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ORCIDIan Holmes
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2010 – 2019
- 2019
[j21]Robert Buels, Shihab Dider
, Colin M. Diesh, James Robinson, Ian Holmes:
Cram-JS: reference-based decompression in node and the browser. Bioinform. 35(21): 4451-4452 (2019)- [c6]Simina M. Boca, David Hanauer, Ian Holmes, Despina Kontos, Juli D. Klemm:
The National Cancer Institute's Informatics Technology for Cancer Research Program: Building a Community of Practice in Cancer Informatics. AMIA 2019 - [e1]Ian Holmes, Carlos Martín-Vide, Miguel A. Vega-Rodríguez:
Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Berkeley, CA, USA, May 28-30, 2019, Proceedings. Lecture Notes in Computer Science 11488, Springer 2019, ISBN 978-3-030-18173-4 [contents] - 2018
- [c5]Jordi Silvestre-Ryan, Ian Holmes:
Consensus Decoding of Recurrent Neural Network Basecallers. AlCoB 2018: 128-139 - 2017
- [j20]Ian Holmes:
Historian: accurate reconstruction of ancestral sequences and evolutionary rates. Bioinform. 33(8): 1227-1229 (2017) - [j19]Ian Holmes:
Solving the master equation for Indels. BMC Bioinform. 18(1): 255:1-255:10 (2017) - [j18]Keith Harris, Todd L. Parsons, Umer Zeeshan Ijaz, Leo Lahti, Ian Holmes, Christopher Quince:
Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process. Proc. IEEE 105(3): 516-529 (2017) - 2016
- [i1]Ian Holmes:
Modular non-repeating codes for DNA storage. CoRR abs/1606.01799 (2016) - 2014
- [c4]Ian Holmes:
A web-based editor for multiplayer choice games. FDG 2014 - 2013
- [j17]Oscar Westesson, Mitchell Skinner, Ian Holmes:
Visualizing next-generation sequencing data with JBrowse. Briefings Bioinform. 14(2): 172-177 (2013) - 2012
- [j16]Søren Mørk, Ian Holmes:
Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. Bioinform. 28(5): 636-642 (2012) - [j15]Oscar Westesson, Lars Barquist, Ian Holmes:
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinform. 28(8): 1170-1171 (2012)
2000 – 2009
- 2009
- [j14]Oscar Westesson, Ian Holmes:
Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments. PLoS Comput. Biol. 5(3) (2009) - [j13]Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian Holmes, Lior Pachter:
Fast Statistical Alignment. PLoS Comput. Biol. 5(5) (2009) - [j12]Robert K. Bradley, Ian Holmes:
Evolutionary Triplet Models of Structured RNA. PLoS Comput. Biol. 5(8) (2009) - 2008
- [j11]Yuri R. Bendaña, Ian Holmes:
Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinform. 24(4): 579-580 (2008) - [j10]Robert K. Bradley, Lior Pachter, Ian Holmes:
Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinform. 24(23): 2677-2683 (2008) - [j9]Lars Barquist, Ian Holmes:
xREI: a phylo-grammar visualization webserver. Nucleic Acids Res. 36(Web-Server-Issue): 65-69 (2008) - 2007
- [j8]Robert K. Bradley, Ian Holmes:
Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinform. 23(23): 3258-3262 (2007) - [j7]Ian Holmes:
Phylocomposer and phylodirector: analysis and visualization of transducer indel models. Bioinform. 23(23): 3263-3264 (2007) - 2006
- [j6]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 Bioinform. 7: 428 (2006) - 2005
- [j5]Ian Holmes:
Using evolutionary Expectation Maximization to estimate indel rates. Bioinform. 21(10): 2294-2300 (2005) - [j4]Ian Holmes:
Accelerated probabilistic inference of RNA structure evolution. BMC Bioinform. 6: 73 (2005) - 2004
- [j3]Ian Holmes:
A probabilistic model for the evolution of RNA structure. BMC Bioinform. 5: 166 (2004) - 2002
- [c3]Ian Holmes, Gerald M. Rubin:
Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars. Pacific Symposium on Biocomputing 2002: 163-174 - 2001
- [j2]Ian Holmes, William J. Bruno:
Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinform. 17(9): 803-820 (2001) - 2000
- [c2]Ian Holmes, William J. Bruno:
Finding Regulatory Elements Using Joint Likelihoods for Sequence and Expression Profile Data. ISMB 2000: 202-210
1990 – 1999
- 1998
- [j1]Ian Holmes, Richard Durbin:
Dynamic Programming Alignment Accuracy. J. Comput. Biol. 5(3): 493-504 (1998) - [c1]Ian Holmes, Richard Durbin:
Dynamic programming alignment accuracy. RECOMB 1998: 102-108
Coauthor Index
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