Ian H. Holmes

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 13

Top Topics

Genome Annotation

Top Venues

PLoS Comput. Biol.

Publications

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
JBrowse Jupyter: a Python interface to JBrowse 2. Bioinform. 39 (1) (2023)
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
GrainGenes: a data-rich repository for small grains genetics and genomics. Database J. Biol. Databases Curation 2022 (2022) (2022)
Elliot A. Hershberg, Garrett Stevens, Colin M. Diesh, Peter Xie, Teresa De Jesus Martinez, Robert Buels, Lincoln Stein, Ian H. Holmes
JBrowseR: an R interface to the JBrowse 2 genome browser. Bioinform. 37 (21) (2021)
Jordi Silvestre-Ryan, Yujie Wang, Mehak Sharma, Stephen Lin, Yolanda Shen, Shihab Dider, Ian H. Holmes
Machine Boss: rapid prototyping of bioinformatic automata. Bioinform. 37 (1) (2021)
Eric Yao, Robert Buels, Lincoln Stein, Taner Z. Sen, Ian H. Holmes
JBrowse Connect: A server API to connect JBrowse instances and users. PLoS Comput. Biol. 16 (8) (2020)
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
Apollo: Democratizing genome annotation. PLoS Comput. Biol. 15 (2) (2019)
Robert Buels, Shihab Dider, Colin M. Diesh, James Robinson, Ian H. Holmes
Cram-JS: reference-based decompression in node and the browser. Bioinform. 35 (21) (2019)
Jordi Silvestre-Ryan, Ian H. Holmes
Consensus Decoding of Recurrent Neural Network Basecallers. AlCoB (2018)
Ian H. Holmes
Historian: accurate reconstruction of ancestral sequences and evolutionary rates. Bioinform. 33 (8) (2017)
Ian H. Holmes, Christopher J. Mungall
BioMake: a GNU make-compatible utility for declarative workflow management. Bioinform. 33 (21) (2017)
Christopher J. Mungall, Ian H. Holmes
WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis. F1000Research 6 (2017)
Keith Harris, Todd L. Parsons, Umer Zeeshan Ijaz, Leo Lahti, Ian H. Holmes, Christopher Quince
Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process. Proc. IEEE 105 (3) (2017)
Ian H. Holmes
Solving the master equation for Indels. BMC Bioinform. 18 (1) (2017)
Oscar Westesson, Mitchell Skinner, Ian H. Holmes
Visualizing next-generation sequencing data with JBrowse. Briefings Bioinform. 14 (2) (2013)
Oscar Westesson, Lars Barquist, Ian H. Holmes
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinform. 28 (8) (2012)
Søren Mørk, Ian H. Holmes
Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. Bioinform. 28 (5) (2012)
Oscar Westesson, Ian H. Holmes
Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments. PLoS Comput. Biol. 5 (3) (2009)
Robert K. Bradley, Ian H. Holmes
Evolutionary Triplet Models of Structured RNA. PLoS Comput. Biol. 5 (8) (2009)
Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter
Fast Statistical Alignment. PLoS Comput. Biol. 5 (5) (2009)
Lars Barquist, Ian H. Holmes
xREI: a phylo-grammar visualization webserver. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Robert K. Bradley, Lior Pachter, Ian H. Holmes
Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinform. 24 (23) (2008)
Yuri R. Bendaña, Ian H. Holmes
Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinform. 24 (4) (2008)
Ian H. Holmes
Phylocomposer and phylodirector: analysis and visualization of transducer indel models. Bioinform. 23 (23) (2007)
Robert K. Bradley, Ian H. Holmes
Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinform. 23 (23) (2007)
Peter S. Klosterman, Andrew V. Uzilov, Yuri R. Bendaña, Robert K. Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, Ian H. Holmes
XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinform. 7 (2006)
Ian H. Holmes
Using evolutionary Expectation Maximization to estimate indel rates. Bioinform. 21 (10) (2005)
Ian H. Holmes
Accelerated probabilistic inference of RNA structure evolution. BMC Bioinform. 6 (2005)
Ian H. Holmes
A probabilistic model for the evolution of RNA structure. BMC Bioinform. 5 (2004)
Ian H. Holmes
Using guide trees to construct multiple-sequence evolutionary HMMs. ISMB (Supplement of Bioinformatics) (2003)