Paper archive for the HolmesLab, Berkeley

Pubmed-indexed journals and conference proceedings

1. Holmes I, Durbin R.  Dynamic programming alignment accuracy.  J Comput Biol. 1998 Fall;5(3):493-504. (pdf)
2. 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. 1999 Dec 7;38(49):16105-14.
3. Holmes I, Bruno WJ.  Finding regulatory elements using joint likelihoods for sequence and expression profile data.  Proc Int Conf Intell Syst Mol Biol. 2000;8:202-10. (pdf)
4. Holmes I, Bruno WJ.  Evolutionary HMMs: a Bayesian approach to multiple alignment.  Bioinformatics. 2001 Sep;17(9):803-20. (pdf)
5. Holmes I, Rubin GM.  Pairwise RNA structure comparison with stochastic context-free grammars.  Pac Symp Biocomput. 2002:163-74. (pdf)
6. Holmes I, Rubin GM.  An expectation maximization algorithm for training hidden substitution models.  J Mol Biol. 2002 Apr 12;317(5):753-64. (pdf)
7. Holmes I.  Transcendent elements: whole-genome transposon screens and open evolutionary questions.  Genome Res. 2002 Aug;12(8):1152-5. (pdf)
8. Holmes I.  Using guide trees to construct multiple-sequence evolutionary HMMs.  Bioinformatics. 2003;19 Suppl 1:i147-57. (pdf) (errata)
9. Miklos I, Lunter GA, Holmes I.  A "Long Indel" model for evolutionary sequence alignment.  Mol Biol Evol. 2004 Mar;21(3):529-40. Epub 2003 Dec 23. (pdf)
10. Holmes I.  A probabilistic model for the evolution of RNA structure.  BMC Bioinformatics. 2004 Oct 26;5:166. (pdf)
11. Holmes I.  Using evolutionary Expectation Maximization to estimate indel rates.  Bioinformatics. 2005 May 15;21(10):2294-300. Epub 2005 Feb 24. (main paper, pdf) (supplement, pdf) (benchmark data)
12. Holmes I.  Accelerated probabilistic inference of RNA structure evolution.  BMC Bioinformatics. 2005 Mar 24;6:73. (pdf)
13. Klosterman PS, Uzilov AV, Bendana YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.  XRate: a fast prototyping, training and annotation tool for phylo-grammars.  BMC Bioinformatics. 2006 Oct 3;7:428. (main paper, pdf) (supplement, pdf)
14. Kosiol C, Holmes I, Goldman N.  An empirical codon model for protein sequence evolution.  Mol Biol Evol. 2007 Jul;24(7):1464-79. Epub 2007 Mar 30.
15. Margulies EH et al.  Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.  Genome Res. 2007 Jun;17(6):760-74.
16. Birney E et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.  Nature. 2007 Jun 14;447(7146):799-816.
17. Holmes I.  Phylocomposer and phylodirector: analysis and visualization of transducer indel models.  Bioinformatics. 2007 Dec 1;23(23):3263-4. Epub 2007 Sep 5. (pdf)
18. Bradley RK, Holmes I.  Transducers: an emerging probabilistic framework for modeling indels on trees.  Bioinformatics. 2007 Dec 1;23(23):3258-62. Epub 2007 Sep 5. (pdf)
19. Clark AG et al.  Evolution of genes and genomes on the Drosophila phylogeny.  Nature. 2007 Nov 8;450(7167):203-18.
20. Bendana YR, Holmes IH.  Colorstock, SScolor, Raton: RNA alignment visualization tools.  Bioinformatics. 2008 Feb 15;24(4):579-80. doi: 10.1093/bioinformatics/btm635. Epub 2008 Jan 24. (pdf)
21. Barquist L, Holmes I.  xREI: a phylo-grammar visualization webserver.  Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W65-9. doi: 10.1093/nar/gkn283. Epub 2008 Jun 3.
22. Bradley RK, Pachter L, Holmes I.  Specific alignment of structured RNA: stochastic grammars and sequence annealing.  Bioinformatics. 2008 Dec 1;24(23):2677-83. doi: 10.1093/bioinformatics/btn495. Epub 2008 Sep 16. (preprint, pdf)
23. Varadarajan A, Bradley RK, Holmes IH.  Tools for simulating evolution of aligned genomic regions with integrated parameter estimation.  Genome Biol. 2008 Oct 8;9(10):R147. doi: 10.1186/gb-2008-9-10-r147.
24. Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E.  Genome-wide nucleotide-level mammalian ancestor reconstruction.  Genome Res. 2008 Nov;18(11):1829-43. doi: 10.1101/gr.076521.108. Epub 2008 Oct 10.
25. Westesson O, Holmes I.  Accurate detection of recombinant breakpoints in whole-genome alignments.  PLoS Comput Biol. 2009 Mar;5(3):e1000318. doi: 10.1371/journal.pcbi.1000318. Epub 2009 Mar 20.
26. Heger A, Ponting CP, Holmes I.  Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins.  Mol Biol Evol. 2009 Aug;26(8):1715-21. doi: 10.1093/molbev/msp080. Epub 2009 Apr 20.
27. Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L.  Fast statistical alignment.  PLoS Comput Biol. 2009 May;5(5):e1000392. doi: 10.1371/journal.pcbi.1000392. Epub 2009 May 29.
28. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH.  JBrowse: a next-generation genome browser.  Genome Res. 2009 Sep;19(9):1630-8. doi: 10.1101/gr.094607.109. Epub 2009 Jul 1.
29. Bradley RK, Uzilov AV, Skinner ME, Bendana YR, Barquist L, Holmes I.  Evolutionary modeling and prediction of non-coding RNAs in Drosophila.  PLoS One. 2009 Aug 11;4(8):e6478. doi: 10.1371/journal.pone.0006478.
30. Bradley RK, Holmes I.  Evolutionary triplet models of structured RNA.  PLoS Comput Biol. 2009 Aug;5(8):e1000483. doi: 10.1371/journal.pcbi.1000483. Epub 2009 Aug 28.
31. Skinner ME, Holmes IH.  Setting up the JBrowse genome browser.  Curr Protoc Bioinformatics. 2010 Dec;Chapter 9:Unit 9.13. doi: 10.1002/0471250953.bi0913s32.
32. Bateman A et al.  RNAcentral: A vision for an international database of RNA sequences.  RNA. 2011 Nov;17(11):1941-6. doi: 10.1261/rna.2750811. Epub 2011 Sep 22.
33. Mork S, Holmes I.  Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.  Bioinformatics. 2012 Mar 1;28(5):636-42. doi: 10.1093/bioinformatics/btr698. Epub 2012 Jan 3.
34. Westesson O, Barquist L, Holmes I.  HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.  Bioinformatics. 2012 Apr 15;28(8):1170-1. doi: 10.1093/bioinformatics/bts058. Epub 2012 Jan 28.
35. Holmes I, Harris K, Quince C.  Dirichlet multinomial mixtures: generative models for microbial metagenomics.  PLoS One. 2012;7(2):e30126. doi: 10.1371/journal.pone.0030126. Epub 2012 Feb 3.
36. Westesson O, Skinner M, Holmes I.  Visualizing next-generation sequencing data with JBrowse.  Brief Bioinform. 2012 Mar 12.
37. Westesson O, Lunter G, Paten B, Holmes I.  Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.  PLoS One. 2012;7(4):e34572. doi: 10.1371/journal.pone.0034572. Epub 2012 Apr 20.
38. Westesson O, Holmes I.  Developing and applying heterogeneous phylogenetic models with XRate.  PLoS One. 2012;7(6):e36898. doi: 10.1371/journal.pone.0036898. Epub 2012 Jun 5.

arXiv.org preprints

• Charles R. Doss, Marc A. Suchard, Ian Holmes, Midori Kato-Maeda, Vladimir N. Minin. Great Expectations: EM Algorithms for Discretely Observed Linear Birth-Death-Immigration Processes. (Submitted on 5 Sep 2010)
• Oscar Westesson, Gerton Lunter, Benedict Paten, Ian Holmes. Phylogenetic automata, pruning, and multiple alignment. (Submitted on 22 Mar 2011)
• Oscar Westesson, Gerton Lunter, Benedict Paten, Ian Holmes. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. (Submitted on 17 Feb 2012)
• Oscar Westesson, Ian Holmes. Developing and applying heterogeneous phylogenetic models with XRate. (Submitted on 17 Feb 2012)

PhD theses

• Westesson, O. PhD thesis. Department of Bioengineering, University of California, Berkeley. 2012. (pdf) (pdf.zip)
• Bradley, R. PhD thesis. Biophysics Graduate Group, University of California, Berkeley. 2008. (pdf)
• Holmes, I. PhD thesis. Dept of Genetics, University of Cambridge; Wellcome Trust Sanger Institute. 1998. (pdf) (ps.gz)