Ian Holmes
Ian Holmes
Associate Professor, Computational Biology, UC Berkeley
Verified email at berkeley.edu
Title
Cited by
Cited by
Year
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
49772007
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium
Nature 450 (7167), 203, 2007
18542007
JBrowse: a next-generation genome browser
ME Skinner, AV Uzilov, LD Stein, CJ Mungall, IH Holmes
Genome research 19 (9), 1630-1638, 2009
6222009
Fast statistical alignment
RK Bradley, A Roberts, M Smoot, S Juvekar, J Do, C Dewey, I Holmes, ...
PLoS computational biology 5 (5), 2009
3392009
Dirichlet multinomial mixtures: generative models for microbial metagenomics
I Holmes, K Harris, C Quince
PloS one 7 (2), 2012
3012012
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), R93, 2013
3002013
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
2322007
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
2241999
Evolutionary HMMs: a Bayesian approach to multiple alignment
I Holmes, WJ Bruno
Bioinformatics 17 (9), 803-820, 2001
2072001
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), 66, 2016
2052016
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
1812008
An empirical codon model for protein sequence evolution
C Kosiol, I Holmes, N Goldman
Molecular biology and evolution 24 (7), 1464-1479, 2007
1752007
Accelerated probabilistic inference of RNA structure evolution
I Holmes
BMC bioinformatics 6 (1), 73, 2005
1542005
Dynamic programming alignment accuracy
I Holmes, R Durbin
Journal of computational biology 5 (3), 493-504, 1998
1521998
A “long indel” model for evolutionary sequence alignment
I Miklós, GA Lunter, I Holmes
Molecular Biology and Evolution 21 (3), 529-540, 2004
1442004
Finding regulatory elements using joint likelihoods for sequence and expression profile data.
I Holmes, WJ Bruno
Ismb 8, 202-210, 2000
1142000
An expectation maximization algorithm for training hidden substitution models
I Holmes, GM Rubin
Journal of molecular biology 317 (5), 753-764, 2002
1062002
Pairwise RNA structure comparison with stochastic context-free grammars
I Holmes, GM Rubin
Biocomputing 2002, 163-174, 2001
842001
XRate: a fast prototyping, training and annotation tool for phylo-grammars
PS Klosterman, AV Uzilov, YR Bendaña, RK Bradley, S Chao, C Kosiol, ...
BMC bioinformatics 7 (1), 428, 2006
712006
Visualizing next-generation sequencing data with JBrowse
O Westesson, M Skinner, I Holmes
Briefings in bioinformatics 14 (2), 172-177, 2013
682013
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