Using guide trees to construct multiple-sequence evolutionary HMMs. - Ian H. Holmes (ISMB (Supplement of Bioinformatics), 2003)

A probabilistic model for the evolution of RNA structure. - Ian H. Holmes (BMC Bioinform., 2004)

Using evolutionary Expectation Maximization to estimate indel rates. - Ian H. Holmes (Bioinform., 2005)

Accelerated probabilistic inference of RNA structure evolution. - Ian H. Holmes (BMC Bioinform., 2005)

XRate: a fast prototyping, training and annotation tool for phylo-grammars. - Peter S. Klosterman; Andrew V. Uzilov; Yuri R. Bendaña; Robert K. Bradley; Sharon Chao; Carolin Kosiol; Nick Goldman; Ian H. Holmes (BMC Bioinform., 2006)

Transducers: an emerging probabilistic framework for modeling indels on trees. - Robert K. Bradley; Ian H. Holmes (Bioinform., 2007)

Phylocomposer and phylodirector: analysis and visualization of transducer indel models. - Ian H. Holmes (Bioinform., 2007)

Colorstock, SScolor, Ratón: RNA alignment visualization tools. - Yuri R. Bendaña; Ian H. Holmes (Bioinform., 2008)

Specific alignment of structured RNA: stochastic grammars and sequence annealing. - Robert K. Bradley; Lior Pachter; Ian H. Holmes (Bioinform., 2008)

xREI: a phylo-grammar visualization webserver. - Lars Barquist; Ian H. Holmes (Nucleic Acids Res., 2008)

Evolutionary Triplet Models of Structured RNA. - Robert K. Bradley; Ian H. Holmes (PLoS Comput. Biol., 2009)

Fast Statistical Alignment. - Robert K. Bradley; Adam Roberts; Michael E. Smoot; Sudeep Juvekar; Jaeyoung Do; Colin N. Dewey; Ian H. Holmes; Lior Pachter (PLoS Comput. Biol., 2009)

Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments. - Oscar Westesson; Ian H. Holmes (PLoS Comput. Biol., 2009)

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. - Søren Mørk; Ian H. Holmes (Bioinform., 2012)

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. - Oscar Westesson; Lars Barquist; Ian H. Holmes (Bioinform., 2012)

Visualizing next-generation sequencing data with JBrowse. - Oscar Westesson; Mitchell Skinner; Ian H. Holmes (Briefings Bioinform., 2013)

Historian: accurate reconstruction of ancestral sequences and evolutionary rates. - Ian H. Holmes (Bioinform., 2017)

BioMake: a GNU make-compatible utility for declarative workflow management. - Ian H. Holmes; Christopher J. Mungall (Bioinform., 2017)

Solving the master equation for Indels. - Ian H. Holmes (BMC Bioinform., 2017)

WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis. - Christopher J. Mungall; Ian H. Holmes (F1000Research, 2017)

Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process. - Keith Harris; Todd L. Parsons; Umer Zeeshan Ijaz; Leo Lahti; Ian H. Holmes; Christopher Quince (Proc. IEEE, 2017)

Consensus Decoding of Recurrent Neural Network Basecallers. - Jordi Silvestre-Ryan; Ian H. Holmes (AlCoB, 2018)

Cram-JS: reference-based decompression in node and the browser. - Robert M. Buels; Shihab Dider; Colin M. Diesh; James Robinson; Ian H. Holmes (Bioinform., 2019)

Apollo: Democratizing genome annotation. - 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 (PLoS Comput. Biol., 2019)

JBrowse Connect: A server API to connect JBrowse instances and users. - Eric Yao; Robert M. Buels; Lincoln Stein; Taner Z. Sen; Ian H. Holmes (PLoS Comput. Biol., 2020)

JBrowseR: an R interface to the JBrowse 2 genome browser. - Elliot A. Hershberg; Garrett Stevens; Colin M. Diesh; Peter Xie; Teresa De Jesus Martinez; Robert M. Buels; Lincoln Stein; Ian H. Holmes (Bioinform., 2021)

Machine Boss: rapid prototyping of bioinformatic automata. - Jordi Silvestre-Ryan; Yujie Wang; Mehak Sharma; Stephen Lin; Yolanda Shen; Shihab Dider; Ian H. Holmes (Bioinform., 2021)

GrainGenes: a data-rich repository for small grains genetics and genomics. - 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; et al. (Database J. Biol. Databases Curation, 2022)

JBrowse Jupyter: a Python interface to JBrowse 2. - 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 (Bioinform., 2023)