Publications

2021

JBrowseR: An R Interface to the JBrowse 2 Genome Browser

Elliot Hershberg , Garrett Stevens , Colin Diesh , Peter Xie , Teresa De Jesus Martinez , Robert Buels , Lincoln Stein , Ian Holmes

Bioinformatics

July, 2021

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

Jordi Silvestre-Ryan , Ian Holmes

Genome Biology

January, 2021

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2020

A model of indel evolution by finite-state, continuous-time machines

Ian Holmes

Genetics

December, 2020

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Machine Boss: rapid prototyping of bioinformatic automata

Jordi Silvestre-Ryan , Yujie Wang , Mehak Sharma , Stephen Lin , Shihab Dider , Ian Holmes

Bioinformatics

July, 2020

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Cellular automata simulation of RNA self-replicators

Ian Holmes

ALIFE 2020: The 2020 Conference on Artificial Life

July, 2020

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2019

Apollo: democratizing genome annotation

Nathan Dunn , Deepak Unni , Colin Diesh , Monica Munoz-Torres , Nomi Harris , Eric Yao , Helena Rasche , Ian Holmes , Christine Elsik , Suzanna Lewis

PLoS Computational Biology

February, 2019

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2017

BioMake: a GNU make-compatible utility for declarative workflow management

Ian Holmes , Christopher Mungall

Bioinformatics

November, 2017

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Historian: accurate reconstruction of ancestral sequences and evolutionary rates

Ian Holmes

Bioinformatics

April, 2017

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2016

JBrowse: a dynamic web platform for genome visualization and analysis

Robert Buels , Eric Yao , Colin Diesh , Richard Hayes , Monica Munoz-Torres , Gregg Helt , David Goodstein , Christine Elsik , Suzanna Lewis , Lincoln Stein , Ian Holmes

Genome Biology

April, 2016

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2015

Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical Dirichlet process

Keith Harris , Todd Parsons , Umer Ijaz , Leo Lahti , Ian Holmes , Christopher Quince

Proceedings of the IEEE

August, 2015

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AAV ancestral reconstruction library enables selection of broadly infectious viral variants

I Holmes , J Santiago-Ortiz , D S Ojala , O Westesson , J R Weinstein , S Y Wong , A Steinsapir , S Kumar , I Holmes , D V Schaffer

Gene Therapy

July, 2015

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