genome sequencing and analysis of the model grass Brachypodium distachyon
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Genome Research
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A Primer on Metagenomics
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Pregel: A System for Large-scale Graph Processing
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ZooKeeper: wait-free coordination for internet-scale systems
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Galaxy CloudMan: delivering cloud compute clusters
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BMC Bioinformatics
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Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler
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PLoS ONE
2009-12-
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A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
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Nature
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Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications
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Next generation transcriptomes for next generation genomes using est2assembly.
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BMC bioinformatics
2009-12-
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Decomposition of Gene Expression State Space Trajectories
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PLoS Comput Biol
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The sequence and de novo assembly of the giant panda genome
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Nature
2009-12-
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Human genomics: The genome finishers
Dolgin, Elie
Nature
2009-12-
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Bacterial Community Variation in Human Body Habitats Across Space and Time
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Science
2009-12-
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Reproducing the manual annotation of multiple sequence alignments using a SVM classifier.
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Bioinformatics (Oxford, England)
2009-12-
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Gates pours cash into agriculture
Birch, Hayley
Nature Biotechnology
2009-12-
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Poor trapped in poverty by disease
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Nature
2009-12-
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The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
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PLoS Comput Biol
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Sequencing firms' court battle
Allison, Malorye
Nature Biotechnology
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Nature Methods
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Updates to the RMAP short-read mapping software
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Nature Methods
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TagDust--a program to eliminate artifacts from next generation sequencing data.
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Bioinformatics (Oxford, England)
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Windshield splatter analysis with the Galaxy metagenomic pipeline
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Genome Research
2009-11-
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Computation of Rank and Select Functions on Hierarchical Binary String and Its Application to Genome Mapping Problems for Short-Read DNA Sequences
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Journal of Computational Biology
2009-11-
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Predicting new molecular targets for known drugs.
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Nature
2009-11-
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The challenges of sequencing by synthesis
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Nature Biotechnology
2009-11-
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Nature Methods
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Global patterns in belowground communities.
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Diagnosing the future of genomics
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A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)
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2009-11-
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Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses.
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2009-10-
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Improved genome annotation for Zymomonas mobilis.
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2009-10-
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PineSAP--sequence alignment and SNP identification pipeline.
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Bioinformatics
2009-10-
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Quantum-mechanics-derived 13C\\alpha\\ chemical shift server (CheShift) for protein structure validation.
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Genome biology
2009-10-
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Training induces changes in white-matter architecture.
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Direct RNA sequencing.
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ABySS-Explorer: visualizing genome sequence assemblies.
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ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
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Bioinformatics
2009-10-
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PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees.
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2009-10-
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Upcoming challenges for multiple sequence alignment methods in the high-throughput era.
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Dopamine Gene Therapy for Parkinson's Disease in a Nonhuman Primate Without Associated Dyskinesia
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Science Translational Medicine
2009-10-
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Why data-sharing policies matter.
Guttmacher, Alan E. and Nabel, Elizabeth G. and Collins, Francis S.
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Genomic DNA k-mer spectra: models and modalities.
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Genome Biol
2009-10-
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Is it virtuous to be virtual? The VC viewpoint.
Chakma, Justin and Calcagno, Jeff L. and Behbahani, Ali and Mojtahedian, Shawn
Nat Biotechnol
2009-10-
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Genome Project Standards in a New Era of Sequencing
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The power of social networking in medicine.
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V3 Loop Sequence Space Analysis Suggests Different Evolutionary Patterns of CCR5- and CXCR4-Tropic HIV
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PLoS ONE
2009-10-
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Models@ run.time
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Computer
2009-10-
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Personalized copy number and segmental duplication maps using next-generation sequencing.
Alkan, Can and Kidd, Jeffrey M. and Marques-Bonet, Tomas and Aksay, Gozde and Antonacci, Francesca and Hormozdiari, Fereydoun and Kitzman, Jacob O. and Baker, Carl and Malig, Maika and Mutlu, Onur and Sahinalp, S. Cenk and Gibbs, Richard A. and Eichler, Evan E.
Nature genetics
2009-10-
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Metagenomics versus Moore's law
Nature Methods
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Genome assembly and comparison using de Bruijn graphs
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WebArrayDB: cross-platform microarray data analysis and public data repository.
Xia, Xiao Q. and McClelland, Michael and Porwollik, Steffen and Song, Wenzhi and Cong, Xianling and Wang, Yipeng
Bioinformatics
2009-09-
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RazerS--fast read mapping with sensitivity control.
Weese, David and Emde, Anne K. and Rausch, Tobias and D\"oring, Andreas and Reinert, Knut
Genome Res
2009-09-
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Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.
Wang, Kai and Saito, Masumichi and Bisikirska, Brygida C. and Alvarez, Mariano J. and Lim, Wei K. and Rajbhandari, Presha and Shen, Qiong and Nemenman, Ilya and Basso, Katia and Margolin, Adam A. and Klein, Ulf and Favera, Riccardo D. and Califano, Andrea
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2009-09-
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JBrowse: a next-generation genome browser.
Skinner, Mitchell E. and Uzilov, Andrew V. and Stein, Lincoln D. and Mungall, Christopher J. and Holmes, Ian H.
Genome Res
2009-09-
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SHREC: a short-read error correction method.
Schr\"oder, Jan and Schr\"oder, Heiko and Puglisi, Simon J. and Sinha, Ranjan and Schmidt, Bertil
Bioinformatics
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Simultaneous alignment of short reads against multiple genomes.
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Genome Biol
2009-09-
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A fast hybrid short read fragment assembly algorithm.
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2009-09-
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Single-molecule sequencing of an individual human genome
Pushkarev, Dmitry and Neff, Norma F. and Quake, Stephen R.
Nat Biotech
2009-09-
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Computer simulations predict that chromosome movements and rotations accelerate mitotic spindle assembly without compromising accuracy.
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Proc Natl Acad Sci U S A
2009-09-
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Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting
Pathania, Ranjana and Zlitni, Soumaya and Barker, Courtney and Das, Rahul and Gerritsma, David A. and Lebert, Julie and Awuah, Emilia and Melacini, Giuseppe and Capretta, Fred A. and Brown, Eric D.
Nature Chemical Biology
2009-09-
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ChIP-seq: advantages and challenges of a maturing technology
Park, Peter J.
Nature Reviews Genetics
2009-09-
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Targeted capture and massively parallel sequencing of 12 human exomes
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Nature
2009-09-
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Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.
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Genome Res
2009-09-
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Why greed works for shortest common superstring problem
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Theoretical Computer Science
2009-09-
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Real Lives and White Lies in the Funding of Scientific Research
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PLoS Biol
2009-09-
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Circos: an information aesthetic for comparative genomics.
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Genome Res
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VarScan: variant detection in massively parallel sequencing of individual and pooled samples
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ParalleX An Advanced Parallel Execution Model for Scaling-Impaired Applications
Kaiser, Hartmut and Brodowicz, Maciek and Sterling, Thomas
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MPI: A Message-Passing Interface Standard Version 2.2
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De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.
Diguistini, Scott and Liao, Nancy and Platt, Darren and Robertson, Gordon and Seidel, Michael and Chan, Simon and Docking, T. Roderick and Birol, Inanc and Holt, Robert and Hirst, Martin and Mardis, Elaine and Marra, Marco and Hamelin, Richard and Bohlmann, Jorg and Breuil, Colette and Jones, Steven
Genome Biol
2009-09-
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Bioinformatics construction of the human cell surfaceome.
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Expression profiling of microRNAs by deep sequencing
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Briefings in Bioinformatics
2009-09-
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Toward Exascale Resilience
Cappello, F. and Geist, A. and Gropp, B. and Kale, L. and Kramer, B. and Snir, M.
International Journal of High Performance Computing Applications
2009-09-
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Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.
Brady, Arthur and Salzberg, Steven L.
Nature Methods
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The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.
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Genome Res
2009-09-
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Nature Methods
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Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree.
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Curr Biol
2009-08-
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Architecture and secondary structure of an entire HIV-1 RNA genome
Watts, Joseph M. and Dang, Kristen K. and Gorelick, Robert J. and Leonard, Christopher W. and Bess, Julian W. and Swanstrom, Ronald and Burch, Christina L. and Weeks, Kevin M.
Nature
2009-08-
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BMC Genomics
2009-08-
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Genetically encoded FRET sensors to monitor intracellular Zn2+ homeostasis
Vinkenborg, Jan L. and Nicolson, Tamara J. and Bellomo, Elisa A. and Koay, Melissa S. and Rutter, Guy A. and Merkx, Maarten
Nature Methods
2009-08-
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Optimizing data intensive GPGPU computations for DNA sequence alignment
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Parallel Computing
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Functional characterization of the antibiotic resistance reservoir in the human microflora.
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Science (New York, N.Y.)
2009-08-
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Equity for Open-Access Journal Publishing
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PLoS Biol
2009-08-
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Evolutionary analysis of the dynamics of viral infectious disease
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Nat Rev Genet
2009-08-
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Bioinformatics
2009-08-
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The Sequence Alignment/Map format and SAMtools
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Bioinformatics
2009-08-
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Identification of protein functions using a machine-learning approach based on sequence-derived properties
Lee, Bum and Shin, Moon and Oh, Young and Oh, Hae and Ryu, Keun
Proteome Science
2009-08-
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Improved base calling for the Illumina Genome Analyzer using machine learning strategies
Kircher, Martin and Stenzel, Udo and Kelso, Janet
Genome Biology
2009-08-
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Missing in action: enzyme functional annotations in biological databases
Furnham, Nicholas and Garavelli, John S. and Apweiler, Rolf and Thornton, Janet M.
Nature Chemical Biology
2009-08-
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ABACAS: algorithm-based automatic contiguation of assembled sequences.
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Bioinformatics
2009-08-
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Nature of the protein universe
Levitt, Michael
Proceedings of the National Academy of Sciences
2009-07-07
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Credit where credit is overdue.
Nat Biotechnol
2009-07-
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TableButler - A tool for combining, handling and processing of huge data tables.
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BMC Bioinformatics
2009-07-
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Mathematical biology education: beyond calculus.
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Science
2009-07-
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Genome assembly reborn: recent computational challenges.
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Brief Bioinform
2009-07-
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Computing has changed biology--biology education must catch up.
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Science
2009-07-
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Dereplication and de novo sequencing of nonribosomal peptides
Ng, Julio and Bandeira, Nuno and Liu, Wei-Ting and Ghassemian, Majid and Simmons, Thomas L. and Gerwick, William H. and Linington, Roger and Dorrestein, Pieter C. and Pevzner, Pavel A.
Nature Methods
2009-07-
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Parametric complexity of sequence assembly: theory and applications to next generation sequencing.
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J Comput Biol
2009-07-
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Quantification of the yeast transcriptome by single-molecule sequencing.
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Nat Biotechnol
2009-07-
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Fast and accurate short read alignment with Burrows-Wheeler transform.
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Bioinformatics
2009-07-
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Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream.
Kyrpides, Nikos C.
Nat Biotechnol
2009-07-
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Production of L-DOPA and dopamine in recombinant bacteria bearing the Vitreoscilla hemoglobin gene.
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Biotechnology journal
2009-07-
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Scale-Free Networks: A Decade and Beyond
Barab\'asi, Albert-L\'aszl\'o
Science
2009-07-
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Ten Simple Rules for Choosing between Industry and Academia
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PLoS Comput Biol
2009-06-
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CloudBurst: highly sensitive read mapping with MapReduce.
Schatz, Michael C.
Bioinformatics (Oxford, England)
2009-06-
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Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: Cardiac arrhythmias, re-entry and the Halting problem.
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Comput Biol Chem
2009-06-
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SNP detection for massively parallel whole-genome resequencing
Li, Ruiqiang and Li, Yingrui and Fang, Xiaodong and Yang, Huanming and Wang, Jian and Kristiansen, Karsten and Wang, Jun
Genome Research
2009-06-
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Circos: An information aesthetic for comparative genomics
Krzywinski, Martin I. and Schein, Jacqueline E. and Birol, Inanc and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J. and Marra, Marco A.
Genome Research
2009-06-
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Supervised machine learning algorithms for protein structure classification.
Jain, Pooja and Garibaldi, Jonathan M. and Hirst, Jonathan D.
Comput Biol Chem
2009-06-
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Whole genome assembly from 454 sequencing output via modified DNA graph concept.
Blazewicz, Jacek and Bryja, Marcin and Figlerowicz, Marek and Gawron, Piotr and Kasprzak, Marta and Kirton, Edward and Platt, Darren and Przybytek, Jakub and Swiercz, Aleksandra and Szajkowski, Lukasz
Comput Biol Chem
2009-06-
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De novo Transcriptome Assembly with ABySS.
Birol, Inan\cc and Jackman, Shaun D. and Nielsen, Cydney and Qian, Jenny Q. and Varhol, Richard and Stazyk, Greg and Morin, Ryan D. and Zhao, Yongjun and Hirst, Martin and Schein, Jacqueline E. and Horsman, Doug E. and Connors, Joseph M. and Gascoyne, Randy D. and Marra, Marco A. and Jones, Steven J.
Bioinformatics
2009-06-
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Cloud computing
Bateman, Alex and Wood, Matt
Bioinformatics
2009-06-
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MapView: visualization of short reads alignment on a desktop computer
Bao, Hua and Guo, Hui and Wang, Jinwei and Zhou, Renchao and Lu, Xuemei and Shi, Suhua
Bioinformatics
2009-06-
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A Message Processing Method for Top-k Query for Traffic Reduction in Ad Hoc Networks
Hagihara, Ryo and Shinohara, Masako and Hara, Takahiro and Nishio, Shojiro
2009 Tenth International Conference on Mobile Data Management: Systems, Services and Middleware
2009-05-18
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How to map billions of short reads onto genomes.
Trapnell, Cole and Salzberg, Steven L.
Nat Biotechnol
2009-05-
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TopHat: discovering splice junctions with RNA-Seq
Trapnell, Cole and Pachter, Lior and Salzberg, Steven L.
Bioinformatics
2009-05-
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Four stages of a scientific discipline; four types of scientist.
Shneider, Alexander M.
Trends Biochem Sci
2009-05-
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SHRiMP: Accurate Mapping of Short Color-space Reads
Rumble, Stephen M. and Lacroute, Phil and Dalca, Adrian V. and Fiume, Marc and Sidow, Arend and Brudno, Michael
PLoS Comput Biol
2009-05-
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A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
Rausch, Tobias and Koren, Sergey and Denisov, Gennady and Weese, David and Emde, Anne-Katrin K. and D\"oring, Andreas and Reinert, Knut
Bioinformatics (Oxford, England)
2009-05-
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A functional role for transposases in a large eukaryotic genome.
Nowacki, Mariusz and Higgins, Brian P. and Maquilan, Genevieve M. and Swart, Estienne C. and Doak, Thomas G. and Landweber, Laura F.
Science
2009-05-
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Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance.
Feng, Jie and Lupien, Andréanne and Gingras, Hél\`ene and Wasserscheid, Jessica and Dewar, Ken and Légaré, Danielle and Ouellette, Marc
Genome Res
2009-05-
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Fast Statistical Alignment
Bradley, Robert K. and Roberts, Adam and Smoot, Michael and Juvekar, Sudeep and Do, Jaeyoung and Dewey, Colin and Holmes, Ian and Pachter, Lior
PLoS Comput Biol
2009-05-
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Visualization of genomic data with the Hilbert curve.
Anders, Simon
Bioinformatics (Oxford, England)
2009-05-
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Defining the scientific method
Nature Methods
2009-04-
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Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
White, James R. and Nagarajan, Niranjan and Pop, Mihai
PLoS Comput Biol
2009-04-
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Ten Simple Rules To Combine Teaching and Research
Vicens, Quentin and Bourne, Philip E.
PLoS Comput Biol
2009-04-
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Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing
Temperton, Ben and Field, Dawn and Oliver, Anna and Tiwari, Bela and Muhling, Martin and Joint, Ian and Gilbert, Jack A.
The ISME Journal
2009-04-
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New strategies and emerging technologies for massively parallel sequencing: applications in medical research.
Mardis, Elaine R.
Genome medicine
2009-04-
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Application of 'next-generation' sequencing technologies to microbial genetics.
MacLean, Daniel and Jones, Jonathan D. G. and Studholme, David J.
Nat Rev Microbiol
2009-04-
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The most influential journals: Impact Factor and Eigenfactor.
Fersht, Alan
Proc Natl Acad Sci U S A
2009-04-
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MOM: maximum oligonucleotide mapping
Eaves, Hugh L. and Gao, Yuan
Bioinformatics
2009-04-
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Quantification of rare allelic variants from pooled genomic DNA.
Druley, Todd E. and Vallania, Francesco L. M. and Wegner, Daniel J. and Varley, Katherine E. and Knowles, Olivia L. and Bonds, Jacqueline A. and Robison, Sarah W. and Doniger, Scott W. and Hamvas, Aaron and Cole, F. Sessions and Fay, Justin C. and Mitra, Robi D.
Nat Methods
2009-04-
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PASS: a program to align short sequences.
Campagna, Davide and Albiero, Alessandro and Bilardi, Alessandra and Caniato, Elisa and Forcato, Claudio and Manavski, Svetlin and Vitulo, Nicola and Valle, Giorgio
Bioinformatics (Oxford, England)
2009-04-
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Sequence assembly.
Alsing, K. Scheibye and Hoffmann, S. and Frankel, A. and Jensen, P. and Stadler, P. F. and Mang, Y. and Tommerup, N. and Gilchrist, M. J. and Nyg\$backslash\$rard, A. B. and Cirera, S. and J\o rgensen, C. B. and Fredholm, M. and Gorodkin, J.
Comput Biol Chem
2009-04-
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Lines of communication
Nature Methods
2009-03-
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Filling the void
Nature
2009-03-
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Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.
Yassour, Moran and Kaplan, Tommy and Fraser, Hunter B. and Levin, Joshua Z. and Pfiffner, Jenna and Adiconis, Xian and Schroth, Gary and Luo, Shujun and Khrebtukova, Irina and Gnirke, Andreas and Nusbaum, Chad and Thompson, Dawn A. and Friedman, Nir and Regev, Aviv
Proc Natl Acad Sci U S A
2009-03-
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Are we training pit bulls to review our manuscripts?
Walbot, Virginia
Journal of Biology
2009-03-
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Comparison of Automated Microarray Detection with Real-Time PCR Assays for Detection of Respiratory Viruses in Specimens Obtained from Children
Raymond, Frédéric and Carbonneau, Julie and Boucher, Nancy and Robitaille, Lynda and Boisvert, Sébastien and Wu, Whei-Kuo and De Serres Gaston and Boivin, Guy and Corbeil, Jacques
Journal of Clinical Microbiology
2009-03-
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven
Genome Biology
2009-03-
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The need for speed.
Flicek, Paul
Genome biology
2009-03-
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Scala Actors: Unifying thread-based and event-based programming
Haller, Philipp and Odersky, Martin
Theoretical Computer Science
2009-02-
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Scala Actors: Unifying thread-based and event-based programming
Haller, Philipp and Odersky, Martin
Theoretical Computer Science
2009-02-
doi:10.1016/j.tcs.2008.09.019
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.
Gnirke, Andreas and Melnikov, Alexandre and Maguire, Jared and Rogov, Peter and LeProust, Emily M. and Brockman, William and Fennell, Timothy and Giannoukos, Georgia and Fisher, Sheila and Russ, Carsten and Gabriel, Stacey and Jaffe, David B. and Lander, Eric S. and Nusbaum, Chad
Nature biotechnology
2009-02-
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Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology.
Fontana, Paolo and Cestaro, Alessandro and Velasco, Riccardo and Formentin, Elide and Toppo, Stefano
PloS one
2009-02-
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AutoGrow: A Novel Algorithm for Protein Inhibitor Design
Durrant, Jacob D. and Amaro, Rommie E. and McCammon, J. Andrew
Chemical Biology & Drug Design
2009-02-
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Understanding genome browsing.
Cline, Melissa S. and Kent, W. James
Nat Biotechnol
2009-02-
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Editorial
Bateman, Alex and Quackenbush, John
Bioinformatics
2009-02-
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Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa.
Winstanley, Craig and Langille, Morgan G. I. and Fothergill, Joanne L. and Ibrulj, Irena K. and Bleau, Catherine P. and Sanschagrin, Fran\ccois and Thomson, Nicholas R. and Winsor, Geoff L. and Quail, Michael A. and Lennard, Nicola and Bignell, Alexandra and Clarke, Louise and Seeger, Kathy and Saunders, David and Harris, David and Parkhill, Julian and Hancock, Robert E. W. and Brinkman, Fiona S. L. and Levesque, Roger C.
Genome Res
2009-01-
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RNA-Seq: a revolutionary tool for transcriptomics.
Wang, Zhong and Gerstein, Mark and Snyder, Michael
Nature reviews. Genetics
2009-01-
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Eventually Consistent
Vogels, Werner
Communications of the ACM
2009-01-
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Slider—maximum use of probability information for alignment of short sequence reads and SNP detection
Malhis, Nawar and Butterfield, Yaron S. N. and Ester, Martin and Jones, Steven J. M.
Bioinformatics
2009-01-
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ARDB—Antibiotic Resistance Genes Database
Liu, Bo and Pop, Mihai
Nucleic Acids Research
2009-01-
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Statistical distributions of pyrosequencing.
Kong, Yong
J Comput Biol
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Parallel short sequence assembly of transcriptomes.
Jackson, Benjamin G. and Schnable, Patrick S. and Aluru, Srinivas
BMC bioinformatics
2009-01-
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The human brain in numbers: a linearly scaled-up primate brain.
Herculano-Houzel, Suzana
Frontiers in human neuroscience
2009-01-
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Real-time DNA sequencing from single polymerase molecules.
Eid, John and Fehr, Adrian and Gray, Jeremy and Luong, Khai and Lyle, John and Otto, Geoff and Peluso, Paul and Rank, David and Baybayan, Primo and Bettman, Brad and Bibillo, Arkadiusz and Bjornson, Keith and Chaudhuri, Bidhan and Christians, Frederick and Cicero, Ronald and Clark, Sonya and Dalal, Ravindra and Dewinter, Alex and Dixon, John and Foquet, Mathieu and Gaertner, Alfred and Hardenbol, Paul and Heiner, Cheryl and Hester, Kevin and Holden, David and Kearns, Gregory and Kong, Xiangxu and Kuse, Ronald and Lacroix, Yves and Lin, Steven and Lundquist, Paul and Ma, Congcong and Marks, Patrick and Maxham, Mark and Murphy, Devon and Park, Insil and Pham, Thang and Phillips, Michael and Roy, Joy and Sebra, Robert and Shen, Gene and Sorenson, Jon and Tomaney, Austin and Travers, Kevin and Trulson, Mark and Vieceli, John and Wegener, Jeffrey and Wu, Dawn and Yang, Alicia and Zaccarin, Denis and Zhao, Peter and Zhong, Frank and Korlach, Jonas and Turner, Stephen
Science
2009-01-
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A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera
Deloger, Marc and Karoui, Meriem E. and Petit, Marie-Agn\`es
Journal of Bacteriology
2009-01-
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Multi-class AdaBoost
Zhu, Ji and Zou, Hui and Rosset, Saharon and Hastie, Trevor
STATISTICS AND ITS INTERFACE VOLUME
2009-xx-
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Multi-way Number Partitioning
Korf, Richard E.
Proceedings of the 21st International Jont Conference on Artifical Intelligence
2009-xx-
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Scalable Work Stealing
Dinan, James and Larkins, D. Brian and Sadayappan, P. and Krishnamoorthy, Sriram and Nieplocha, Jarek
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
2009-xx-
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Characterizing the Performance of "Big Memory" on Blue Gene Linux
Yoshii, Kazutomo and Iskra, Kamil and Naik, Harish and Beckmanm, Pete and Broekema, P. Chris
Proceedings of the 2009 International Conference on Parallel Processing Workshops
2009-xx-
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Q&A: What have we found out about the influenza A (H1N1) 2009 pandemic virus?
Turner, Stephen and Brown, Lorena and Doherty, Peter and Kelso, Anne
Journal of Biology
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ABySS: A parallel assembler for short read sequence data.
Simpson, Jared T. and Wong, Kim and Jackman, Shaun D. and Schein, Jacqueline E. and Jones, Steven J. M. and Birol, Inan\cc
Genome Research
2009-xx-
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Skittle: A 2-Dimensional Genome Visualization Tool
Seaman, Josiah and Sanford, John
BMC Bioinformatics
2009-xx-
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Natively Supporting True One-Sided Communication in  MPI on Multi-core Systems with InfiniBand
Santhanaraman, G. and Balaji, P. and Gopalakrishnan, K. and Thakur, R. and Gropp, W. and Panda, D. K.
2009 9th IEEE/ACM International Symposium on Cluster Computing and the Grid
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Natively Supporting True One-Sided Communication in  MPI on Multi-core Systems with InfiniBand
Santhanaraman, G. and Balaji, P. and Gopalakrishnan, K. and Thakur, R. and Gropp, W. and Panda, D. K.
2009 9th IEEE/ACM International Symposium on Cluster Computing and the Grid
2009-xx-
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Managing and Analyzing Next-Generation Sequence Data
Richter, Brent G. and Sexton, David P.
PLoS Comput Biol
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Cloud technologies for bioinformatics applications
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Proceedings of the 2nd Workshop on Many-Task Computing on Grids and Supercomputers
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Coordinated gene expression by post-transcriptional regulons in African trypanosomes
Ouellette, Marc and Papadopoulou, Barbara
Journal of Biology
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Winning a 60 second dash with a yellow elephant
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Establishing a Successful Bioinformatics Core Facility Team
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PLoS Comput Biol
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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Genome Biol
2009-xx-
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Make Room for Computing
Klymkowsky, M. W.
Science
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Charm++ and AMPI: Adaptive Runtime Strategies via Migratable Objects
Kale, Laxmikant V. and Zheng, Gengbin
Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications
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Assembly of Large Genomes from Paired Short Reads
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Bioinformatics and Computational Biology
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Parallel short sequence assembly of transcriptomes.
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BMC bioinformatics
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Crystallizing short-read assemblies around seeds.
Hossain, Mohammad S. and Azimi, Navid and Skiena, Steven
BMC Bioinformatics
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Formal kinetics of H1N1 epidemic.
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Theor Biol Med Model
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Assisted assembly: how to improve a de novo genome assembly by using related species.
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Genome Biol
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Nature Methods
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Metagenomics: Read Length Matters
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Applied and Environmental Microbiology
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Bioinformatics
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Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies
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BMC Microbiology
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Nature Methods
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Using quality scores and longer reads improves accuracy of Solexa read mapping
Smith, Andrew and Xuan, Zhenyu and Zhang, Michael
BMC Bioinformatics
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The RAST Server: rapid annotations using subsystems technology.
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BMC genomics
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Nature Methods
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Proceedings of the Royal Society B: Biological Sciences
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FastBLAST: homology relationships for millions of proteins.
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ACM SIGPLAN Notices
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Dean, Jeffrey and Ghemawat, Sanjay
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Combinatorial methods in computational genomics : mammalian phylogenetics using microinversions and fragment assembly with short reads
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The average mutual information profile as a genomic signature.
Bauer, Mark and Schuster, Sheldon M. and Sayood, Khalid
BMC bioinformatics
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An Efficient Parallel Approach for Identifying Protein Families in Large-scale Metagenomic Data Sets
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Genome Biol
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The second chance story of HIV-1 DNA: Unintegrated? Not a problem!
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Retrovirology
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Genome Biol
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Evaluating the Effect of Replacing CNK with Linux on the Compute-nodes of Blue Gene/L
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BMC Genomics
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Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome
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Genome assembly forensics: finding the elusive mis-assembly.
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Genome Biol
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BMC Bioinformatics
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Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks.
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A weighted average difference method for detecting differentially expressed genes from microarray data.
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BMC Bioinformatics
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Can Children with Autism Recover? If So, How?
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Genetic analysis of the human infective trypanosome Trypanosoma brucei gambiense: chromosomal segregation, crossing over, and the construction of a genetic map.
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Blast2GO: A comprehensive suite for functional analysis in plant genomics.
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HIV-1 coreceptor usage determination in clinical isolates using clonal and population-based genotypic and phenotypic assays.
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Genome biology
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Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
Warnecke, Falk and Luginbuhl, Peter and Ivanova, Natalia and Ghassemian, Majid and Richardson, Toby H. and Stege, Justin T. and Cayouette, Michelle and McHardy, Alice C. and Djordjevic, Gordana and Aboushadi, Nahla and Sorek, Rotem and Tringe, Susannah G. and Podar, Mircea and Martin, Hector G. and Kunin, Victor and Dalevi, Daniel and Madejska, Julita and Kirton, Edward and Platt, Darren and Szeto, Ernest and Salamov, Asaf and Barry, Kerrie and Mikhailova, Natalia and Kyrpides, Nikos C. and Matson, Eric G. and Ottesen, Elizabeth A. and Zhang, Xinning and Hernandez, Myriam and Murillo, Catalina and Acosta, Luis G. and Rigoutsos, Isidore and Tamayo, Giselle and Green, Brian D. and Chang, Cathy and Rubin, Edward M. and Mathur, Eric J. and Robertson, Dan E. and Hugenholtz, Philip and Leadbetter, Jared R.
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Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer
Sorek, Rotem and Zhu, Yiwen and Creevey, Christopher J. and Francino, M. Pilar and Bork, Peer and Rubin, Edward M.
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Extending assembly of short DNA sequences to handle error.
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Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome.
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Genome Res
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Current opinion in microbiology
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Pseudomonas aeruginosa May Accumulate Drug Resistance Mechanisms without Losing Its Ability To Cause Bloodstream Infections
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Dynamo: amazon's highly available key-value store
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PLoS Biol
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Wang, Chunlin and Mitsuya, Yumi and Gharizadeh, Baback and Ronaghi, Mostafa and Shafer, Robert W.
Genome Res
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Pyrosequencing enumerates and contrasts soil microbial diversity.
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ChIP-seq: welcome to the new frontier
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Nat Meth
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International Journal of High Performance Computing Applications
2007-08-
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Dissecting biological ” dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
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2007-07-17
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Comparative genomic analysis of three Leishmania species that cause diverse human disease.
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Nature genetics
2007-07-
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Proceedings of the National Academy of Sciences
2007-07-
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Bioinformatics
2007-07-
http://www.google.com/search?hl=en&site=&q=\\F\\ast model-based protein homology detection without alignment&btnG=Search
Supervised reconstruction of biological networks with local models
Bleakley, Kevin and Biau, Gerard and Vert, Jean-Philippe
Bioinformatics
2007-07-
doi:10.1093/bioinformatics/btm204
A View from the Dark Side
Searls, David B.
PLoS Comput Biol
2007-06-
doi:10.1371/journal.pcbi.0030105
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
Mavromatis, Konstantinos and Ivanova, Natalia and Barry, Kerrie and Shapiro, Harris and Goltsman, Eugene and McHardy, Alice C. and Rigoutsos, Isidore and Salamov, Asaf and Korzeniewski, Frank and Land, Miriam and Lapidus, Alla and Grigoriev, Igor and Richardson, Paul and Hugenholtz, Philip and Kyrpides, Nikos C.
Nat Meth
2007-06-
doi:10.1038/nmeth1043
Genomorama: genome visualization and analysis
Gans, Jason and Wolinsky, Murray
BMC Bioinformatics
2007-06-
doi:10.1186/1471-2105-8-204
PTC124 targets genetic disorders caused by nonsense mutations.
Welch, Ellen M. and Barton, Elisabeth R. and Zhuo, Jin and Tomizawa, Yuki and Friesen, Westley J. and Trifillis, Panayiota and Paushkin, Sergey and Patel, Meenal and Trotta, Christopher R. and Hwang, Seongwoo and Wilde, Richard G. and Karp, Gary and Takasugi, James and Chen, Guangming and Jones, Stephen and Ren, Hongyu and Moon, Young-Choon C. and Corson, Donald and Turpoff, Anthony A. and Campbell, Jeffrey A. and Conn, Morgan M. and Khan, Atiyya and Almstead, Neil G. and Hedrick, Jean and Mollin, Anna and Risher, Nicole and Weetall, Marla and Yeh, Shirley and Branstrom, Arthur A. and Colacino, Joseph M. and Babiak, John and Ju, William D. and Hirawat, Samit and Northcutt, Valerie J. and Miller, Langdon L. and Spatrick, Phyllis and He, Feng and Kawana, Masataka and Feng, Huisheng and Jacobson, Allan and Peltz, Stuart W. and Sweeney, H. Lee
Nature
2007-05-
doi:10.1038/nature05756
What's the 'meta' with metagenomics?
Steward, Grieg F. and Rappe, Michael S.
The ISME Journal
2007-05-
doi:10.1038/ismej.2007.25
On the Advantages of an Alternative MPI Execution Model for Grids
Sena, A. C. and Nascimento, A. P. and Da Silva J. A. and Vianna, D. Q. C. and Boeres, C. and Rebello, V. E. F.
Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid '07)
2007-05-
doi:10.1109/CCGRID.2007.74
Ten Principles to Improve the Likelihood of Publication of a Scientific Manuscript
Provenzale, James M.
Am. J. Roentgenol.
2007-05-
doi:10.2214/ajr.06.1003
Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing
Mwangi, Michael M. and Wu, Shang W. and Zhou, Yanjiao and Sieradzki, Krzysztof and de Lencastre, Herminia and Richardson, Paul and Bruce, David and Rubin, Edward and Myers, Eugene and Siggia, Eric D. and Tomasz, Alexander
Proceedings of the National Academy of Sciences
2007-05-
doi:10.1073/pnas.0609839104
Writing intelligible English prose for biomedical journals.
Ludbrook, John
Clinical and experimental pharmacology & physiology
2007-05-
doi:10.1111/j.1440-1681.2007.04603.x
Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition.
Lefébure, Tristan and Stanhope, Michael J.
Genome biology
2007-05-
doi:10.1186/gb-2007-8-5-r71
Reducing Connection Memory Requirements of MPI for InfiniBand Clusters: A Message Coalescing Approach
Koop, Matthew J. and Jones, Terry and Panda, Dhabaleswar K.
Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid '07)
2007-05-
doi:10.1109/CCGRID.2007.92
Population-based sequencing of the V3 region of env for predicting the coreceptor usage of human immunodeficiency virus type 1 quasispecies.
Delobel, Pierre and Nugeyre, Marie T. and Cazabat, Michelle and Pasquier, Christophe and Marchou, Bruno and Massip, Patrice and Sinoussi, Fran\ccoise B. and Isra\"el, Nicole and Izopet, Jacques
J Clin Microbiol
2007-05-
doi:10.1128/JCM.02090-06
Evolutionary and biomedical insights from the rhesus macaque genome.
Rhesus Macaque Genome Sequencing and Analysis Consortium and Gibbs, Richard A. and Rogers, Jeffrey and Katze, Michael G. and Bumgarner, Roger and Weinstock, George M. and Mardis, Elaine R. and Remington, Karin A. and Strausberg, Robert L. and Venter, J. Craig and Wilson, Richard K. and Batzer, Mark A. and Bustamante, Carlos D. and Eichler, Evan E. and Hahn, Matthew W. and Hardison, Ross C. and Makova, Kateryna D. and Miller, Webb and Milosavljevic, Aleksandar and Palermo, Robert E. and Siepel, Adam and Sikela, James M. and Attaway, Tony and Bell, Stephanie and Bernard, Kelly E. and Buhay, Christian J. and Chandrabose, Mimi N. and Dao, Marvin and Davis, Clay and Delehaunty, Kimberly D. and Ding, Yan and Dinh, Huyen H. and Dugan-Rocha, Shannon and Fulton, Lucinda A. and Gabisi, Ramatu A. and Garner, Toni T. and Godfrey, Jennifer and Hawes, Alicia C. and Hernandez, Judith and Hines, Sandra and Holder, Michael and Hume, Jennifer and Jhangiani, Shalini N. and Joshi, Vandita and Khan, Ziad M. and Kirkness, Ewen F. and Cree, Andrew and Fowler, R. Gerald and Lee, Sandra and Lewis, Lora R. and Li, Zhangwan and Liu, Yih-Shin S. and Moore, Stephanie M. and Muzny, Donna and Nazareth, Lynne V. and Ngo, Dinh N. and Okwuonu, Geoffrey O. and Pai, Grace and Parker, David and Paul, Heidie A. and Pfannkoch, Cynthia and Pohl, Craig S. and Rogers, Yu-Hui H. and Ruiz, San J. and Sabo, Aniko and Santibanez, Jireh and Schneider, Brian W. and Smith, Scott M. and Sodergren, Erica and Svatek, Amanda F. and Utterback, Teresa R. and Vattathil, Selina and Warren, Wesley and White, Courtney S. and Chinwalla, Asif T. and Feng, Yucheng and Halpern, Aaron L. and Hillier, Ladeana W. and Huang, Xiaoqiu and Minx, Pat and Nelson, Joanne O. and Pepin, Kymberlie H. and Qin, Xiang and Sutton, Granger G. and Venter, Eli and Walenz, Brian P. and Wallis, John W. and Worley, Kim C. and Yang, Shiaw-Pyng P. and Jones, Steven M. and Marra, Marco A. and Rocchi, Mariano and Schein, Jacqueline E. and Baertsch, Robert and Clarke, Laura and Cs\"ur\"os, Mikl\'os and Glasscock, Jarret and Harris, R. Alan and Havlak, Paul and Jackson, Andrew R. and Jiang, Huaiyang and Liu, Yue and Messina, David N. and Shen, Yufeng and Song, Henry X. and Wylie, Todd and Zhang, Lan and Birney, Ewan and Han, Kyudong and Konkel, Miriam K. and Lee, Jungnam and Smit, Arian F. and Ullmer, Brygg and Wang, Hui and Xing, Jinchuan and Burhans, Richard and Cheng, Ze and Karro, John E. and Ma, Jian and Raney, Brian and She, Xinwei and Cox, Michael J. and Demuth, Jeffery P. and Dumas, Laura J. and Han, Sang-Gook G. and Hopkins, Janet and Karimpour-Fard, Anis and Kim, Young H. and Pollack, Jonathan R. and Vinar, Tomas and Addo-Quaye, Charles and Degenhardt, Jeremiah and Denby, Alexandra and Hubisz, Melissa J. and Indap, Amit and Kosiol, Carolin and Lahn, Bruce T. and Lawson, Heather A. and Marklein, Alison and Nielsen, Rasmus and Vallender, Eric J. and Clark, Andrew G. and Ferguson, Betsy and Hernandez, Ryan D. and Hirani, Kashif and Kehrer-Sawatzki, Hildegard and Kolb, Jessica and Patil, Shobha and Pu, Ling-Ling L. and Ren, Yanru and Smith, David G. and Wheeler, David A. and Schenck, Ian and Ball, Edward V. and Chen, Rui and Cooper, David N. and Giardine, Belinda and Hsu, Fan and Kent, W. James and Lesk, Arthur and Nelson, David L. and O'brien, William E. and Pr\"ufer, Kay and Stenson, Peter D. and Wallace, James C. and Ke, Hui and Liu, Xiao-Ming M. and Wang, Peng and Xiang, Andy P. and Yang, Fan and Barber, Galt P. and Haussler, David and Karolchik, Donna and Kern, Andy D. and Kuhn, Robert M. and Smith, Kayla E. and Zwieg, Ann S.
Science (New York, N.Y.)
2007-04-
doi:10.1126/science.1139247
Gepard: a rapid and sensitive tool for creating dotplots on genome scale.
Krumsiek, Jan and Arnold, Roland and Rattei, Thomas
Bioinformatics (Oxford, England)
2007-04-
doi:10.1093/bioinformatics/btm039
Social software
Nature Methods
2007-03-
doi:10.1038/nmeth0307-189
CAMERA: A Community Resource for Metagenomics
Seshadri, Rekha and Kravitz, Saul A. and Smarr, Larry and Gilna, Paul and Frazier, Marvin
PLoS Biol
2007-03-
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Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage.
Sander, Oliver and Sing, Tobias and Sommer, Ingolf and Low, Andrew J. and Cheung, Peter K. and Harrigan, P. Richard and Lengauer, Thomas and Domingues, Francisco S.
PLoS Comput Biol
2007-03-
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The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
Rusch, Douglas B. and Halpern, Aaron L. and Sutton, Granger and Heidelberg, Karla B. and Williamson, Shannon and Yooseph, Shibu and Wu, Dongying and Eisen, Jonathan A. and Hoffman, Jeff M. and Remington, Karin and Beeson, Karen and Tran, Bao and Smith, Hamilton and Baden-Tillson, Holly and Stewart, Clare and Thorpe, Joyce and Freeman, Jason and Andrews-Pfannkoch, Cynthia and Venter, Joseph E. and Li, Kelvin and Kravitz, Saul and Heidelberg, John F. and Utterback, Terry and Rogers, Yu-Hui and Falc\'on, Luisa I. and Souza, Valeria and Bonilla-Rosso, Germ\'an and Eguiarte, Luis E. and Karl, David M. and Sathyendranath, Shubha and Platt, Trevor and Bermingham, Eldredge and Gallardo, Victor and Tamayo-Castillo, Giselle and Ferrari, Michael R. and Strausberg, Robert L. and Nealson, Kenneth and Friedman, Robert and Frazier, Marvin and Venter, J. Craig
PLoS Biol
2007-03-
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A human phenome-interactome network of protein complexes implicated in genetic disorders
Lage, Kasper and Karlberg, E. Olof and Storling, Zenia M. and Olason, Pall I. and Pedersen, Anders G. and Rigina, Olga and Hinsby, Anders M. and Tumer, Zeynep and Pociot, Flemming and Tommerup, Niels and Moreau, Yves and Brunak, Soren
Nature Biotechnology
2007-03-
doi:10.1038/nbt1295
The Data Vortex, an All Optical Path Multicomputer Interconnection Network
Hawkins, Cory and Small, Benjamin and Wills, D. and Bergman, Keren
IEEE Transactions on Parallel and Distributed Systems
2007-03-
doi:10.1109/TPDS.2007.48
Same computational analysis, different miRNA target predictions
Hatzigeorgiou, Artemis G.
Nature Methods
2007-03-
doi:10.1038/nmeth0307-191b
ParalleX: A Study of A New Parallel Computation Model
Gao, Guang R. and Sterling, Thomas and Stevens, Rick and Hereld, Mark and Zhu, Weirong
2007 IEEE International Parallel and Distributed Processing Symposium
2007-03-
doi:10.1109/IPDPS.2007.370484
Identifying bacterial genes and endosymbiont DNA with Glimmer.
Delcher, Arthur L. and Bratke, Kirsten A. and Powers, Edwin C. and Salzberg, Steven L.
Bioinformatics
2007-03-
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The D programming language
Armaly, Ameer
Linux J.
2007-03-
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Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.
Albert, Istvan and Mavrich, Travis N. and Tomsho, Lynn P. and Qi, Ji and Zanton, Sara J. and Schuster, Stephan C. and Pugh, B. Franklin
Nature
2007-03-
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Assembling millions of short DNA sequences using SSAKE.
Warren, René L. and Sutton, Granger G. and Jones, Steven J. M. and Holt, Robert A.
Bioinformatics
2007-02-
doi:10.1093/bioinformatics/btl629
\\D\\etermining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model
Skrabal, K. and Low, A. J. and Dong, W. and Sing, T. and Cheung, P. K. and Mammano, F. and Harrigan, P. R.
J. Clin. Microbiol.
2007-02-
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Oligonucleotide microarray identification of Bacillus anthracis strains using support vector machines.
Doran, M. and Raicu, D. S. and Furst, J. D. and Settimi, R. and Schipma, M. and Chandler, D. P.
Bioinformatics
2007-02-
doi:10.1093/bioinformatics/btl626
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
McNeil, Leslie Klis K. and Reich, Claudia and Aziz, Ramy K. and Bartels, Daniela and Cohoon, Matthew and Disz, Terry and Edwards, Robert A. and Gerdes, Svetlana and Hwang, Kaitlyn and Kubal, Michael and Margaryan, Gohar Rem R. and Meyer, Folker and Mihalo, William and Olsen, Gary J. and Olson, Robert and Osterman, Andrei and Paarmann, Daniel and Paczian, Tobias and Parrello, Bruce and Pusch, Gordon D. and Rodionov, Dmitry A. and Shi, Xinghua and Vassieva, Olga and Vonstein, Veronika and Zagnitko, Olga and Xia, Fangfang and Zinner, Jenifer and Overbeek, Ross and Stevens, Rick
Nucleic acids research
2007-01-01
doi:10.1093/nar/gkl947
PATRIC: the VBI PathoSystems Resource Integration Center.
Snyder, E. E. and Kampanya, N. and Lu, J. and Nordberg, E. K. and Karur, H. R. and Shukla, M. and Soneja, J. and Tian, Y. and Xue, T. and Yoo, H. and Zhang, F. and Dharmanolla, C. and Dongre, N. V. and Gillespie, J. J. and Hamelius, J. and Hance, M. and Huntington, K. I. and Jukneliene, D. and Koziski, J. and Mackasmiel, L. and Mane, S. P. and Nguyen, V. and Purkayastha, A. and Shallom, J. and Yu, G. and Guo, Y. and Gabbard, J. and Hix, D. and Azad, A. F. and Baker, S. C. and Boyle, S. M. and Khudyakov, Y. and Meng, X. J. and Rupprecht, C. and Vinje, J. and Crasta, O. R. and Czar, M. J. and Dickerman, A. and Eckart, J. D. and Kenyon, R. and Will, R. and Setubal, J. C. and Sobral, B. W.
Nucleic acids research
2007-01-
doi:10.1093/nar/gkl858
Morpheus unbound: reimagining the morphogen gradient.
Lander, Arthur D.
Cell
2007-01-
doi:10.1016/j.cell.2007.01.004
Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins.
Axelsen, Jacob B. and Yan, Koon-Kiu and Maslov, Sergei
Biology direct
2007-01-
doi:10.1186/1745-6150-2-32
ApiDB: integrated resources for the apicomplexan bioinformatics resource center.
Aurrecoechea, Cristina and Heiges, Mark and Wang, Haiming and Wang, Zhiming and Fischer, Steve and Rhodes, Philippa and Miller, John and Kraemer, Eileen and Stoeckert, Christian J. and Roos, David S. and Kissinger, Jessica C.
Nucleic Acids Res
2007-01-
doi:10.1093/nar/gkl880
Reducing Traffic of Messages in Distributed Editing Systems
Hui, Huaihai and Liang, Gongqian and Ma, Jiancheng and Yang, Jianxv
Wireless Communications, Networking and Mobile Computing, 2007. WiCom 2007. International Conference on
2007-xx-
doi:10.1109/wicom.2007.1445
Why do amusement parks only charge a fixed admission fee?
Wu, Dachrahn and Liu, Nien P.
Economics Letters
2007-xx-
doi:10.1016/j.econlet.2006.09.030
Modern Operating Systems
Tanenbaum, Andrew S.
2007-xx-
http://portal.acm.org/citation.cfm?id=1410217
Whole-genome sequencing and assembly with high-throughput, short-read technologies.
Sundquist, Andreas and Ronaghi, Mostafa and Tang, Haixu and Pevzner, Pavel and Batzoglou, Serafim
PLoS ONE
2007-xx-
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Minimus: a fast, lightweight genome assembler.
Sommer, Daniel D. and Delcher, Arthur L. and Salzberg, Steven L. and Pop, Mihai
BMC Bioinformatics
2007-xx-
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\\P\\redicting \\H\\\\I\\\\V\\ coreceptor usage on the basis of genetic and clinical covariates
Sing, T. and Low, A. J. and Beerenwinkel, N. and Sander, O. and Cheung, P. K. and Domingues, F. S. and B\"uch, J. and D\"aumer, M. and Kaiser, R. and Lengauer, T. and Harrigan, P. R.
Antivir. Ther. (Lond.)
2007-xx-
http://www.google.com/search?hl=en&site=&q=\\P\\redicting \\H\\\\I\\\\V\\ coreceptor usage on the basis of genetic and clinical covariates&btnG=Search
High-throughput sequence alignment using Graphics Processing Units
Schatz, Michael and Trapnell, Cole and Delcher, Arthur and Varshney, Amitabh
BMC Bioinformatics
2007-xx-
doi:10.1186/1471-2105-8-474
Hawkeye: an interactive visual analytics tool for genome assemblies.
Schatz, Michael C. and Phillippy, Adam M. and Shneiderman, Ben and Salzberg, Steven L.
Genome Biol
2007-xx-
doi:10.1186/gb-2007-8-3-r34
Coordination Models and Languages
2007-xx-
doi:10.1007/978-3-540-72794-1
Computability of Models for Sequence Assembly
Medvedev, Paul and Georgiou, Konstantinos and Myers, Gene and Brudno, Michael
Algorithms in Bioinformatics
2007-xx-
doi:10.1007/978-3-540-74126-8_27
CLUSS: clustering of protein sequences based on a new similarity measure.
Kelil, Abdellali and Wang, Shengrui and Brzezinski, Ryszard and Fleury, Alain
BMC Bioinformatics
2007-xx-
doi:10.1186/1471-2105-8-286
Dryad: Distributed Data-parallel Programs from Sequential Building Blocks
Isard, Michael and Budiu, Mihai and Yu, Yuan and Birrell, Andrew and Fetterly, Dennis
Proceedings of the 2Nd ACM SIGOPS/EuroSys European Conference on Computer Systems 2007
2007-xx-
doi:10.1145/1272996.1273005
Revised Loss Bounds for the Set Covering Machine and Sample-Compression Loss Bounds for Imbalanced Data
Hussain, Zakria and Laviolette, Fran\ccois and Marchand, Mario and Taylor, John S. and Brubaker, Spencer C. and Mullin, Matthew D.
J. Mach. Learn. Res.
2007-xx-
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Accuracy and quality of massively parallel DNA pyrosequencing.
Huse, Susan M. and Huber, Julie A. and Morrison, Hilary G. and Sogin, Mitchell L. and Welch, David M.
Genome Biol
2007-xx-
doi:10.1186/gb-2007-8-7-r143
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.
Gross, Samuel S. and Do, Chuong B. and Sirota, Marina and Batzoglou, Serafim
Genome Biol
2007-xx-
doi:10.1186/gb-2007-8-12-r269
Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats.
Fankhauser, Niklaus and Ha, Tien M. and Adler, Jo\"el and M\"aser, Pascal
Proteome Sci
2007-xx-
doi:10.1186/1477-5956-5-20
Identifying sources of Operating System Jitter through fine-grained kernel instrumentation
De, Pradipta and Kothari, Ravi and Mann, Vijay
2007 IEEE International Conference on Cluster Computing
2007-xx-
doi:10.1109/CLUSTR.2007.4629247
Identifying sources of Operating System Jitter through fine-grained kernel instrumentation
De, Pradipta and Kothari, Ravi and Mann, Vijay
2007 IEEE International Conference on Cluster Computing
2007-xx-
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Colored de Bruijn graphs and the genome halving problem.
Alekseyev, Max A. and Pevzner, Pavel A.
IEEE/ACM Trans Comput Biol Bioinform
2007-xx-
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What is a support vector machine?
Noble, William S.
Nat Biotechnol
2006-12-
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Reconstructing contiguous regions of an ancestral genome.
Ma, Jian and Zhang, Louxin and Suh, Bernard B. and Raney, Brian J. and Burhans, Richard C. and Kent, W. James and Blanchette, Mathieu and Haussler, David and Miller, Webb
Genome Res
2006-12-
doi:10.1101/gr.5383506
When to use splay trees
Lee, Eric K. and Martel, Charles U.
Software: Practice and Experience
2006-12-
doi:10.1002/spe.813
Software Routing and Aggregation of Messages to Optimize the Performance of HPCC Randomaccess Benchmark
Garg, R. and Sabharwal, Y.
SC 2006 Conference, Proceedings of the ACM/IEEE
2006-11-
doi:10.1109/sc.2006.56
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Stamatakis, Alexandros
Bioinformatics (Oxford, England)
2006-11-
doi:10.1093/bioinformatics/btl446
UPC: unified parallel C
El-Ghazawi, Tarek and Smith, Lauren
Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06
2006-11-
doi:10.1145/1188455.1188483
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Berger, Michael F. and Philippakis, Anthony A. and Qureshi, Aaron M. and He, Fangxue S. and Estep, Preston W. and Bulyk, Martha L.
Nature biotechnology
2006-11-
doi:10.1038/nbt1246
TreeDyn: towards dynamic graphics and annotations for analyses of trees
Chevenet, Francois and Brun, Christine and Banuls, Anne L. and Jacq, Bernard and Christen, Richard
BMC Bioinformatics
2006-10-
doi:10.1186/1471-2105-7-439
Dealing with repetitions in sequencing by hybridization.
Blazewicz, Jacek and Glover, Fred and Kasprzak, Marta and Markiewicz, Wojciech T. and O\$backslash\$uguz, Ceyda and Schuhmann, Dietrich R. and Swiercz, Aleksandra
Comput Biol Chem
2006-10-
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\\R\\emote homology detection based on oligomer distances
Lingner, T. and Meinicke, P.
Bioinformatics
2006-09-
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Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates.
Zhang, Zhang and Yu, Jun
Genomics, proteomics & bioinformatics / Beijing Genomics Institute
2006-08-
doi:10.1016/s1672-0229(06)60030-2
Microbial diversity in the deep sea and the underexplored "rare biosphere".
Sogin, Mitchell L. and Morrison, Hilary G. and Huber, Julie A. and Mark Welch David and Huse, Susan M. and Neal, Phillip R. and Arrieta, Jesus M. and Herndl, Gerhard J.
Proceedings of the National Academy of Sciences of the United States of America
2006-08-
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SVM-based detection of distant protein structural relationships using pairwise probabilistic suffix trees.
O\$backslash\$ugul, Hasan and Mumcuo\$backslash\$uglu, Erkan U.
Comput Biol Chem
2006-08-
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ScalaBLAST: A Scalable Implementation of BLAST for High-Performance Data-Intensive Bioinformatics Analysis
Oehmen, C. and Nieplocha, J.
IEEE Transactions on Parallel and Distributed Systems
2006-08-
doi:10.1109/TPDS.2006.112
UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context.
Lozupone, Catherine and Hamady, Micah and Knight, Rob
BMC bioinformatics
2006-08-
doi:10.1186/1471-2105-7-371
Highly parallel genomic assays
Fan, Jian-Bing and Chee, Mark S. and Gunderson, Kevin L.
Nature Reviews Genetics
2006-08-
doi:10.1038/nrg1901
Comprehensive association testing of common mitochondrial DNA variation in metabolic disease.
Saxena, Richa and de Bakker, Paul I. W. and Singer, Karyn and Mootha, Vamsi and Burtt, Noel and Hirschhorn, Joel N. and Gaudet, Daniel and Isomaa, Bo and Daly, Mark J. and Groop, Leif and Ardlie, Kristin G. and Altshuler, David
Am J Hum Genet
2006-07-
doi:10.1086/504926
MINIX 3: a highly reliable, self-repairing operating system
Herder, Jorrit N. and Bos, Herbert and Gras, Ben and Homburg, Philip and Tanenbaum, Andrew S.
SIGOPS Oper. Syst. Rev.
2006-07-
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A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes.
Goldberg, Susanne M. D. and Johnson, Justin and Busam, Dana and Feldblyum, Tamara and Ferriera, Steve and Friedman, Robert and Halpern, Aaron and Khouri, Hoda and Kravitz, Saul A. and Lauro, Federico M. and Li, Kelvin and Rogers, Yu H. and Strausberg, Robert and Sutton, Granger and Tallon, Luke and Thomas, Torsten and Venter, Eli and Frazier, Marvin and Venter, J. Craig
Proc Natl Acad Sci U S A
2006-07-
doi:10.1073/pnas.0604351103
It is time to end the patenting of software
Quackenbush, John and Salzberg, Steven L.
Bioinformatics
2006-06-
doi:10.1093/bioinformatics/btl167
A maximum likelihood framework for protein design
Kleinman, Claudia and Rodrigue, Nicolas and Bonnard, Cecile and Philippe, Herve and Lartillot, Nicolas
BMC Bioinformatics
2006-06-
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Metagenomic analysis of the human distal gut microbiome.
Gill, Steven R. and Pop, Mihai and Deboy, Robert T. and Eckburg, Paul B. and Turnbaugh, Peter J. and Samuel, Buck S. and Gordon, Jeffrey I. and Relman, David A. and Fraser-Liggett, Claire M. and Nelson, Karen E.
Science
2006-06-
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An introduction to ROC analysis
Fawcett, Tom
Pattern Recognition Letters
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Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
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Optimizing the Synchronization Operations in Message Passing Interface One-Sided Communication
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Applied and Environmental Microbiology
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Isotropic fractionator: a simple, rapid method for the quantification of total cell and neuron numbers in the brain.
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The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
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Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi.
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Sand DNA - a genetic library of life at the water's edge
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Salminen, S. and Gibson, G. R. and McCartney, A. L. and Isolauri, E.
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De novo repeat classification and fragment assembly.
Pevzner, Pavel A. and Pevzner, Paul A. and Tang, Haixu and Tesler, Glenn
Genome Res
2004-09-
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Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians.
Pevzner, Pavel A.
Bioinformatics
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Fragment assembly with short reads.
Chaisson, Mark and Pevzner, Pavel and Tang, Haixu
Bioinformatics
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Fault Tolerance in Message Passing Interface Programs
Gropp, William and Lusk, Ewing
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Where did the BLOSUM62 alignment score matrix come from?
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Saigo, H. and Vert, J. P. and Ueda, N. and Akutsu, T.
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Measuring quality of research: what do they mean and why they mean so?
Konopka, Andrzej K.
Comput Biol Chem
2004-07-
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Me write pretty one day
Wells, William A.
The Journal of Cell Biology
2004-06-
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A Calculus of Purpose
Lander, Arthur D.
PLoS Biol
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Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance
Holden, Matthew T. G. and Feil, Edward J. and Lindsay, Jodi A. and Peacock, Sharon J. and Day, Nicholas P. J. and Enright, Mark C. and Foster, Tim J. and Moore, Catrin E. and Hurst, Laurence and Atkin, Rebecca and Barron, Andrew and Bason, Nathalie and Bentley, Stephen D. and Chillingworth, Carol and Chillingworth, Tracey and Churcher, Carol and Clark, Louise and Corton, Craig and Cronin, Ann and Doggett, Jon and Dowd, Linda and Feltwell, Theresa and Hance, Zahra and Harris, Barbara and Hauser, Heidi and Holroyd, Simon and Jagels, Kay and James, Keith D. and Lennard, Nicola and Line, Alexandra and Mayes, Rebecca and Moule, Sharon and Mungall, Karen and Ormond, Douglas and Quail, Michael A. and Rabbinowitsch, Ester and Rutherford, Kim and Sanders, Mandy and Sharp, Sarah and Simmonds, Mark and Stevens, Kim and Whitehead, Sally and Barrell, Bart G. and Spratt, Brian G. and Parkhill, Julian
Proceedings of the National Academy of Sciences of the United States of America
2004-06-
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Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.
Chevreux, Bastien and Pfisterer, Thomas and Drescher, Bernd and Driesel, Albert J. and M\"uller, Werner E. G. and Wetter, Thomas and Suhai, S\'andor
Genome Res
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Software company bans competitive users
Giles, Jim
Nature
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Incongruence between test statistics and P values in medical papers.
Berthou, Emili G. and Alcaraz, Carles
BMC Med Res Methodol
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A new approach to fault-tolerant wormhole routing for mesh-connected parallel computers
Ho, Ching-Tien and Stockmeyer, Larry
Computers, IEEE Transactions on
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Aligning multiple genomic sequences with the threaded blockset aligner.
Blanchette, Mathieu and Kent, W. James and Riemer, Cathy and Elnitski, Laura and Smit, Arian F. A. and Roskin, Krishna M. and Baertsch, Robert and Rosenbloom, Kate and Clawson, Hiram and Green, Eric D. and Haussler, David and Miller, Webb
Genome Res
2004-04-
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\\M\\ismatch string kernels for discriminative protein classification
Leslie, C. S. and Eskin, E. and Cohen, A. and Weston, J. and Noble, W. S.
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Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, Gene W. and Chapman, Jarrod and Hugenholtz, Philip and Allen, Eric E. and Ram, Rachna J. and Richardson, Paul M. and Solovyev, Victor V. and Rubin, Edward M. and Rokhsar, Daniel S. and Banfield, Jillian F.
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2004-02-
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All we need is truth.
Konopka, Andrzej K.
Comput Biol Chem
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Adult outcome for children with autism
Howlin, Patricia and Goode, Susan and Hutton, Jane and Rutter, Michael
Journal of Child Psychology and Psychiatry
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Introductory Science and Mathematics Education for 21st-Century Biologists
Bialek, William and Botstein, David
Science
2004-02-
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Network biology: understanding the cell's functional organization
Barabasi, Albert-Laszlo and Oltvai, Zoltan N.
Nature Reviews Genetics
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Hierarchical scaffolding with Bambus.
Pop, Mihai and Kosack, Daniel S. and Salzberg, Steven L.
Genome Res
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The EMBL Nucleotide Sequence Database
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Nucleic Acids Research
2004-01-
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The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
Camon, Evelyn and Magrane, Michele and Barrell, Daniel and Lee, Vivian and Dimmer, Emily and Maslen, John and Binns, David and Harte, Nicola and Lopez, Rodrigo and Apweiler, Rolf
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Locality-sensitive Hashing Scheme Based on P-stable Distributions
Datar, Mayur and Immorlica, Nicole and Indyk, Piotr and Mirrokni, Vahab S.
Proceedings of the Twentieth Annual Symposium on Computational Geometry
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Kernel Methods for Pattern Analysis
Taylor, J. Shawe and Cristianini, N.
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The limits of log-ratios
Sharov, Vasily and Kwong, Ka and Frank, Bryan and Chen, Emily and Hasseman, Jeremy and Gaspard, Renee and Yu, Yan and Yang, Ivana and Quackenbush, John
BMC Biotechnology
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Trilinos Tutorial
Sala, Marzio and Heroux, Michael A. and Day, David M.
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A preprocessor for shotgun assembly of large genomes.
Roberts, Michael and Hunt, Brian R. and Yorke, James A. and Bolanos, Randall A. and Delcher, Arthur L.
Journal of computational biology : a journal of computational molecular cell biology
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High performance MPI-2 one-sided communication over infinilband
Panda, D. K. and Gropp, W. and Thakur, R.
IEEE International Symposium on Cluster Computing and the Grid, 2004. CCGrid 2004.
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Panda, D. K. and Gropp, W. and Thakur, R.
IEEE International Symposium on Cluster Computing and the Grid, 2004. CCGrid 2004.
2004-xx-
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An Event-driven Architecture for MPI Libraries
Majumder, Supratik and Rixner, Scott
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Versatile and open software for comparing large genomes.
Kurtz, Stefan and Phillippy, Adam and Delcher, Arthur L. and Smoot, Michael and Shumway, Martin and Antonescu, Corina and Salzberg, Steven L.
Genome Biol
2004-xx-
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Recent Advances in Parallel Virtual Machine and Message Passing Interface
2004-xx-
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Local alignment kernels for biological sequences
Hiroto, Saigo and Vert, Jean P. and Nobuhisa, Ueda and Tatsuya, Akutsu
Kernel Methods in Computational Biology
2004-xx-
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Open MPI: Goals, Concept, and Design of a Next Generation MPI Implementation
Gabriel, Edgar and Fagg, Graham and Bosilca, George and Angskun, Thara and Dongarra, Jack and Squyres, Jeffrey and Sahay, Vishal and Kambadur, Prabhanjan and Barrett, Brian and Lumsdaine, Andrew and Castain, Ralph and Daniel, David and Graham, Richard and Woodall, Timothy and Fagg, Graham E. and Dongarra, Jack J. and Squyres, Jeffrey M. and Castain, Ralph H. and Daniel, David J. and Graham, Richard L. and Woodall, Timothy S.
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2004-xx-
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A fully distributed architecture for massively multiplayer online games
Dickey, Chris G. and Zappala, Daniel and Lo, Virginia
Proceedings of 3rd ACM SIGCOMM workshop on Network and system support for games
2004-xx-
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Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data
Baerends, Richard and Smits, Wiep and de Jong, Anne and Hamoen, Leendert and Kok, Jan and Kuipers, Oscar
Genome Biology
2004-xx-
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The role of dynamics in allosteric regulation
Kern, Dorothee and Zuiderweg, Erik R. P.
Current Opinion in Structural Biology
2003-12-
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Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences.
Jensen, Mark A. and Li, Fu S. and van 't Wout Angélique B. and Nickle, David C. and Shriner, Daniel and He, Hong X. and McLaughlin, Sherry and Shankarappa, Raj and Margolick, Joseph B. and Mullins, James I.
J Virol
2003-12-
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Protein folding and misfolding
Dobson, Christopher M.
Nature
2003-12-
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GENOMICS: Microarrays--Guilt by Association
Quackenbush, John
Science
2003-10-
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The Google File System
Ghemawat, Sanjay and Gobioff, Howard and Leung, Shun T.
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2003-10-
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Making a Case for Efficient Supercomputing
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Metagenomic Analyses of an Uncultured Viral Community from Human Feces
Breitbart, Mya and Hewson, Ian and Felts, Ben and Mahaffy, Joseph M. and Nulton, James and Salamon, Peter and Rohwer, Forest
Journal of Bacteriology
2003-10-
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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, Li and Stoeckert, Christian J. and Roos, David S.
Genome Research
2003-09-01
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PCAP: a whole-genome assembly program.
Huang, Xiaoqiu and Wang, Jianmin and Aluru, Srinivas and Yang, Shiaw-Pyng P. and Hillier, LaDeana
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Automatic registration of microarray images. II. Hexagonal grid.
Galinsky, Vitaly L.
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Galinsky, Vitaly L.
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2003-09-
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ClustalW-MPI: ClustalW analysis using distributed and parallel computing
Li, Kuo-Bin
Bioinformatics
2003-08-12
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Estimating the Repeat Structure and Length of DNA Sequences Using l-Tuples
Li, Xiaoman and Waterman, Michael S.
Genome Research
2003-08-
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A new bioinformatic approach to detect common 3D sites in protein structures
Jambon, Martin and Imberty, Anne and Deleage, Gilbert and Geourjon, Christophe
Proteins: Structure, Function, and Genetics
2003-08-
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Mfold web server for nucleic acid folding and hybridization prediction.
Zuker, Michael
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2003-07-
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EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae.
Florea, Liliana and McClelland, Michael and Riemer, Cathy and Schwartz, Scott and Miller, Webb
Nucleic acids research
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Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites.
Chaussabel, Damien and Semnani, Roshanak T. and McDowell, Mary A. and Sacks, David and Sher, Alan and Nutman, Thomas B.
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2003-07-
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Scientific publishing picks up speed.
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Efficient clustering of large EST data sets on parallel computers
Kalyanaraman, Anantharaman and Aluru, Srinivas and Kothari, Suresh and Brendel, Volker
Nucleic Acids Research
2003-06-
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The way we write.
Netzel, Rebecca and Perez-Iratxeta, Carolina and Bork, Peer and Andrade, Miguel A.
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Selected dreams and nightmares about computational biology.
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Comput Biol Chem
2003-05-
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GenDB--an open source genome annotation system for prokaryote genomes.
Meyer, Folker and Goesmann, Alexander and McHardy, Alice C. and Bartels, Daniela and Bekel, Thomas and Clausen, J\"orn and Kalinowski, J\"orn and Linke, Burkhard and Rupp, Oliver and Giegerich, Robert and P\"uhler, Alfred
Nucleic acids research
2003-04-15
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Alignment-free sequence comparison—a review
Vinga, Susana and Almeida, Jonas
Bioinformatics
2003-03-
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Massive parallelism, randomness and genomic advances
Venter, J. Craig and Levy, Samuel and Stockwell, Tim and Remington, Karin and Halpern, Aaron
Nature Genetics
2003-03-
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
Hucka, M. and Finney, A. and Sauro, H. M. and Bolouri, H. and Doyle, J. C. and Kitano, H. and and the rest of the SBML Forum: and Arkin, A. P. and Bornstein, B. J. and Bray, D. and Cornish-Bowden, A. and Cuellar, A. A. and Dronov, S. and Gilles, E. D. and Ginkel, M. and Gor, V. and Goryanin, I. I. and Hedley, W. J. and Hodgman, T. C. and Hofmeyr, J. H. and Hunter, P. J. and Juty, N. S. and Kasberger, J. L. and Kremling, A. and Kummer, U. and Le Nov\`ere N. and Loew, L. M. and Lucio, D. and Mendes, P. and Minch, E. and Mjolsness, E. D. and Nakayama, Y. and Nelson, M. R. and Nielsen, P. F. and Sakurada, T. and Schaff, J. C. and Shapiro, B. E. and Shimizu, T. S. and Spence, H. D. and Stelling, J. and Takahashi, K. and Tomita, M. and Wagner, J. and Wang, J.
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2003-03-
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Parallel biological sequence comparison using prefix computations
Aluru, Srinivas and Futamura, Natsuhiko and Mehrotra, Kishan
Journal of Parallel and Distributed Computing
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The independence of our genome assemblies
Adams, Mark D. and Sutton, Granger G. and Smith, Hamilton O. and Myers, Eugene W. and Venter, J. Craig
Proceedings of the National Academy of Sciences
2003-03-
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A Part of the Human Genome Sequence
Venter, J. C.
Science
2003-02-
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Chord: A Scalable Peer-to-peer Lookup Protocol for Internet Applications
Stoica, Ion and Morris, Robert and Nowell, David L. and Karger, David R. and Kaashoek, M. Frans and Dabek, Frank and Balakrishnan, Hari
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Pillai, Satish and Good, Benjamin and Richman, Douglas and Corbeil, Jacques
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2003-01-
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The phusion assembler.
Mullikin, James C. and Ning, Zemin
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2003-01-
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Whole-genome sequence assembly for mammalian genomes: Arachne 2.
Jaffe, David B. and Butler, Jonathan and Gnerre, Sante and Mauceli, Evan and Toh, Kerstin L. and Mesirov, Jill P. and Zody, Michael C. and Lander, Eric S.
Genome Res
2003-01-
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The Design, Implementation, and Evaluation of mpiBLAST
Darling, Aaron E. and Carey, Lucas and Feng, Wu-chun
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Velterop, Jan
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String kernels, Fisher kernels and finite state automata
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The set covering machine
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The Set Covering Machine with Data-Dependent Half-Spaces
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Space Efficient Linear Time Construction of Suffix Arrays
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Combinatorial Pattern Matching
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Predicting HIV-1 coreceptor usage with sequence analysis.
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Hur, Asa B. and Brutlag, Douglas
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Enterprise Integration Patterns: Designing, Building, and Deploying Messaging Solutions
Hohpe, Gregor and Woolf, Bobby
2003-xx-
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An Overview of Trilinos
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Trilinos Developers Guide
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2003-xx-
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Trilinos Developers Guide Part II: ASCI Software Quality Engineering Practices Version 1.0
Heroux, Michael A. and Willenbring, James M. and Heaphy, Robert
2003-xx-
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Trilinos Users Guide
Heroux, Michael A. and Willenbring, James M.
2003-xx-
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Recent Advances in Parallel Virtual Machine and Message Passing Interface
2003-xx-
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VEGAN, a package of R functions for community ecology
Dixon, Philip
Journal of Vegetation Science
2003-xx-
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Merrimac: Supercomputing with Streams
Dally, William J. and Labonte, Francois and Das, Abhishek and Hanrahan, Patrick and Ahn, Jung H. and Gummaraju, Jayanth and Erez, Mattan and Jayasena, Nuwan and Buck, Ian and Knight, Timothy J. and Kapasi, Ujval J.
Proceedings of the 2003 ACM/IEEE Conference on Supercomputing
2003-xx-
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Making Reliable Distributed Systems in the Presence of Software Errors
Armstrong, Joe
2003-xx-
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Quackenbush, John
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MIT Artificial Intelligence Laboratory Working Papers
1977-05-
http://dspace.mit.edu/handle/1721.1/41962
A new method for sequencing DNA.
Maxam, A. M. and Gilbert, W.
Proc Natl Acad Sci U S A
1977-02-
http://www.google.com/search?hl=en&site=&q=A new method for sequencing DNA.&btnG=Search
DNA sequencing with chain-terminating inhibitors.
Sanger, F. and Nicklen, S. and Coulson, A. R.
Proceedings of the National Academy of Sciences
1977-xx-
doi:10.1073/pnas.74.12.5463
Graph Theory With Applications
Bondy, John A.
1976-xx-
http://portal.acm.org/citation.cfm?id=1097029
Editorial: Dopa decarboxylase inhibitors.
British medical journal
1974-11-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1612227/
A universal modular ACTOR formalism for artificial intelligence
Hewitt, Carl and Bishop, Peter and Steiger, Richard
1973-08-
http://dl.acm.org/citation.cfm?id=1624775.1624804
Planar 3-colorability is polynomial complete
Stockmeyer, Larry
SIGACT News
1973-xx-
http://www.google.com/search?hl=en&site=&q=Planar 3-colorability is polynomial complete&btnG=Search
A universal modular ACTOR formalism for artificial intelligence
Hewitt, Carl and Bishop, Peter and Steiger, Richard
Proceedings of the 3rd international joint conference on Artificial intelligence
1973-xx-
http://ijcai.org/Past Proceedings/IJCAI-73/PDF/027B.pdf
Matching sequences under deletion-insertion constraints.
Sankoff, D.
Proc Natl Acad Sci U S A
1972-01-
http://www.pnas.org/content/69/1/4.abstract
Reducibility among combinatorial problems
Karp, Richard M.
1972-xx-
http://www.cs.berkeley.edu/~luca/cs172/karp.pdf
Space/Time Trade-offs in Hash Coding with Allowable Errors
Bloom, Burton H.
Commun. ACM
1970-07-
doi:10.1145/362686.362692
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
Needleman, S. B. and Wunsch, C. D.
J Mol Biol
1970-03-
doi:10.1016/0022-2836(70)90057-4
L-dopa in Parkinsonism.
British medical journal
1969-04-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1983096/
Evaluation of polymer sequence fragment data using graph theory.
Hutchinson, G.
Bulletin of Mathematical Biophysics
1969-xx-
doi:10.1007/BF02476636
L-Dopa for Parkinsonism
N Engl J Med
1968-03-
doi:10.1056/nejm196803142781127
Some genetic programs to supplement self-instruction in FORTRAN.
MacCluer, J. W. and Griffith, R. and Sing, C. F. and Schull, W. J.
American journal of human genetics
1967-05-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1706278/
Dependence of the melting temperature of DNA on salt concentration
Schildkraut, C. and Lifson, S.
Biopolymers
1965-04-
doi:10.1002/bip.360030207
Upper Atmosphere Densities from Minitrack Observations on Sputnik I
Harris, I. and Jastrow, R.
Science
1958-02-
doi:10.1126/science.127.3296.471-a
Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.
Watson, J. D. and Crick, F. H.
Nature
1953-04-
doi:10.1038/171737a0
A Combinatorial Problem
de Bruijn, N. G.
Koninklijke Nederlandse Akademie v. Wetenschappen
1946-xx-
http://www.dwc.knaw.nl/DL/publications/PU00018235.pdf
DIDA: Distributed Indexing Dispatched Alignment.
Mohamadi, Hamid and Vandervalk, Benjamin P. and Raymond, Anthony and Jackman, Shaun D. and Chu, Justin and Breshears, Clay P. and Birol, Inanc
PloS one
-xx-
http://view.ncbi.nlm.nih.gov/pubmed/25923767
Cochrane review questions effectiveness of neuraminidase inhibitors
Torjesen, Ingrid
BMJ : British Medical Journal
-xx-
doi:10.1136/bmj.g2675
A simulation of demand-driven dataflow: translation from Lucid into MDC language
Thiruvathukal, G. K. and Christopher, T. W.
[1991] Proceedings. The Fifth International Parallel Processing Symposium
-xx-
doi:10.1109/IPPS.1991.153848
Documents Cannot Be Edited
Renear, Allen H. and Wickett, Karen M.
-xx-
doi:10.4242/balisagevol3.renear01
New Execution Models are Required for Big Data at Exascale
Lumsdaine, Andrew
-xx-
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.294.5071}
Time, Clocks, and the Ordering of Events in a Distributed System
Lamport, Leslie
-xx-
http://citeseerx.ist.psu.edu/viewdoc/summary;jsessionid=AFABE868FC74D1BB2FCB80762CBEBD7B?doi=10.1.1.142.3682}
D4M 2.0 Schema: A General Purpose High Performance Schema for the Accumulo Database
Kepner, Jeremy and Anderson, Christian and Arc, William and Bestor, David and Bergeron, Bill and Byun, Chansup and Hubbell, Matthew and Michaleas, Peter and Mullen, Julie and Prout, Andrew and Reuther, Albert and Rosa, Antonio and Yee, Charles
-xx-
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.381.155}
Concurrent Programming in ERLANG
Armstrong, Joe and Virding, Robert and Wikstrom, Claes and Williams, Mike
-xx-
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.33.6333}
Artificial Intelligence A Universal Modular ACTOR Formalism for Artificial Intelligence
Hewitt, Carl and Bishop, Peter and Steiger, Richard
-xx-
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.77.7898}
Erlang - A survey of the language and its industrial applications
Armstrong, Joe
-xx-
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.146.5459}
Parallel Programming with Migratable Objects: Charm++ in Practice
Acun, Bilge and Gupta, Abhishek and Jain, Nikhil and Langer, Akhil and Menon, Harshitha and Mikida, Eric and Ni, Xiang and Robson, Michael and Sun, Yanhua and Totoni, Ehsan and Others
-xx-
http://www.google.com/search?hl=en&site=&q=Parallel Programming with Migratable Objects: Charm++ in Practice&btnG=Search