Difference between revisions of "Paper Archive"
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* Oscar Westesson, Ian Holmes. [http://arxiv.org/abs/1202.3834 Developing and applying heterogeneous phylogenetic models with XRate.] ''(Submitted on 17 Feb 2012)'' | * Oscar Westesson, Ian Holmes. [http://arxiv.org/abs/1202.3834 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. [http://arxiv.org/abs/1410.4038 Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process.] ''(Submitted on 15 Oct 2014)'' | * Keith Harris, Todd L Parsons, Umer Z Ijaz, Leo Lahti, Ian Holmes, Christopher Quince. [http://arxiv.org/abs/1410.4038 Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process.] ''(Submitted on 15 Oct 2014)'' | ||
+ | * Ian Holmes. [https://arxiv.org/abs/1606.01799 Modular non-repeating codes for DNA storage] ''(Submitted on 6 Jun 2016)'' | ||
== PhD theses == | == PhD theses == |
Revision as of 19:31, 6 September 2017
Contents
Paper archive for the Holmes Lab, Berkeley
Pubmed-indexed journals and conference proceedings
- Holmes & Durbin: Dynamic programming alignment accuracy. J. Comput. Biol. 1998;5:493-504.
(pdf)
- Newman et al.: Haloalkane dehalogenases: structure of a Rhodococcus enzyme. Biochemistry 1999;38:16105-14.
- 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)
- Holmes & Bruno: Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics 2001;17:803-20.
(pdf)
- Holmes & Rubin: Pairwise RNA structure comparison with stochastic context-free grammars. Pac Symp Biocomput 2002;:163-74.
(pdf)
- Holmes & Rubin: An expectation maximization algorithm for training hidden substitution models. J. Mol. Biol. 2002;317:753-64.
(pdf)
- Holmes &: Transcendent elements: whole-genome transposon screens and open evolutionary questions. Genome Res. 2002;12:1152-5.
(pdf)
- Holmes &: Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics 2003;19 Suppl 1:i147-57.
(pdf) (errata)
- Miklós et al.: A "Long Indel" model for evolutionary sequence alignment. Mol. Biol. Evol. 2004;21:529-40.
(pdf)
- Holmes &: A probabilistic model for the evolution of RNA structure. BMC Bioinformatics 2004;5:166.
(pdf)
- Holmes &: Using evolutionary Expectation Maximization to estimate indel rates. Bioinformatics 2005;21:2294-300.
(main paper, pdf)
(supplement, pdf)
(benchmark data)
- Holmes &: Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 2005;6:73.
(pdf)
- Klosterman et al.: XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics 2006;7:428.
(main paper, pdf)
(supplement, pdf)
- Kosiol et al.: An empirical codon model for protein sequence evolution. Mol. Biol. Evol. 2007;24:1464-79.
- Margulies et al.: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007;17:760-74.
- 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.
- Holmes &: Phylocomposer and phylodirector: analysis and visualization of transducer indel models. Bioinformatics 2007;23:3263-4.
(pdf)
- Bradley & Holmes: Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics 2007;23:3258-62.
(pdf)
- Clark et al.: Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007;450:203-18.
- Bendaña & Holmes: Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinformatics 2008;24:579-80.
(pdf)
- Barquist & Holmes: xREI: a phylo-grammar visualization webserver. Nucleic Acids Res. 2008;36:W65-9.
- Bradley et al.: Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics 2008;24:2677-83. [[Stemloc AMAPreprint|
(preprint, pdf)]]
- Varadarajan et al.: Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol. 2008;9:R147.
- Paten et al.: Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res. 2008;18:1829-43.
- Westesson & Holmes: Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput. Biol. 2009;5:e1000318.
- Heger et al.: Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins. Mol. Biol. Evol. 2009;26:1715-21.
- Bradley et al.: Fast statistical alignment. PLoS Comput. Biol. 2009;5:e1000392.
- Skinner et al.: JBrowse: a next-generation genome browser. Genome Res. 2009;19:1630-8.
- Bradley et al.: Evolutionary modeling and prediction of non-coding RNAs in Drosophila. PLoS ONE 2009;4:e6478.
- Bradley & Holmes: Evolutionary triplet models of structured RNA. PLoS Comput. Biol. 2009;5:e1000483.
- Skinner & Holmes: Setting up the JBrowse genome browser. Curr Protoc Bioinformatics 2010;Chapter 9:Unit 9.13.
- Bateman et al.: RNAcentral: A vision for an international database of RNA sequences. RNA 2011;17:1941-6.
- Mørk & Holmes: Evaluating bacterial gene-finding HMM structures as probabilistic logic programs. Bioinformatics 2012;28:636-42.
- Westesson et al.: HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction. Bioinformatics 2012;28:1170-1.
- Holmes et al.: Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS ONE 2012;7:e30126.
- Westesson et al.: Visualizing next-generation sequencing data with JBrowse. Brief. Bioinformatics 2013;14:172-7.
- Westesson et al.: Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS ONE 2012;7:e34572.
- Westesson & Holmes: Developing and applying heterogeneous phylogenetic models with XRate. PLoS ONE 2012;7:e36898.
- De Maio et al.: Estimating empirical codon hidden Markov models. Mol. Biol. Evol. 2013;30:725-36.
- Lee et al.: Web Apollo: a web-based genomic annotation editing platform. Genome Biol. 2013;14:R93.
- Santiago-Ortiz et al.: AAV ancestral reconstruction library enables selection of broadly infectious viral variants. Gene Ther. 2015;22:934-46.
- Buels et al.: JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66.
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)