| Structure, function and diversity of the healthy human microbiome C Huttenhower, D Gevers, R Knight, S Abubucker, JH Badger, ... nature 486 (7402), 207, 2012 | 4824 | 2012 |
| De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis BJ Haas, A Papanicolaou, M Yassour, M Grabherr, PD Blood, J Bowden, ... Nature protocols 8 (8), 1494, 2013 | 3393 | 2013 |
| A framework for human microbiome research BA Methé, KE Nelson, M Pop, HH Creasy, MG Giglio, C Huttenhower, ... nature 486 (7402), 215, 2012 | 1285 | 2012 |
| Genome sequence of Aedes aegypti, a major arbovirus vector V Nene, JR Wortman, D Lawson, B Haas, C Kodira, ZJ Tu, B Loftus, Z Xi, ... Science 316 (5832), 1718-1723, 2007 | 1060 | 2007 |
| The TIGR rice genome annotation resource: improvements and new features S Ouyang, W Zhu, J Hamilton, H Lin, M Campbell, K Childs, ... Nucleic acids research 35 (suppl_1), D883-D887, 2006 | 897 | 2006 |
| Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments BJ Haas, SL Salzberg, W Zhu, M Pertea, JE Allen, J Orvis, O White, ... Genome biology 9 (1), R7, 2008 | 652 | 2008 |
| A catalog of reference genomes from the human microbiome. KE Nelson, GM Weinstock, SK Highlander, KC Worley, HH Creasy, ... Science (New York, NY) 328 (5981), 994-999, 2010 | 537 | 2010 |
| Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus ND Fedorova, N Khaldi, VS Joardar, R Maiti, P Amedeo, MJ Anderson, ... PLoS genetics 4 (4), e1000046, 2008 | 441 | 2008 |
| Draft genome sequence of the oilseed species Ricinus communis AP Chan, J Crabtree, Q Zhao, H Lorenzi, J Orvis, D Puiu, ... Nature biotechnology 28 (9), 951, 2010 | 429 | 2010 |
| Strains, functions and dynamics in the expanded Human Microbiome Project J Lloyd-Price, A Mahurkar, G Rahnavard, J Crabtree, J Orvis, AB Hall, ... Nature 550 (7674), 61, 2017 | 279 | 2017 |
| The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations GC Cerqueira, MB Arnaud, DO Inglis, MS Skrzypek, G Binkley, M Simison, ... Nucleic acids research 42 (D1), D705-D710, 2013 | 193 | 2013 |
| The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources MB Arnaud, GC Cerqueira, DO Inglis, MS Skrzypek, J Binkley, ... Nucleic acids research 40 (D1), D653-D659, 2011 | 133 | 2011 |
| The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community MB Arnaud, MC Chibucos, MC Costanzo, J Crabtree, DO Inglis, A Lotia, ... Nucleic acids research 38 (suppl_1), D420-D427, 2009 | 115 | 2009 |
| Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium TF Ducey, MB Carson, J Orvis, AP Stintzi, DW Dyer Journal of bacteriology 187 (14), 4865-4874, 2005 | 111 | 2005 |
| A catalog of reference genomes from the human microbiome Human Microbiome Jumpstart Reference Strains Consortium Science 328 (5981), 994-999, 2010 | 110 | 2010 |
| The IGS standard operating procedure for automated prokaryotic annotation K Galens, J Orvis, S Daugherty, HH Creasy, S Angiuoli, O White, ... Standards in genomic sciences 4 (2), 244, 2011 | 106 | 2011 |
| Ergatis: a web interface and scalable software system for bioinformatics workflows J Orvis, J Crabtree, K Galens, A Gussman, JM Inman, E Lee, S Nampally, ... Bioinformatics 26 (12), 1488-1492, 2010 | 99 | 2010 |
| The Staphylococcus aureus NCTC 8325 genome AF Gillaspy, V Worrell, J Orvis, BA Roe, DW Dyer, JJ Iandolo Gram-Positive Pathogens, Second Edition, 381-412, 2006 | 95 | 2006 |
| Transcriptional and functional analysis of the Neisseria gonorrhoeae Fur regulon LA Jackson, TF Ducey, MW Day, JB Zaitshik, J Orvis, DW Dyer Journal of bacteriology 192 (1), 77-85, 2010 | 60 | 2010 |
| Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities J Martin, S Sykes, S Young, K Kota, R Sanka, N Sheth, J Orvis, ... PLoS One 7 (6), e36427, 2012 | 53 | 2012 |