Paper Archive

Paper archive for the Holmes Lab, Berkeley

Pubmed-indexed journals and conference proceedings

1. Holmes & Durbin: Dynamic programming alignment accuracy. J. Comput. Biol. 1998;5:493-504. (pdf)
2. Newman et al.: Haloalkane dehalogenases: structure of a Rhodococcus enzyme. Biochemistry 1999;38:16105-14.
3. Holmes & Bruno: 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 & Bruno: Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics 2001;17:803-20. (pdf)
5. Holmes & Rubin: Pairwise RNA structure comparison with stochastic context-free grammars. Pac Symp Biocomput 2002;:163-74. (pdf)
6. Holmes & Rubin: An expectation maximization algorithm for training hidden substitution models. J. Mol. Biol. 2002;317:753-64. (pdf)
7. Holmes &: Transcendent elements: whole-genome transposon screens and open evolutionary questions. Genome Res. 2002;12:1152-5. (pdf)
8. Holmes &: Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics 2003;19 Suppl 1:i147-57. (pdf) (errata)
9. Miklós et al.: A "Long Indel" model for evolutionary sequence alignment. Mol. Biol. Evol. 2004;21:529-40. (pdf)
10. Holmes &: A probabilistic model for the evolution of RNA structure. BMC Bioinformatics 2004;5:166. (pdf)
11. Holmes &: Using evolutionary Expectation Maximization to estimate indel rates. Bioinformatics 2005;21:2294-300. (main paper, pdf) (supplement, pdf) (benchmark data)
12. Holmes &: Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 2005;6:73. (pdf)
13. Klosterman et al.: XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics 2006;7:428. (main paper, pdf) (supplement, pdf)
14. Kosiol et al.: An empirical codon model for protein sequence evolution. Mol. Biol. Evol. 2007;24:1464-79.
15. Margulies et al.: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007;17:760-74.
16. Birney et al.: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447:799-816.
17. Holmes &: Phylocomposer and phylodirector: analysis and visualization of transducer indel models. Bioinformatics 2007;23:3263-4. (pdf)
18. Bradley & Holmes: Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics 2007;23:3258-62. (pdf)
19. Clark et al.: Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007;450:203-18.
20. Bendaña & Holmes: Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinformatics 2008;24:579-80. (pdf)
21. Barquist & Holmes: xREI: a phylo-grammar visualization webserver. Nucleic Acids Res. 2008;36:W65-9.
22. Bradley et al.: Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics 2008;24:2677-83. [[Stemloc AMAPreprint| (preprint, pdf)]]
23. Varadarajan et al.: Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol. 2008;9:R147.
24. Paten et al.: Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res. 2008;18:1829-43.
25. Westesson & Holmes: Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput. Biol. 2009;5:e1000318.
26. Heger et al.: Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins. Mol. Biol. Evol. 2009;26:1715-21.
27. Bradley et al.: Fast statistical alignment. PLoS Comput. Biol. 2009;5:e1000392.
28. Skinner et al.: JBrowse: a next-generation genome browser. Genome Res. 2009;19:1630-8.
29. Bradley et al.: Evolutionary modeling and prediction of non-coding RNAs in Drosophila. PLoS ONE 2009;4:e6478.
30. Bradley & Holmes: Evolutionary triplet models of structured RNA. PLoS Comput. Biol. 2009;5:e1000483.
31. Skinner & Holmes: Setting up the JBrowse genome browser. Curr Protoc Bioinformatics 2010;Chapter 9:Unit 9.13.
32. Bateman et al.: RNAcentral: A vision for an international database of RNA sequences. RNA 2011;17:1941-6.
33. Mørk & Holmes: Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. Bioinformatics 2012;28:636-42.
34. Westesson et al.: HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinformatics 2012;28:1170-1.
35. Holmes et al.: Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS ONE 2012;7:e30126.
36. Westesson et al.: Visualizing next-generation sequencing data with JBrowse. Brief. Bioinformatics 2013;14:172-7.
37. Westesson et al.: Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS ONE 2012;7:e34572.
38. Westesson & Holmes: Developing and applying heterogeneous phylogenetic models with XRate. PLoS ONE 2012;7:e36898.
39. De Maio et al.: Estimating empirical codon hidden Markov models. Mol. Biol. Evol. 2013;30:725-36.
40. Lee et al.: Web Apollo: a web-based genomic annotation editing platform. Genome Biol. 2013;14:R93.
41. Santiago-Ortiz et al.: AAV ancestral reconstruction library enables selection of broadly infectious viral variants. Gene Ther. 2015;22:934-46.
42. Buels et al.: JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66.
43. Holmes &: Historian: accurate reconstruction of ancestral sequences and evolutionary rates. Bioinformatics 2017;33:1227-1229.
44. Holmes & Mungall: BioMake: a GNU Make-compatible utility for declarative workflow management. Bioinformatics 2017;:.
45. Holmes &: Solving the master equation for Indels. BMC Bioinformatics 2017;18:255.
46. Keith Harris; Todd L. Parsons; Umer Z. Ijaz; Leo Lahti; Ian Holmes; Christopher Quince. Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process. Proceedings of the IEEE, 105(3). Special issue: Bioinformatics of DNA (2017).
47. Silvestre-Ryan J and Holmes IH. Consensus Decoding of Recurrent Neural Network Basecallers. Proceedings, 5th International Conference for Algorithms in Computational Biology (AlCoB 2018). Springer.
48. Dunn et al.: Apollo: Democratizing genome annotation. PLoS Comput. Biol. 2019;15:e1006790.
49. Buels et al.: Cram-JS: reference-based decompression in node and the browser. Bioinformatics 2019;35:4451-4452.

biorXiv.org preprints

• Jordi Silvestre-Ryan and Ian Holmes. Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing. (2020)
• Eric Yao, Robert Buels, Taner Sen, Lincoln Stein, Ian Holmes. JBrowse Connect: A server API to connect JBrowse instances and users. (2020)
• J. Silvestre-Ryan, Y. Wang, M. Sharma, S. Lin, Y. Shen, S. Dider, I. Holmes. Machine Boss: Rapid Prototyping of Bioinformatic Automata. (2020)

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)
• Keith Harris, Todd L Parsons, Umer Z Ijaz, Leo Lahti, Ian Holmes, Christopher Quince. Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process. (Submitted on 15 Oct 2014)
• Ian Holmes. Modular non-repeating codes for DNA storage (Submitted on 6 Jun 2016)

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)