List of works - Ian Holmes

A "Long Indel" model for evolutionary sequence alignment

scientific article published on 23 December 2003

A probabilistic model for the evolution of RNA structure

scientific article

Accelerated probabilistic inference of RNA structure evolution

scientific article

Accurate detection of recombinant breakpoints in whole-genome alignments

scientific article

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

scientific article

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

scientific article

An Empirical Codon Model for Protein Sequence Evolution

scientific article published in 2007

An empirical codon model for protein sequence evolution

scientific article

An expectation maximization algorithm for training hidden substitution models.

scientific article

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

scientific article published in June 2007

Colorstock, SScolor, Ratón: RNA alignment visualization tools

scientific article published on 24 January 2008

Developing and applying heterogeneous phylogenetic models with XRate

scientific article

Dirichlet multinomial mixtures: generative models for microbial metagenomics

scientific article (publication date: 2012)

Estimating empirical codon hidden Markov models

scientific article published on 27 November 2012

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs

scientific article published on 3 January 2012

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolutionary modeling and prediction of non-coding RNAs in Drosophila

scientific article

Evolutionary triplet models of structured RNA

scientific article

Fast statistical alignment

scientific article

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

scientific article

Genome-wide nucleotide-level mammalian ancestor reconstruction

scientific article (publication date: November 2008)

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

scientific article

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

scientific article published in June 2007

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

scientific article published in 2023

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

scientific article published on 18 August 2020

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

JBrowse: a dynamic web platform for genome visualization and analysis

scientific article published on 12 April 2016

JBrowse: a next-generation genome browser

scientific article

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

Phylocomposer and phylodirector: analysis and visualization of transducer indel models.

scientific article published on 5 September 2007

Pipeline

1988 video game

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

Setting up the JBrowse genome browser

scientific article

Solving the master equation for Indels

scientific article published on 12 May 2017

Specific alignment of structured RNA: stochastic grammars and sequence annealing

scientific article published on 16 September 2008

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

scientific article published on 8 October 2008

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

scientific article

Transducers: an emerging probabilistic framework for modeling indels on trees

article

Using evolutionary Expectation Maximization to estimate indel rates

article

Using guide trees to construct multiple-sequence evolutionary HMMs

article

Visualizing next-generation sequencing data with JBrowse

scientific article

Web Apollo: a web-based genomic annotation editing platform

scientific article (publication date: 30 August 2013)

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

scientific article

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

xREI: a phylo-grammar visualization webserver

scientific article published on 3 June 2008

List of works by Ian Holmes

A "Long Indel" model for evolutionary sequence alignment

A probabilistic model for the evolution of RNA structure

Accelerated probabilistic inference of RNA structure evolution

Accurate detection of recombinant breakpoints in whole-genome alignments

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

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

An Empirical Codon Model for Protein Sequence Evolution

An empirical codon model for protein sequence evolution

An expectation maximization algorithm for training hidden substitution models.

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

Colorstock, SScolor, Ratón: RNA alignment visualization tools

Developing and applying heterogeneous phylogenetic models with XRate

Dirichlet multinomial mixtures: generative models for microbial metagenomics

Estimating empirical codon hidden Markov models

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs

Evolution of genes and genomes on the Drosophila phylogeny

Evolutionary modeling and prediction of non-coding RNAs in Drosophila

Evolutionary triplet models of structured RNA

Fast statistical alignment

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

Genome-wide nucleotide-level mammalian ancestor reconstruction

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

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

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

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

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

JBrowse: a dynamic web platform for genome visualization and analysis

JBrowse: a next-generation genome browser

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

Phylocomposer and phylodirector: analysis and visualization of transducer indel models.

Pipeline

RNAcentral: A vision for an international database of RNA sequences

Setting up the JBrowse genome browser

Solving the master equation for Indels

Specific alignment of structured RNA: stochastic grammars and sequence annealing

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

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

Transducers: an emerging probabilistic framework for modeling indels on trees

Using evolutionary Expectation Maximization to estimate indel rates

Using guide trees to construct multiple-sequence evolutionary HMMs

Visualizing next-generation sequencing data with JBrowse

Web Apollo: a web-based genomic annotation editing platform

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

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

xREI: a phylo-grammar visualization webserver