Publications by authors named "Matt Simison"

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Data navigation on the ENCODE portal.
Meenakshi S Kagda, Bonita Lam, Casey Litton, Corinn Small, Cricket A Sloan, Matt Simison

Nat Commun· October 2025

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The ENCODE Uniform Analysis Pipelines.
Benjamin C Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S Kagda, Keenan Graham, Matt Simison

Res Sq· July 2023

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The ENCODE Uniform Analysis Pipelines.
Benjamin C Hitz, Lee Jin-Wook, Otto Jolanki, Meenakshi S Kagda, Keenan Graham, Matt Simison

bioRxiv· April 2023

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New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources.
Stacia R Engel, Edith D Wong, Robert S Nash, Suzi Aleksander, Micheal Alexander, Matt Simison

Genetics· April 2022

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Transcriptome visualization and data availability at the Saccharomyces Genome Database.
Patrick C Ng, Edith D Wong, Kevin A MacPherson, Suzi Aleksander, Joanna Argasinska, Matt Simison

Nucleic Acids Res· January 2020

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Saccharomyces genome database informs human biology.
Marek S Skrzypek, Robert S Nash, Edith D Wong, Kevin A MacPherson, Sage T Hellerstedt, Matt Simison

Nucleic Acids Res· January 2018

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The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.
Marek S Skrzypek, Jonathan Binkley, Gail Binkley, Stuart R Miyasato, Matt Simison

Nucleic Acids Res· January 2017

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Ontology application and use at the ENCODE DCC.
Venkat S Malladi, Drew T Erickson, Nikhil R Podduturi, Laurence D Rowe, Esther T Chan, Matt Simison

Database (Oxford)· September 2015

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The reference genome sequence of Saccharomyces cerevisiae: then and now.
Stacia R Engel, Fred S Dietrich, Dianna G Fisk, Gail Binkley, Rama Balakrishnan, Matt Simison

G3 (Bethesda)· March 2014

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The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny.
Jonathan Binkley, Martha B Arnaud, Diane O Inglis, Marek S Skrzypek, Prachi Shah, Matt Simison

Nucleic Acids Res· January 2014

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The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations.
Gustavo C Cerqueira, Martha B Arnaud, Diane O Inglis, Marek S Skrzypek, Gail Binkley, Matt Simison

Nucleic Acids Res· January 2014

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The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.
Diane O Inglis, Martha B Arnaud, Jonathan Binkley, Prachi Shah, Marek S Skrzypek, Matt Simison

Nucleic Acids Res· January 2012

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The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources.
Martha B Arnaud, Gustavo C Cerqueira, Diane O Inglis, Marek S Skrzypek, Jonathan Binkley, Matt Simison

Nucleic Acids Res· January 2012

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Saccharomyces Genome Database: the genomics resource of budding yeast.
J Michael Cherry, Eurie L Hong, Craig Amundsen, Rama Balakrishnan, Gail Binkley, Matt Simison

Nucleic Acids Res· January 2012

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