Paper archive for the Holmes Lab, Berkeley

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 Sep 5;. (pdf)
18. Bradley RK, Holmes I.  Transducers: An Emerging Probabilistic Framework for Modeling Indels on Trees.  Bioinformatics. 2007 Sep 5;. (pdf)
19. Clark AG et al.  Evolution of genes and genomes on the Drosophila phylogeny.  Nature. 2007 Nov 8;450(7167):203-218.
20. Bendana YR, Holmes IH.  Colorstock, SScolor, Raton: RNA Alignment Visualization Tools.  Bioinformatics. 2008 Jan 24;. (pdf)
21. Barquist L, Holmes I.  xREI: a phylo-grammar visualization webserver.  Nucleic Acids Res. 2008 Jun 3;.
22. Bradley RK, Pachter L, Holmes I.  Specific Alignment of Structured RNA: Stochastic Grammars and Sequence Annealing.  Bioinformatics. 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.
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 Oct 10.
25. Westesson O, Holmes I.  Accurate detection of recombinant breakpoints in whole-genome alignments.  PLoS Comput Biol. 2009 Mar;5(3):e1000318. 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 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. Epub 2009 May 29.

PhD theses

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