Ian Holmes, Ph.D. - Publications

Affiliations: 
Bioengineering University of California, Berkeley, Berkeley, CA 

42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes IH. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biology. 17: 66. PMID 27072794 DOI: 10.1186/s13059-016-0924-1  1
2015 Santiago-Ortiz J, Ojala DS, Westesson O, Weinstein JR, Wong SY, Steinsapir A, Kumar S, Holmes I, Schaffer DV. AAV ancestral reconstruction library enables selection of broadly infectious viral variants. Gene Therapy. PMID 26186661 DOI: 10.1038/gt.2015.74  1
2013 Doss CR, Suchard MA, Holmes I, Kato-Maeda M, Minin VN. Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting. The Annals of Applied Statistics. 7: 2315-2335. PMID 26702330 DOI: 10.1214/13-AOAS673  1
2013 Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers CP, Buels RM, Stein L, Holmes IH, Elsik CG, Lewis SE. Web Apollo: a web-based genomic annotation editing platform. Genome Biology. 14: R93. PMID 24000942 DOI: 10.1186/gb-2013-14-8-r93  1
2013 De Maio N, Holmes I, Schlötterer C, Kosiol C. Estimating empirical codon hidden Markov models. Molecular Biology and Evolution. 30: 725-36. PMID 23188590 DOI: 10.1093/molbev/mss266  1
2013 Westesson O, Skinner M, Holmes I. Visualizing next-generation sequencing data with JBrowse. Briefings in Bioinformatics. 14: 172-7. PMID 22411711 DOI: 10.1093/bib/bbr078  1
2012 Westesson O, Holmes I. Developing and applying heterogeneous phylogenetic models with XRate. Plos One. 7: e36898. PMID 22693624 DOI: 10.1371/journal.pone.0036898  1
2012 Westesson O, Lunter G, Paten B, Holmes I. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. Plos One. 7: e34572. PMID 22536326 DOI: 10.1371/journal.pone.0034572  1
2012 Holmes I, Harris K, Quince C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. Plos One. 7: e30126. PMID 22319561 DOI: 10.1371/journal.pone.0030126  1
2012 Westesson O, Barquist L, Holmes I. HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinformatics (Oxford, England). 28: 1170-1. PMID 22285828 DOI: 10.1093/bioinformatics/bts058  1
2012 Mørk S, Holmes I. Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. Bioinformatics (Oxford, England). 28: 636-42. PMID 22215819 DOI: 10.1093/bioinformatics/btr698  1
2011 Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, et al. RNAcentral: A vision for an international database of RNA sequences. Rna (New York, N.Y.). 17: 1941-6. PMID 21940779 DOI: 10.1261/rna.2750811  1
2010 Skinner ME, Holmes IH. Setting up the JBrowse genome browser. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 9.13. PMID 21154710 DOI: 10.1002/0471250953.bi0913s32  1
2009 Bradley RK, Holmes I. Evolutionary triplet models of structured RNA. Plos Computational Biology. 5: e1000483. PMID 19714212 DOI: 10.1371/journal.pcbi.1000483  1
2009 Bradley RK, Uzilov AV, Skinner ME, Bendaña YR, Barquist L, Holmes I. Evolutionary modeling and prediction of non-coding RNAs in Drosophila. Plos One. 4: e6478. PMID 19668382 DOI: 10.1371/journal.pone.0006478  1
2009 Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Research. 19: 1630-8. PMID 19570905 DOI: 10.1101/gr.094607.109  1
2009 Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Fast statistical alignment. Plos Computational Biology. 5: e1000392. PMID 19478997 DOI: 10.1371/journal.pcbi.1000392  1
2009 Heger A, Ponting CP, Holmes I. Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins. Molecular Biology and Evolution. 26: 1715-21. PMID 19380462 DOI: 10.1093/molbev/msp080  1
2009 Westesson O, Holmes I. Accurate detection of recombinant breakpoints in whole-genome alignments. Plos Computational Biology. 5: e1000318. PMID 19300487 DOI: 10.1371/journal.pcbi.1000318  1
2008 Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research. 18: 1829-43. PMID 18849525 DOI: 10.1101/gr.076521.108  1
2008 Varadarajan A, Bradley RK, Holmes IH. Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biology. 9: R147. PMID 18840304 DOI: 10.1186/gb-2008-9-10-r147  1
2008 Bradley RK, Pachter L, Holmes I. Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics (Oxford, England). 24: 2677-83. PMID 18796475 DOI: 10.1093/bioinformatics/btn495  1
2008 Barquist L, Holmes I. xREI: a phylo-grammar visualization webserver. Nucleic Acids Research. 36: W65-9. PMID 18522975 DOI: 10.1093/nar/gkn283  1
2008 Bendaña YR, Holmes IH. Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinformatics (Oxford, England). 24: 579-80. PMID 18218657 DOI: 10.1093/bioinformatics/btm635  1
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Holmes I, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/nature06341  0.01
2007 Bradley RK, Holmes I. Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics (Oxford, England). 23: 3258-62. PMID 17804440 DOI: 10.1093/bioinformatics/btm402  1
2007 Holmes I. Phylocomposer and phylodirector: analysis and visualization of transducer indel models. Bioinformatics (Oxford, England). 23: 3263-4. PMID 17804439 DOI: 10.1093/bioinformatics/btm432  1
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Holmes I, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/gr.6034307  1
2007 Kosiol C, Holmes I, Goldman N. An empirical codon model for protein sequence evolution. Molecular Biology and Evolution. 24: 1464-79. PMID 17400572 DOI: 10.1093/molbev/msm064  1
2006 Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I. XRate: a fast prototyping, training and annotation tool for phylo-grammars. Bmc Bioinformatics. 7: 428. PMID 17018148 DOI: 10.1186/1471-2105-7-428  1
2005 Holmes I. Accelerated probabilistic inference of RNA structure evolution. Bmc Bioinformatics. 6: 73. PMID 15790387 DOI: 10.1186/1471-2105-6-73  1
2005 Holmes I. Using evolutionary Expectation Maximization to estimate indel rates. Bioinformatics (Oxford, England). 21: 2294-300. PMID 15731213 DOI: 10.1093/bioinformatics/bti177  1
2004 Holmes I. A probabilistic model for the evolution of RNA structure. Bmc Bioinformatics. 5: 166. PMID 15507142 DOI: 10.1186/1471-2105-5-166  1
2004 Miklós I, Lunter GA, Holmes I. A "Long Indel" model for evolutionary sequence alignment. Molecular Biology and Evolution. 21: 529-40. PMID 14694074 DOI: 10.1093/molbev/msh043  1
2003 Holmes I. Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics (Oxford, England). 19: i147-57. PMID 12855451 DOI: 10.1093/bioinformatics/btg1019  1
2002 Holmes I. Transcendent elements: whole-genome transposon screens and open evolutionary questions. Genome Research. 12: 1152-5. PMID 12176921 DOI: 10.1101/gr.453102  1
2002 Holmes I, Rubin GM. An expectation maximization algorithm for training hidden substitution models. Journal of Molecular Biology. 317: 753-64. PMID 11955022 DOI: 10.1006/jmbi.2002.5405  1
2002 Holmes I, Rubin GM. Pairwise RNA structure comparison with stochastic context-free grammars. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 163-74. PMID 11928472  1
2001 Holmes I, Bruno WJ. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics (Oxford, England). 17: 803-20. PMID 11590097  1
2000 Holmes I, Bruno WJ. Finding regulatory elements using joint likelihoods for sequence and expression profile data. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 202-10. PMID 10977081  1
1999 Newman J, Peat TS, Richard R, Kan L, Swanson PE, Affholter JA, Holmes IH, Schindler JF, Unkefer CJ, Terwilliger TC. Haloalkane dehalogenases: structure of a Rhodococcus enzyme. Biochemistry. 38: 16105-14. PMID 10587433 DOI: 10.1021/bi9913855  1
1998 Holmes I, Durbin R. Dynamic programming alignment accuracy. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 5: 493-504. PMID 9773345  1
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