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| The transcriptional landscape of the mammalian genome P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, ... science 309 (5740), 1559-1563, 2005 | 4134 | 2005 |
| 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, 1-22, 2008 | 2863 | 2008 |
| Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii JM Carlton, SV Angiuoli, BB Suh, TW Kooij, M Pertea, JC Silva, ... Nature 419 (6906), 512-519, 2002 | 915 | 2002 |
| The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans BJ Loftus, E Fung, P Roncaglia, D Rowley, P Amedeo, D Bruno, ... Science 307 (5713), 1321-1324, 2005 | 882 | 2005 |
| Draft genome of the filarial nematode parasite Brugia malayi E Ghedin, S Wang, D Spiro, E Caler, Q Zhao, J Crabtree, JE Allen, ... Science 317 (5845), 1756-1760, 2007 | 728 | 2007 |
| Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes MJ Gardner, R Bishop, T Shah, EP De Villiers, JM Carlton, N Hall, Q Ren, ... Science 309 (5731), 134-137, 2005 | 397 | 2005 |
| Scalable metagenomic taxonomy classification using a reference genome database SK Ames, DA Hysom, SN Gardner, GS Lloyd, MB Gokhale, JE Allen Bioinformatics 29 (18), 2253-2260, 2013 | 239 | 2013 |
| Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14 MJ Gardner, SJ Shallom, JM Carlton, SL Salzberg, V Nene, A Shoaibi, ... Nature 419 (6906), 531-534, 2002 | 236 | 2002 |
| Improved protein–ligand binding affinity prediction with structure-based deep fusion inference D Jones, H Kim, X Zhang, A Zemla, G Stevenson, WFD Bennett, ... Journal of chemical information and modeling 61 (4), 1583-1592, 2021 | 214 | 2021 |
| JIGSAW: integration of multiple sources of evidence for gene prediction JE Allen, SL Salzberg Bioinformatics 21 (18), 3596-3603, 2005 | 205 | 2005 |
| Computational gene prediction using multiple sources of evidence JE Allen, M Pertea, SL Salzberg Genome research 14 (1), 142-148, 2004 | 188 | 2004 |
| Predicting tumor cell line response to drug pairs with deep learning F Xia, M Shukla, T Brettin, C Garcia-Cardona, J Cohn, JE Allen, S Maslov, ... BMC bioinformatics 19, 71-79, 2018 | 132 | 2018 |
| FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science H Sichtig, T Minogue, Y Yan, C Stefan, A Hall, L Tallon, L Sadzewicz, ... Nature communications 10 (1), 3313, 2019 | 128 | 2019 |
| Metagenomic analysis of the airborne environment in urban spaces NA Be, JB Thissen, VY Fofanov, JE Allen, M Rojas, G Golovko, Y Fofanov, ... Microbial Ecology 69, 346-355, 2015 | 114 | 2015 |
| Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces C Urbaniak, AC Sielaff, KG Frey, JE Allen, N Singh, C Jaing, K Wheeler, ... Scientific reports 8 (1), 814, 2018 | 112 | 2018 |
| JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions JE Allen, WH Majoros, M Pertea, SL Salzberg Genome Biology 7, 1-13, 2006 | 104 | 2006 |
| Microbiomes of the built environment: a research agenda for indoor microbiology, human health, and buildings National Academies of Sciences, Division on Engineering, ... National Academies Press, 2017 | 101 | 2017 |
| AMPL: a data-driven modeling pipeline for drug discovery AJ Minnich, K McLoughlin, M Tse, J Deng, A Weber, N Murad, BD Madej, ... Journal of chemical information and modeling 60 (4), 1955-1968, 2020 | 82 | 2020 |
| nGASP–the nematode genome annotation assessment project A Coghlan, TJ Fiedler, SJ McKay, P Flicek, TW Harris, D Blasiar, ... BMC bioinformatics 9, 1-13, 2008 | 82 | 2008 |
Kevin S. McLoughlinLawrence Livermore National LaboratoryVerified email at llnl.gov
