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Author Details

Ian Holmes
University of California berkeley
1998
57
25
PMIDPaper TitleJournal TitlePublished Year
36648320JBrowse Jupyter: a Python interface to JBrowse 2.Bioinformatics2023
36648320JBrowse Jupyter: a Python interface to JBrowse 2.Bioinformatics2023
37069644JBrowse 2: a modular genome browser with views of synteny and structural variation.Genome Biol2023
37069644JBrowse 2: a modular genome browser with views of synteny and structural variation.Genome Biol2023
35616118GrainGenes: a data-rich repository for small grains genetics and genomics.Database (Oxford)2022
35616118GrainGenes: a data-rich repository for small grains genetics and genomics.Database (Oxford)2022
32683444Machine Boss: rapid prototyping of bioinformatic automata.Bioinformatics2021
33468205Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.Genome Biol2021
34196689JBrowseR: an R interface to the JBrowse 2 genome browser.Bioinformatics2021
32683444Machine Boss: rapid prototyping of bioinformatic automata.Bioinformatics2021
34817058CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.Gigascience2021
34817058CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.Gigascience2021
34196689JBrowseR: an R interface to the JBrowse 2 genome browser.Bioinformatics2021
33468205Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.Genome Biol2021
33020189A Model of Indel Evolution by Finite-State, Continuous-Time Machines.Genetics2020
32810130JBrowse Connect: A server API to connect JBrowse instances and users.PLoS Comput Biol2020
33020189A Model of Indel Evolution by Finite-State, Continuous-Time Machines.Genetics2020
32810130JBrowse Connect: A server API to connect JBrowse instances and users.PLoS Comput Biol2020
30726205Apollo: Democratizing genome annotation.PLoS Comput Biol2019
30726205Apollo: Democratizing genome annotation.PLoS Comput Biol2019
31099383Cram-JS: reference-based decompression in node and the browser.Bioinformatics2019
31099383Cram-JS: reference-based decompression in node and the browser.Bioinformatics2019
28494756Solving the master equation for Indels.BMC Bioinformatics2017
28494756Solving the master equation for Indels.BMC Bioinformatics2017
28486579BioMake: a GNU make-compatible utility for declarative workflow management.Bioinformatics2017
28104629Historian: accurate reconstruction of ancestral sequences and evolutionary rates.Bioinformatics2017
28486579BioMake: a GNU make-compatible utility for declarative workflow management.Bioinformatics2017
28104629Historian: accurate reconstruction of ancestral sequences and evolutionary rates.Bioinformatics2017
27072794JBrowse: a dynamic web platform for genome visualization and analysis.Genome Biol2016
27072794JBrowse: a dynamic web platform for genome visualization and analysis.Genome Biol2016
26186661AAV ancestral reconstruction library enables selection of broadly infectious viral variants.Gene Ther2015
26186661AAV ancestral reconstruction library enables selection of broadly infectious viral variants.Gene Ther2015
22411711Visualizing next-generation sequencing data with JBrowse.Brief Bioinform2013
26702330Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting.Ann Appl Stat2013
22411711Visualizing next-generation sequencing data with JBrowse.Brief Bioinform2013
24000942Web Apollo: a web-based genomic annotation editing platform.Genome Biol2013
23188590Estimating empirical codon hidden Markov models.Mol Biol Evol2013
26702330Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting.Ann Appl Stat2013
24000942Web Apollo: a web-based genomic annotation editing platform.Genome Biol2013
23188590Estimating empirical codon hidden Markov models.Mol Biol Evol2013
22285828HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.Bioinformatics2012
22693624Developing and applying heterogeneous phylogenetic models with XRate.PLoS One2012
22536326Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.PLoS One2012
22285828HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.Bioinformatics2012
22319561Dirichlet multinomial mixtures: generative models for microbial metagenomics.PLoS One2012
22215819Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.Bioinformatics2012
22693624Developing and applying heterogeneous phylogenetic models with XRate.PLoS One2012
22536326Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.PLoS One2012
22215819Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.Bioinformatics2012
22319561Dirichlet multinomial mixtures: generative models for microbial metagenomics.PLoS One2012
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Collaborators

Robert K Bradley
Fred Hutchinson Cancer Research Center, University of Washington
Co-authored papers 8
Robert M Buels
University of California berkeley
Co-authored papers 7
Colin Diesh
University of California berkeley
Co-authored papers 7
Lincoln Stein
Ontario Institute for Cancer Research, University Avenue
Co-authored papers 7
Lior Pachter
Co-authored papers 5
Benedict Paten
UC Santa Cruz Genomics Institute, University of California
Co-authored papers 4
Ewan Birney
European Bioinformatics Institute
Co-authored papers 4
Nick Goldman
Co-authored papers 4
Eric Yao
Western Regional Research Center, Crop Improvement and Genetics Research Unit
Co-authored papers 4
Mitchell E Skinner
University of California at Berkeley
Co-authored papers 4
Monica C Munoz-Torres
University of Colorado Anschutz Medical Campus
Co-authored papers 3
Christine G Elsik
University of Missouri
Co-authored papers 3
Richard K Wilson
The Ohio State University
Co-authored papers 3
David B Jaffe
Co-authored papers 3
Kerstin Lindblad-Toh
Uppsala University
Co-authored papers 3
Robert S Fulton
McDonnell Genome Institute, Washington University School of Medicine
Co-authored papers 3
Angie S Hinrichs
Co-authored papers 3
Eric S Lander
Vanderbilt-Ingram Cancer Center, Vanderbilt University
Co-authored papers 3
Andrew V Uzilov
University of California Santa Cruz
Co-authored papers 3
Suzanna E Lewis
Lawrence Berkeley National Laboratory
Co-authored papers 3
Serafim Batzoglou
Co-authored papers 3
Colin N Dewey
Co-authored papers 3
Sante Gnerre
Co-authored papers 3
Jean L Chang
Co-authored papers 3
Daryl J Thomas
University of California at Santa Cruz
Co-authored papers 2
Michele Clamp
Harvard University
Co-authored papers 2
Nancy F Hansen
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 2
Ross C Hardison
Co-authored papers 2
Donna Karolchik
Co-authored papers 2
Kim D Pruitt
National Center for Biotechnology Information, National Institutes of Health
Co-authored papers 2
Release 1.2