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Journal Articles
- 2023
[j26]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)- 2022
- [j25]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) - 2021
- [j24]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): 29-35 (2021) - [j23]Elliot A. Hershberg, Garrett Stevens, Colin M. Diesh, Peter Xie, Teresa De Jesus Martinez, Robert M. Buels, Lincoln Stein, Ian H. Holmes:
JBrowseR: an R interface to the JBrowse 2 genome browser. Bioinform. 37(21): 3914-3915 (2021) - 2020
- [j22]Eric Yao, Robert M. 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) - 2019
- [j21]Robert M. Buels, Shihab Dider, Colin M. Diesh, James Robinson, Ian H. Holmes:
Cram-JS: reference-based decompression in node and the browser. Bioinform. 35(21): 4451-4452 (2019) - [j20]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) - 2017
- [j19]Ian H. Holmes:
Historian: accurate reconstruction of ancestral sequences and evolutionary rates. Bioinform. 33(8): 1227-1229 (2017) - [j18]Ian H. Holmes, Christopher J. Mungall:
BioMake: a GNU make-compatible utility for declarative workflow management. Bioinform. 33(21): 3502-3504 (2017) - [j17]Ian H. Holmes:
Solving the master equation for Indels. BMC Bioinform. 18(1): 255:1-255:10 (2017) - [j16]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): 516-529 (2017) - 2013
- [j15]Oscar Westesson, Mitchell Skinner, Ian H. Holmes:
Visualizing next-generation sequencing data with JBrowse. Briefings Bioinform. 14(2): 172-177 (2013) - 2012
- [j14]Søren Mørk, Ian H. Holmes:
Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. Bioinform. 28(5): 636-642 (2012) - [j13]Oscar Westesson, Lars Barquist, Ian H. Holmes:
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinform. 28(8): 1170-1171 (2012) - 2009
- [j12]Oscar Westesson, Ian H. Holmes:
Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments. PLoS Comput. Biol. 5(3) (2009) - [j11]Robert K. Bradley, Adam Roberts, Michael E. Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter:
Fast Statistical Alignment. PLoS Comput. Biol. 5(5) (2009) - [j10]Robert K. Bradley, Ian H. Holmes:
Evolutionary Triplet Models of Structured RNA. PLoS Comput. Biol. 5(8) (2009) - 2008
- [j9]Yuri R. Bendaña, Ian H. Holmes:
Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinform. 24(4): 579-580 (2008) - [j8]Robert K. Bradley, Lior Pachter, Ian H. Holmes:
Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinform. 24(23): 2677-2683 (2008) - [j7]Lars Barquist, Ian H. Holmes:
xREI: a phylo-grammar visualization webserver. Nucleic Acids Res. 36(Web-Server-Issue): 65-69 (2008) - 2007
- [j6]Robert K. Bradley, Ian H. Holmes:
Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinform. 23(23): 3258-3262 (2007) - [j5]Ian H. Holmes:
Phylocomposer and phylodirector: analysis and visualization of transducer indel models. Bioinform. 23(23): 3263-3264 (2007) - 2006
- [j4]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: 428 (2006) - 2005
- [j3]Ian H. Holmes:
Using evolutionary Expectation Maximization to estimate indel rates. Bioinform. 21(10): 2294-2300 (2005) - [j2]Ian H. Holmes:
Accelerated probabilistic inference of RNA structure evolution. BMC Bioinform. 6: 73 (2005) - 2004
- [j1]Ian H. Holmes:
A probabilistic model for the evolution of RNA structure. BMC Bioinform. 5: 166 (2004)
Conference and Workshop Papers
- 2018
- [c2]Jordi Silvestre-Ryan, Ian H. Holmes:
Consensus Decoding of Recurrent Neural Network Basecallers. AlCoB 2018: 128-139 - 2003
- [c1]Ian H. Holmes:
Using guide trees to construct multiple-sequence evolutionary HMMs. ISMB (Supplement of Bioinformatics) 2003: 147-157
Editorship
- 2019
- [e1]Ian H. 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]
Informal and Other Publications
- 2017
- [i1]Christopher J. Mungall, Ian H. Holmes:
WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis. F1000Research 6: 423- (2017)
Coauthor Index
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last updated on 2024-05-02 21:48 CEST by the dblp team
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