Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing von Silvestre-Ryan, Jordi, Holmes, Ian

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Apollo: Democratizing genome annotation von Dunn, Nathan A, Unni, Deepak R, Diesh, Colin, Munoz-Torres, Monica, Harris, Nomi L, Yao, Eric, Rasche, Helena, Holmes, Ian H, Elsik, Christine G, Lewis, Suzanna E

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Dirichlet multinomial mixtures: generative models for microbial metagenomics von Holmes, Ian, Harris, Keith, Quince, Christopher

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JBrowse 2: a modular genome browser with views of synteny and structural variation von Diesh, Colin, Stevens, Garrett J, Xie, Peter, De Jesus Martinez, Teresa, Hershberg, Elliot A, Leung, Angel, Guo, Emma, Dider, Shihab, Zhang, Junjun, Bridge, Caroline, Hogue, Gregory, Duncan, Andrew, Morgan, Matthew, Flores, Tia, Bimber, Benjamin N, Haw, Robin, Cain, Scott, Buels, Robert M, Stein, Lincoln D, Holmes, Ian H

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JBrowse: a dynamic web platform for genome visualization and analysis von Buels, Robert, Yao, Eric, Diesh, Colin M, Hayes, Richard D, Munoz-Torres, Monica, Helt, Gregg, Goodstein, David M, Elsik, Christine G, Lewis, Suzanna E, Stein, Lincoln, Holmes, Ian H

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Solving the master equation for Indels von Holmes, Ian H

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Historian: accurate reconstruction of ancestral sequences and evolutionary rates von Holmes, Ian H

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JBrowse: a next-generation genome browser von Skinner, Mitchell E, Uzilov, Andrew V, Stein, Lincoln D, Mungall, Christopher J, Holmes, Ian H

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Accelerated probabilistic inference of RNA structure evolution von Holmes, Ian

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CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing von Suvakov, Milovan, Panda, Arijit, Diesh, Colin, Holmes, Ian, Abyzov, Alexej

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Chemically Catalyzed Asymmetric Cyanohydrin Syntheses von Brunel, Jean-Michel, Holmes, Ian P.

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Fast statistical alignment von Bradley, Robert K, Roberts, Adam, Smoot, Michael, Juvekar, Sudeep, Do, Jaeyoung, Dewey, Colin, Holmes, Ian, Pachter, Lior

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Web Apollo: a web-based genomic annotation editing platform von Lee, Eduardo, Helt, Gregg A, Reese, Justin T, Munoz-Torres, Monica C, Childers, Chris P, Buels, Robert M, Stein, Lincoln, Holmes, Ian H, Elsik, Christine G, Lewis, Suzanna E

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A Model of Indel Evolution by Finite-State, Continuous-Time Machines von Holmes, Ian

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JBrowseR: an R interface to the JBrowse 2 genome browser von Hershberg, Elliot A, Stevens, Garrett, Diesh, Colin, Xie, Peter, De Jesus Martinez, Teresa, Buels, Robert, Stein, Lincoln, Holmes, Ian

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Endoscopic Mucosal Resection versus Endoscopic Submucosal Dissection for Large Polyps: A Western Colonoscopist's View von Holmes, Ian, Friedland, Shai

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BioMake: a GNU make-compatible utility for declarative workflow management von Holmes, Ian H, Mungall, Christopher J

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Avulsion is superior to argon plasma coagulation for treatment of visible residual neoplasia during EMR of colorectal polyps (with videos) von Holmes, Ian, MD, Kim, Hyun Gun, MD, Yang, Dong-Hoon, MD, Friedland, Shai, MD

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A probabilistic model for the evolution of RNA structure von Holmes, Ian

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Genome-wide nucleotide-level mammalian ancestor reconstruction von Paten, Benedict, Herrero, Javier, Fitzgerald, Stephen, Beal, Kathryn, Flicek, Paul, Holmes, Ian, Birney, Ewan

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