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Ian Holmes
Ian Holmes
Professor, Computational Biology and Bioengineering, 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
56312007
Evolution of genes and genomes on the Drosophila phylogeny
AG Clark, L Pachter
Nature 450 (7167), 203-218, 2007
20932007
JBrowse: a next-generation genome browser
ME Skinner, AV Uzilov, LD Stein, CJ Mungall, IH Holmes
Genome research 19 (9), 1630-1638, 2009
7412009
Dirichlet multinomial mixtures: generative models for microbial metagenomics
I Holmes, K Harris, C Quince
PloS one 7 (2), e30126, 2012
5232012
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
5022016
Fast statistical alignment
RK Bradley, A Roberts, M Smoot, S Juvekar, J Do, C Dewey, I Holmes, ...
PLoS computational biology 5 (5), e1000392, 2009
3752009
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
3382013
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
2471999
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
2412007
Evolutionary HMMs: a Bayesian approach to multiple alignment
I Holmes, WJ Bruno
Bioinformatics 17 (9), 803-820, 2001
2232001
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
2152008
An empirical codon model for protein sequence evolution
C Kosiol, I Holmes, N Goldman
Molecular biology and evolution 24 (7), 1464-1479, 2007
1932007
Dynamic programming alignment accuracy
I Holmes, R Durbin
Journal of computational biology 5 (3), 493-504, 1998
1651998
A “long indel” model for evolutionary sequence alignment
I Miklós, GA Lunter, I Holmes
Molecular Biology and Evolution 21 (3), 529-540, 2004
1612004
Accelerated probabilistic inference of RNA structure evolution
I Holmes
BMC bioinformatics 6 (1), 1-22, 2005
1562005
Finding regulatory elements using joint likelihoods for sequence and expression profile data.
I Holmes, WJ Bruno
Ismb 8, 202-210, 2000
1272000
An expectation maximization algorithm for training hidden substitution models
I Holmes, GM Rubin
Journal of molecular biology 317 (5), 753-764, 2002
1222002
Apollo: democratizing genome annotation
NA Dunn, DR Unni, C Diesh, M Munoz-Torres, NL Harris, E Yao, ...
PLoS computational biology 15 (2), e1006790, 2019
1202019
Pairwise RNA structure comparison with stochastic context-free grammars
I Holmes, GM Rubin
Biocomputing 2002, 163-174, 2001
862001
Visualizing next-generation sequencing data with JBrowse
O Westesson, M Skinner, I Holmes
Briefings in bioinformatics 14 (2), 172-177, 2013
772013
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