Ian H. Holmes

According to our database, Ian H. Holmes authored at least 29 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

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., January, 2023

2022

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, David P. Eickholt, Taner Z. Sen

Database J. Biol. Databases Curation, 2022

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

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

2020

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

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

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

2018

Consensus Decoding of Recurrent Neural Network Basecallers.

Jordi Silvestre-Ryan, Ian H. Holmes

Proceedings of the Algorithms for Computational Biology - 5th International Conference, 2018

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

WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis.

Christopher J. Mungall, Ian H. Holmes

F1000Research, 2017

Solving the master equation for Indels.

Ian H. Holmes

BMC Bioinform., 2017

BioMake: a GNU make-compatible utility for declarative workflow management.

Ian H. Holmes, Christopher J. Mungall

Bioinform., 2017

Historian: accurate reconstruction of ancestral sequences and evolutionary rates.

Ian H. Holmes

Bioinform., 2017

2013

Visualizing next-generation sequencing data with JBrowse.

Oscar Westesson, Mitchell Skinner, Ian H. Holmes

Briefings Bioinform., 2013

2012

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.

Oscar Westesson, Lars Barquist, Ian H. Holmes

Bioinform., 2012

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.

Søren Mørk, Ian H. Holmes

Bioinform., 2012

2009

Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments.

Oscar Westesson, 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

Evolutionary Triplet Models of Structured RNA.

Robert K. Bradley, Ian H. Holmes

PLoS Comput. Biol., 2009

2008

xREI: a phylo-grammar visualization webserver.

Lars Barquist, Ian H. Holmes

Nucleic Acids Res., 2008

Specific alignment of structured RNA: stochastic grammars and sequence annealing.

Robert K. Bradley, Lior Pachter, Ian H. Holmes

Bioinform., 2008

Colorstock, SScolor, Ratón: RNA alignment visualization tools.

Yuri R. Bendaña, Ian H. Holmes

Bioinform., 2008

2007

Phylocomposer and phylodirector: analysis and visualization of transducer indel models.

Ian H. Holmes

Bioinform., 2007

Transducers: an emerging probabilistic framework for modeling indels on trees.

Robert K. Bradley, Ian H. Holmes

Bioinform., 2007

2006

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

2005

Accelerated probabilistic inference of RNA structure evolution.

Ian H. Holmes

BMC Bioinform., 2005

Using evolutionary Expectation Maximization to estimate indel rates.

Ian H. Holmes

Bioinform., 2005

2004

A probabilistic model for the evolution of RNA structure.

Ian H. Holmes

BMC Bioinform., 2004

2003

Using guide trees to construct multiple-sequence evolutionary HMMs.

Ian H. Holmes

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003