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
54192007
Evolution of genes and genomes on the Drosophila phylogeny
AG Clark, MB Eisen, DR Smith, CM Bergman, B Oliver, TA Markow, ...
Nature 450 (7167), 203-218, 2007
20262007
JBrowse: a next-generation genome browser
ME Skinner, AV Uzilov, LD Stein, CJ Mungall, IH Holmes
Genome research 19 (9), 1630-1638, 2009
7052009
Dirichlet multinomial mixtures: generative models for microbial metagenomics
I Holmes, K Harris, C Quince
PloS one 7 (2), e30126, 2012
4402012
Fast statistical alignment
RK Bradley, A Roberts, M Smoot, S Juvekar, J Do, C Dewey, I Holmes, ...
PLoS computational biology 5 (5), e1000392, 2009
3712009
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
3692016
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
3202013
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
2422007
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
2401999
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
2042008
An empirical codon model for protein sequence evolution
C Kosiol, I Holmes, N Goldman
Molecular biology and evolution 24 (7), 1464-1479, 2007
1922007
Dynamic programming alignment accuracy
I Holmes, R Durbin
Journal of computational biology 5 (3), 493-504, 1998
1611998
A “long indel” model for evolutionary sequence alignment
I Miklós, GA Lunter, I Holmes
Molecular Biology and Evolution 21 (3), 529-540, 2004
1582004
Accelerated probabilistic inference of RNA structure evolution
I Holmes
BMC bioinformatics 6 (1), 1-22, 2005
1572005
Finding regulatory elements using joint likelihoods for sequence and expression profile data.
I Holmes, WJ Bruno
Ismb 8, 202-210, 2000
1232000
An expectation maximization algorithm for training hidden substitution models
I Holmes, GM Rubin
Journal of molecular biology 317 (5), 753-764, 2002
1202002
A cross-package Bioconductor workflow for analysing methylation array data
J Maksimovic, B Phipson, A Oshlack
F1000Research 5, 2016
862016
Pairwise RNA structure comparison with stochastic context-free grammars
I Holmes, GM Rubin
Biocomputing 2002, 163-174, 2001
862001
Apollo: democratizing genome annotation
NA Dunn, DR Unni, C Diesh, M Munoz-Torres, NL Harris, E Yao, ...
PLoS computational biology 15 (2), e1006790, 2019
752019
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