Ian Holmes

Oscar Westesson, Mitchell Skinner, Ian Holmes: Visualizing next-generation sequencing data with JBrowse. Briefings in Bioinformatics 14(2): 172-177 (2013)

Søren Mørk, Ian Holmes: Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. Bioinformatics 28(5): 636-642 (2012)

Oscar Westesson, Lars Barquist, Ian Holmes: HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinformatics 28(8): 1170-1171 (2012)

Oscar Westesson, Ian Holmes: Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments. PLoS Computational Biology 5(3) (2009)

Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian Holmes, Lior Pachter: Fast Statistical Alignment. PLoS Computational Biology 5(5) (2009)

Robert K. Bradley, Ian Holmes: Evolutionary Triplet Models of Structured RNA. PLoS Computational Biology 5(8) (2009)

Yuri R. Bendaña, Ian Holmes: Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinformatics 24(4): 579-580 (2008)

Robert K. Bradley, Lior Pachter, Ian Holmes: Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics 24(23): 2677-2683 (2008)

Lars Barquist, Ian Holmes: xREI: a phylo-grammar visualization webserver. Nucleic Acids Research 36(Web-Server-Issue): 65-69 (2008)

Robert K. Bradley, Ian Holmes: Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics 23(23): 3258-3262 (2007)

Ian Holmes: Phylocomposer and phylodirector: analysis and visualization of transducer indel models. Bioinformatics 23(23): 3263-3264 (2007)

Peter S. Klosterman, Andrew V. Uzilov, Yuri R. Bendaña, Robert K. Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, Ian Holmes: XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics 7: 428 (2006)

Ian Holmes: Using evolutionary Expectation Maximization to estimate indel rates. Bioinformatics 21(10): 2294-2300 (2005)

Ian Holmes: Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 6: 73 (2005)

Ian Holmes: A probabilistic model for the evolution of RNA structure. BMC Bioinformatics 5: 166 (2004)

Ian Holmes, Gerald M. Rubin: Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars. Pacific Symposium on Biocomputing 2002: 163-174

Ian Holmes, William J. Bruno: Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics 17(9): 803-820 (2001)

Ian Holmes, William J. Bruno: Finding Regulatory Elements Using Joint Likelihoods for Sequence and Expression Profile Data. ISMB 2000: 202-210

Ian Holmes, Richard Durbin: Dynamic Programming Alignment Accuracy. Journal of Computational Biology 5(3): 493-504 (1998)

Ian Holmes, Richard Durbin: Dynamic programming alignment accuracy. RECOMB 1998: 102-108