Ian H. Holmes

30 papers Journal 27Unranked 2
YearRankTypeTitle / Venue / Authors
2023 J jnl
JBrowse Jupyter: a Python interface to JBrowse 2.
Bioinform.
Teresa De Jesus Martinez, Elliot A. Hershberg, Emma Guo, Garrett Stevens, Colin M. Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes
2022 J jnl
GrainGenes: a data-rich repository for small grains genetics and genomics.
Database J. Biol. Databases Curation
Eric Yao, Victoria C. Blake, Laurel Cooper, Charlene P. Wight, Steve L. Michel, H. Busra Cagirici, Gerard R. Lazo, Clayton L. Birkett, David J. Waring, Jean-Luc Jannink, Ian H. Holmes, Amanda J. Waters, David P. Eickholt, Taner Z. Sen
2021 J jnl
JBrowseR: an R interface to the JBrowse 2 genome browser.
Bioinform.
Elliot A. Hershberg, Garrett Stevens, Colin M. Diesh, Peter Xie, Teresa De Jesus Martinez, Robert M. Buels, Lincoln Stein, Ian H. Holmes
2021 J jnl
Machine Boss: rapid prototyping of bioinformatic automata.
Bioinform.
Jordi Silvestre-Ryan, Yujie Wang, Mehak Sharma, Stephen Lin, Yolanda Shen, Shihab Dider, Ian H. Holmes
2020 J jnl
JBrowse Connect: A server API to connect JBrowse instances and users.
PLoS Comput. Biol.
Eric Yao, Robert M. Buels, Lincoln Stein, Taner Z. Sen, Ian H. Holmes
2019 — ed.
Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Berkeley, CA, USA, May 28-30, 2019, Proceedings
AlCoB
Ian H. Holmes, Carlos Martín-Vide, Miguel A. Vega-Rodríguez
2019 J jnl
Apollo: Democratizing genome annotation.
PLoS Comput. Biol.
Nathan A. Dunn, Deepak R. Unni, Colin M. Diesh, Monica C. Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis
2019 J jnl
Cram-JS: reference-based decompression in node and the browser.
Bioinform.
Robert M. Buels, Shihab Dider, Colin M. Diesh, James Robinson, Ian H. Holmes
2018 — conf
Consensus Decoding of Recurrent Neural Network Basecallers.
AlCoB
Jordi Silvestre-Ryan, Ian H. Holmes
2017 J jnl
BioMake: a GNU make-compatible utility for declarative workflow management.
Bioinform.
Ian H. Holmes, Christopher J. Mungall
2017 J jnl
Historian: accurate reconstruction of ancestral sequences and evolutionary rates.
Bioinform.
Ian H. Holmes
2017 J jnl
Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process.
Proc. IEEE
Keith Harris, Todd L. Parsons, Umer Zeeshan Ijaz, Leo Lahti, Ian H. Holmes, Christopher Quince
2017 J jnl
Solving the master equation for Indels.
BMC Bioinform.
Ian H. Holmes
2017 J jnl
WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis.
F1000Research
Christopher J. Mungall, Ian H. Holmes
2013 J jnl
Visualizing next-generation sequencing data with JBrowse.
Briefings Bioinform.
Oscar Westesson, Mitchell Skinner, Ian H. Holmes
2012 J jnl
Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.
Bioinform.
Søren Mørk, Ian H. Holmes
2012 J jnl
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.
Bioinform.
Oscar Westesson, Lars Barquist, Ian H. Holmes
2009 J jnl
Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments.
PLoS Comput. Biol.
Oscar Westesson, Ian H. Holmes
2009 J jnl
Evolutionary Triplet Models of Structured RNA.
PLoS Comput. Biol.
Robert K. Bradley, Ian H. Holmes
2009 J jnl
Fast Statistical Alignment.
PLoS Comput. Biol.
Robert K. Bradley, Adam Roberts, Michael E. Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter
2008 J jnl
Colorstock, SScolor, Ratón: RNA alignment visualization tools.
Bioinform.
Yuri R. Bendaña, Ian H. Holmes
2008 J jnl
Specific alignment of structured RNA: stochastic grammars and sequence annealing.
Bioinform.
Robert K. Bradley, Lior Pachter, Ian H. Holmes
2008 J jnl
xREI: a phylo-grammar visualization webserver.
Nucleic Acids Res.
Lars Barquist, Ian H. Holmes
2007 J jnl
Phylocomposer and phylodirector: analysis and visualization of transducer indel models.
Bioinform.
Ian H. Holmes
2007 J jnl
Transducers: an emerging probabilistic framework for modeling indels on trees.
Bioinform.
Robert K. Bradley, Ian H. Holmes
2006 J jnl
XRate: a fast prototyping, training and annotation tool for phylo-grammars.
BMC Bioinform.
Peter S. Klosterman, Andrew V. Uzilov, Yuri R. Bendaña, Robert K. Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, Ian H. Holmes
2005 J jnl
Accelerated probabilistic inference of RNA structure evolution.
BMC Bioinform.
Ian H. Holmes
2005 J jnl
Using evolutionary Expectation Maximization to estimate indel rates.
Bioinform.
Ian H. Holmes
2004 J jnl
A probabilistic model for the evolution of RNA structure.
BMC Bioinform.
Ian H. Holmes
2003 — conf
Using guide trees to construct multiple-sequence evolutionary HMMs.
ISMB (Supplement of Bioinformatics)
Ian H. Holmes