Publications by authors named "Matthew DeJongh"

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The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.
Samuel M D Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, José P Faria, Matthew DeJongh

Nucleic Acids Res· January 2021

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The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.
Samuel M D Seaver, Filipe Liu, Qizhi Zhang, James Jeffryes, José P Faria, Matthew DeJongh

Nucleic Acids Res· January 2021

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Implementing and evaluating a Gaussian mixture framework for identifying gene function from TnSeq data.
Kevin Li, Rachel Chen, William Lindsey, Aaron Best, Matthew DeJongh

Pac Symp Biocomput· August 2019

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KBase: The United States Department of Energy Systems Biology Knowledgebase.
Adam P Arkin, Robert W Cottingham, Christopher S Henry, Nomi L Harris, Rick L Stevens, Matthew DeJongh

Nat Biotechnol· July 2018

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IDENTIFICATION AND ANALYSIS OF BACTERIAL GENOMIC METABOLIC SIGNATURES.
Nathaniel Bowerman, Nathan Tintle, Matthew Dejongh, Aaron A Best

Pac Symp Biocomput· July 2017

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Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.
José P Faria, James J Davis, Janaka N Edirisinghe, Ronald C Taylor, Pamela Weisenhorn, Matthew DeJongh

Front Microbiol· November 2016

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A Bayesian Framework for the Classification of Microbial Gene Activity States.
Craig Disselkoen, Brian Greco, Kaitlyn Cook, Kristin Koch, Reginald Lerebours, Matthew DeJongh

Front Microbiol· August 2016

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Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.
Scott Devoid, Ross Overbeek, Matthew DeJongh, Veronika Vonstein, Aaron A Best

Methods Mol Biol· July 2013

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Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data.
Nathan L Tintle, Alexandra Sitarik, Benjamin Boerema, Kylie Young, Aaron A Best, Matthew Dejongh

BMC Bioinformatics· August 2012

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CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED.
Matthew DeJongh, Benjamin Bockstege, Paul Frybarger, Nicholas Hazekamp, Joshua Kammeraad

Bioinformatics· March 2012

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Connecting genotype to phenotype in the era of high-throughput sequencing.
Christopher S Henry, Ross Overbeek, Fangfang Xia, Aaron A Best, Elizabeth Glass, Matthew Dejongh

Biochim Biophys Acta· October 2011

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Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence.
Dmitry A Ravcheev, Aaron A Best, Nathan Tintle, Matthew Dejongh, Andrei L Osterman

J Bacteriol· July 2011

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High-throughput generation, optimization and analysis of genome-scale metabolic models.
Christopher S Henry, Matthew DeJongh, Aaron A Best, Paul M Frybarger, Ben Linsay

Nat Biotechnol· September 2010

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Gene set analyses for interpreting microarray experiments on prokaryotic organisms.
Nathan L Tintle, Aaron A Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron

BMC Bioinformatics· November 2008

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The RAST Server: rapid annotations using subsystems technology.
Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz

BMC Genomics· February 2008

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Linking molecular function and biological process terms in the ontology for gene expression data analysis.
Matthew Dejongh, Pamela Van Dort, Benjamin Ramsay

Conf Proc IEEE Eng Med Biol Soc· June 2007

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Toward the automated generation of genome-scale metabolic networks in the SEED.
Matthew DeJongh, Kevin Formsma, Paul Boillot, John Gould, Matthew Rycenga

BMC Bioinformatics· April 2007

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