I. Holmes

发表

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Colin N. Dewey, Richard A. Moore, James B. Brown, 2007, Genome research.

Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics

I. Holmes, B. Paten, G. Lunter, 2012, PloS one.

A "Long Indel" model for evolutionary sequence alignment.

I. Holmes, I. Miklós, G. Lunter, 2003, Molecular biology and evolution.

Evolution of genes and genomes on the Drosophila phylogeny

Melanie A. Huntley, Sonja J. Prohaska, Albert J. Vilella, 2007, Nature.

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

I. Holmes, R. Bradley, A. Varadarajan, 2008, Genome Biology.

JBrowse: a next-generation genome browser.

L. Stein, C. Mungall, I. Holmes, 2009, Genome research.

Finding Regulatory Elements Using Joint Likelihoods for Sequence and Expression Profile Data

Ian Holmes, William J. Bruno, I. Holmes, 2000, ISMB.

RNAcentral: A vision for an international database of RNA sequences.

Anton J. Enright, Albert J. Vilella, Mathew W. Wright, 2011, RNA.

JBrowse: a dynamic web platform for genome visualization and analysis

Suzanna E Lewis, Colin M. Diesh, Monica Munoz-Torres, 2016, Genome Biology.

Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila

Ian Holmes, Lars Barquist, Yuri R. Bendaña, 2009, PloS one.

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

C. Quince, I. Holmes, Keith Harris, 2012, PloS one.

Modular non-repeating codes for DNA storage

I. Holmes, 2016, bioRxiv.

Genome-wide nucleotide-level mammalian ancestor reconstruction.

E. Birney, P. Flicek, I. Holmes, 2008, Genome research.

Phylogenetic automata, pruning, and multiple alignment

I. Holmes, B. Paten, G. Lunter, 2011, 1103.4347.

Web Apollo: a web-based genomic annotation editing platform

Monica C Munoz-Torres, Suzanna E Lewis, Lincoln Stein, 2013, Genome Biology.

Fast Statistical Alignment

Lior Pachter, Jaeyoung Do, Ian Holmes, 2009, PLoS Comput. Biol..

Historian: accurate reconstruction of ancestral sequences and evolutionary rates

I. Holmes, 2016, bioRxiv.

WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis

C. Mungall, I. Holmes, 2017, bioRxiv.

Approximation of Indel Evolution by Differential Calculus of Finite State Automata

I. Holmes, 2020, bioRxiv.

Transcendent elements: whole-genome transposon screens and open evolutionary questions.

I. Holmes, 2002, Genome research.

Estimation of Rearrangement Break Rates Across the Genome

I. Holmes, John W. Taylor, Christopher Hann-Soden, 2018, bioRxiv.

An alignment-free generalization to indels of Felsenstein's phylogenetic pruning algorithm

I. Holmes, B. Paten, G. Lunter, 2011 .

Colorstock, SScolor, Ratón: RNA alignment visualization tools

Yuri R. Bendaña, I. Holmes, 2008, Bioinform..

Lawrence Berkeley National Laboratory Recent Work Title JBrowse : A dynamic web platform for genome visualization and analysis

Richard D. Hayes, S. Lewis, L. Stein, 2016 .

Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins.

C. Ponting, A. Heger, I. Holmes, 2009, Molecular biology and evolution.

Developing and Applying Heterogeneous Phylogenetic Models with XRate

I. Holmes, Oscar Westesson, 2012, PloS one.

JBrowse 2: a modular genome browser with views of synteny and structural variation

Colin M. Diesh, Elliot A. Hershberg, R. Haw, 2022, bioRxiv.

JBrowse Jupyter: A Python interface to JBrowse 2

Elliot A. Hershberg, R. Haw, I. Holmes, 2022, bioRxiv.

Solving the master equation for Indels

I. Holmes, 2017, BMC Bioinformatics.

Evidence of stock connectivity, hybridization and misidentification in white anglerfish support the need of a genetics-informed fisheries management framework

I. Holmes, N. Rodríguez‐Ezpeleta, H. Gerritsen, 2021, bioRxiv.

A probabilistic model for the evolution of RNA structure

Ian Holmes, I. Holmes, 2004, BMC Bioinformatics.

Stem Stem Stem Stem Loop Loop Loop LoopLoop Loop Loop Loop Loop Loop Loop

Ian Holmes, I. Holmes, Ian H. Holmes, 2005 .

Machine Boss: rapid prototyping of bioinformatic automata

Yujie Wang, Stephen Lin, Ian Holmes, 2020, bioRxiv.

Fast Statistical Alignment : Text S 1

Lior Pachter, Jaeyoung Do, Ian Holmes, 2009 .

xREI: a phylo-grammar visualization webserver

Ian Holmes, Lars Barquist, I. Holmes, 2008, Nucleic Acids Res..

XRate: a fast prototyping, training and annotation tool for phylo-grammars

Ian Holmes, Carolin Kosiol, Nick Goldman, 2006, BMC Bioinformatics.

Dynamic programming alignment accuracy

Ian Holmes, Richard Durbin, R. Durbin, 1998, RECOMB '98.

Studies in Probabilistic Sequence Alignment and Evolution

Ian H. Holmes, I. Holmes, 1998 .

An empirical codon model for protein sequence evolution.

Ian Holmes, Nick Goldman, Carolin Kosiol, 2007, Molecular biology and evolution.

CNVpytor: a tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing

Colin M. Diesh, A. Abyzov, I. Holmes, 2021, bioRxiv.

Evolutionary Triplet Models of Structured RNA

Ian Holmes, Robert K. Bradley, I. Holmes, 2009, PLoS Comput. Biol..

JBrowse Connect: A server API to connect JBrowse instances and users

Lincoln Stein, Taner Z. Sen, Ian Holmes, 2019, bioRxiv.

JBrowse: a dynamic web platform for genome visualization and analysis

Colin M. Diesh, Richard D. Hayes, S. Lewis, 2016, Genome Biology.

Modular non-repeating codes for DNA storage

Ian Holmes, I. Holmes, 2016, bioRxiv.

Estimating Empirical Codon Hidden Markov Models

Ian Holmes, Christian Schlötterer, Nicola De Maio, 2012, Molecular biology and evolution.

Fitting Birth-Death Processes to Panel Data with Applications to Bacterial DNA Fingerprinting.

Marc A Suchard, Vladimir N Minin, Ian Holmes, 2010, The annals of applied statistics.

An expectation maximization algorithm for training hidden substitution models.

I Holmes, G M Rubin, G. Rubin, 2002, Journal of molecular biology.

Evolutionary HMMs: a Bayesian approach to multiple alignment

Ian Holmes, William J. Bruno, I. Holmes, 2001, Bioinform..

Apollo: Democratizing genome annotation

Colin Diesh, Suzanna E Lewis, Colin M. Diesh, 2019, bioRxiv.

Specific alignment of structured RNA: stochastic grammars and sequence annealing

Lior Pachter, Ian Holmes, Robert K. Bradley, 2008, Bioinform..

Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments

Oscar Westesson, Ian Holmes, I. Holmes, 2009, PLoS Comput. Biol..

AAV ANCESTRAL RECONSTRUCTION LIBRARY ENABLES SELECTION OF BROADLY INFECTIOUS VIRAL VARIANTS

I. Holmes, D. Schaffer, Oscar Westesson, 2015, Gene Therapy.

Transducers: an emerging probabilistic framework for modeling indels on trees

Ian Holmes, Robert K. Bradley, I. Holmes, 2007, Bioinform..

Using evolutionary Expectation Maximization to estimate indel rates

Ian Holmes, I. Holmes, 2005, Bioinform..

CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing

Colin M. Diesh, A. Abyzov, I. Holmes, 2021, GigaScience.

Using guide trees to construct multiple-sequence evolutionary HMMs

I. Holmes, I. Holmes, 2003, ISMB.

Visualizing next-generation sequencing data with JBrowse

Oscar Westesson, Ian Holmes, Mitchell Skinner, 2013, Briefings Bioinform..

Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process

Ian Holmes, Umer Zeeshan Ijaz, Leo Lahti, 2014, Proceedings of the IEEE.

SI Appendix: 1) Large Population Limits for a Neutral Metacommunity and 2) Gibbs Sampling for the UNTB-HDP

C. Quince, I. Holmes, U. Ijaz, 2015 .

k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction

Christopher J. Mungall, Melissa Haendel, Sebastian Koehler, 2016, bioRxiv.

Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing

Ian Holmes, Jordi Silvestre-Ryan, I. Holmes, 2020, Genome Biology.

CellScape: Protein structure visualization with vector graphics cartoons

I. Holmes, D. Fletcher, J. Silvestre-Ryan, 2022, bioRxiv.

Historian: accurate reconstruction of ancestral sequences and evolutionary rates

Ian Holmes, I. Holmes, 2016, bioRxiv.

Setting Up the JBrowse Genome Browser

Ian H Holmes, Mitchell E Skinner, I. Holmes, 2010, Current protocols in bioinformatics.

Abstract 6400: JBrowse 2: An extensible open-source platform for modern genome analysis

Colin M. Diesh, Elliot A. Hershberg, R. Haw, 2022, Cancer Research.

GrainGenes: a data-rich repository for small grains genetics and genomics

Steve L Michel, I. Holmes, L. Cooper, 2022, Database J. Biol. Databases Curation.

Great Expectations: EM Algorithms for Discretely Observed Linear Birth-Death-Immigration Processes

Charles R. Doss, M. Suchard, I. Holmes, 2010 .

JBrowseR: an R interface to the JBrowse 2 genome browser

Colin M. Diesh, Lincoln Stein, Robert Buels, 2021, Bioinform..

Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars

Ian Holmes, Gerald M. Rubin, G. Rubin, 2001, Pacific Symposium on Biocomputing.

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

Oscar Westesson, Ian Holmes, Lars Barquist, 2012, Bioinform..

Solving the master equation for Indels

Ian Holmes, I. Holmes, 2017, BMC Bioinformatics.

Using evolutionary Expectation Maximization to estimate indel rates

I. Holmes, 2005, Bioinform..

Consensus Decoding of Recurrent Neural Network Basecallers

Ian Holmes, Jordi Silvestre-Ryan, I. Holmes, 2018, AlCoB.