עקוב אחר
Ian Holmes
Ian Holmes
Professor, Computational Biology and Bioengineering, UC Berkeley
כתובת אימייל מאומתת בדומיין berkeley.edu
כותרת
צוטט על ידי
צוטט על ידי
שנה
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ...
nature 447 (7146), 799-816, 2007
61332007
Evolution of genes and genomes on the Drosophila phylogeny
AG Clark, MB Eisen, DR Smith, CM Bergman, B Oliver, TA Markow, ...
Nature 450 (7167), 203-18, 2007
22892007
Dirichlet multinomial mixtures: generative models for microbial metagenomics
I Holmes, K Harris, C Quince
PloS one 7 (2), e30126, 2012
8422012
JBrowse: a next-generation genome browser
ME Skinner, AV Uzilov, LD Stein, CJ Mungall, IH Holmes
Genome research 19 (9), 1630-1638, 2009
8332009
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, 1-12, 2016
7752016
JBrowse 2: a modular genome browser with views of synteny and structural variation
C Diesh, GJ Stevens, P Xie, T De Jesus Martinez, EA Hershberg, A Leung, ...
Genome biology 24 (1), 74, 2023
5062023
Fast statistical alignment
RK Bradley, A Roberts, M Smoot, S Juvekar, J Do, C Dewey, I Holmes, ...
PLoS computational biology 5 (5), e1000392, 2009
4222009
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, 1-13, 2013
3972013
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
2721999
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
2542007
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
2372008
Evolutionary HMMs: a Bayesian approach to multiple alignment
I Holmes, WJ Bruno
Bioinformatics 17 (9), 803-820, 2001
2302001
Apollo: democratizing genome annotation
NA Dunn, DR Unni, C Diesh, M Munoz-Torres, NL Harris, E Yao, ...
PLoS computational biology 15 (2), e1006790, 2019
2272019
An empirical codon model for protein sequence evolution
C Kosiol, I Holmes, N Goldman
Molecular biology and evolution 24 (7), 1464-1479, 2007
2242007
A “long indel” model for evolutionary sequence alignment
I Miklós, GA Lunter, I Holmes
Molecular Biology and Evolution 21 (3), 529-540, 2004
1742004
Dynamic programming alignment accuracy
I Holmes, R Durbin
Proceedings of the second annual international conference on Computational …, 1998
1721998
Accelerated probabilistic inference of RNA structure evolution
I Holmes
BMC bioinformatics 6, 1-22, 2005
1672005
An expectation maximization algorithm for training hidden substitution models
I Holmes, GM Rubin
Journal of molecular biology 317 (5), 753-764, 2002
1282002
Finding regulatory elements using joint likelihoods for sequence and expression profile data.
I Holmes, WJ Bruno
Ismb 8, 202-210, 2000
1252000
AAV ancestral reconstruction library enables selection of broadly infectious viral variants
J Santiago-Ortiz, DS Ojala, O Westesson, JR Weinstein, SY Wong, ...
Gene therapy 22 (12), 934-946, 2015
952015
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מאמרים 1–20