| Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project ENCODE Project Consortium nature 447 (7146), 799, 2007 | 5631 | 2007 |
| Evolution of genes and genomes on the Drosophila phylogeny AG Clark, L Pachter Nature 450 (7167), 203-218, 2007 | 2093 | 2007 |
| JBrowse: a next-generation genome browser ME Skinner, AV Uzilov, LD Stein, CJ Mungall, IH Holmes Genome research 19 (9), 1630-1638, 2009 | 741 | 2009 |
| Dirichlet multinomial mixtures: generative models for microbial metagenomics I Holmes, K Harris, C Quince PloS one 7 (2), e30126, 2012 | 523 | 2012 |
| JBrowse: a dynamic web platform for genome visualization and analysis R Buels, E Yao, CM Diesh, RD Hayes, M Munoz-Torres, G Helt, ... Genome biology 17 (1), 1-12, 2016 | 502 | 2016 |
| Fast statistical alignment RK Bradley, A Roberts, M Smoot, S Juvekar, J Do, C Dewey, I Holmes, ... PLoS computational biology 5 (5), e1000392, 2009 | 375 | 2009 |
| Web Apollo: a web-based genomic annotation editing platform E Lee, GA Helt, JT Reese, MC Munoz-Torres, CP Childers, RM Buels, ... Genome biology 14 (8), 1-13, 2013 | 338 | 2013 |
| Haloalkane Dehalogenases: Structure of a Rhodococcus Enzyme, J Newman, TS Peat, R Richard, L Kan, PE Swanson, JA Affholter, ... Biochemistry 38 (49), 16105-16114, 1999 | 247 | 1999 |
| Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome EH Margulies, GM Cooper, G Asimenos, DJ Thomas, CN Dewey, A Siepel, ... Genome research 17 (6), 760-774, 2007 | 241 | 2007 |
| Evolutionary HMMs: a Bayesian approach to multiple alignment I Holmes, WJ Bruno Bioinformatics 17 (9), 803-820, 2001 | 223 | 2001 |
| Genome-wide nucleotide-level mammalian ancestor reconstruction B Paten, J Herrero, S Fitzgerald, K Beal, P Flicek, I Holmes, E Birney Genome research 18 (11), 1829-1843, 2008 | 215 | 2008 |
| An empirical codon model for protein sequence evolution C Kosiol, I Holmes, N Goldman Molecular biology and evolution 24 (7), 1464-1479, 2007 | 193 | 2007 |
| Dynamic programming alignment accuracy I Holmes, R Durbin Journal of computational biology 5 (3), 493-504, 1998 | 165 | 1998 |
| A “long indel” model for evolutionary sequence alignment I Miklós, GA Lunter, I Holmes Molecular Biology and Evolution 21 (3), 529-540, 2004 | 161 | 2004 |
| Accelerated probabilistic inference of RNA structure evolution I Holmes BMC bioinformatics 6 (1), 1-22, 2005 | 156 | 2005 |
| Finding regulatory elements using joint likelihoods for sequence and expression profile data. I Holmes, WJ Bruno Ismb 8, 202-210, 2000 | 127 | 2000 |
| An expectation maximization algorithm for training hidden substitution models I Holmes, GM Rubin Journal of molecular biology 317 (5), 753-764, 2002 | 122 | 2002 |
| Apollo: democratizing genome annotation NA Dunn, DR Unni, C Diesh, M Munoz-Torres, NL Harris, E Yao, ... PLoS computational biology 15 (2), e1006790, 2019 | 120 | 2019 |
| Pairwise RNA structure comparison with stochastic context-free grammars I Holmes, GM Rubin Biocomputing 2002, 163-174, 2001 | 86 | 2001 |
| Visualizing next-generation sequencing data with JBrowse O Westesson, M Skinner, I Holmes Briefings in bioinformatics 14 (2), 172-177, 2013 | 77 | 2013 |
