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Author Details

Matthew DeJongh
Hope College
2000
19
11
PMIDPaper TitleJournal TitlePublished Year
32986834The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.Nucleic Acids Res2021
33179751The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.Nucleic Acids Res2021
30864320Implementing and evaluating a Gaussian mixture framework for identifying gene function from TnSeq data.Pac Symp Biocomput2019
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
27896957IDENTIFICATION AND ANALYSIS OF BACTERIAL GENOMIC METABOLIC SIGNATURES.Pac Symp Biocomput2017
27555837A Bayesian Framework for the Classification of Microbial Gene Activity States.Front Microbiol2016
27933038Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.Front Microbiol2016
26167162Cautions about the reliability of pairwise gene correlations based on expression data.Front Microbiol2015
23417797Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.Methods Mol Biol2013
22210867CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED.Bioinformatics2012
22873695Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data.BMC Bioinformatics2012
21421023Connecting genotype to phenotype in the era of high-throughput sequencing.Biochim Biophys Acta2011
21531804Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence.J Bacteriol2011
20802497High-throughput generation, optimization and analysis of genome-scale metabolic models.Nat Biotechnol2010
18261238The RAST Server: rapid annotations using subsystems technology.BMC Genomics2008
18986519Gene set analyses for interpreting microarray experiments on prokaryotic organisms.BMC Bioinformatics2008
17462086Toward the automated generation of genome-scale metabolic networks in the SEED.BMC Bioinformatics2007
17270905Linking molecular function and biological process terms in the ontology for gene expression data analysis.Conf Proc IEEE Eng Med Biol Soc2004
10977085An evaluation of ontology exchange languages for bioinformatics.Proc Int Conf Intell Syst Mol Biol2000
  • 1 - 19 of 19

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Collaborators

Aaron A Best
Hope College
Co-authored papers 16
Nathan Tintle
The Fatty Acid Research Institute
Co-authored papers 9
Christopher S Henry
Argonne National Laboratory
Co-authored papers 8
Rick Stevens
Argonne National Laboratory
Co-authored papers 5
Robert Olson
University of Chicago
Co-authored papers 4
Jos?? P Faria
Argonne National Laboratory
Co-authored papers 4
Janaka N Edirisinghe
Computation Institute, University of Chicago
Co-authored papers 4
Paul M Frybarger
Argonne National Laboratory
Co-authored papers 3
Erik Pearson
E.O. Lawrence Berkeley National Laboratory
Co-authored papers 3
Shane Canon
Lawrence Berkeley National Laboratory
Co-authored papers 3
Samuel M D Seaver
Argonne National Laboratory
Co-authored papers 3
Bruce Parrello
University of Chicago
Co-authored papers 3
Robert W Cottingham
Oak Ridge National Laboratory
Co-authored papers 3
Scott Devoid
Argonne National Laboratory
Co-authored papers 3
Folker Meyer
Institute for Artificial Intelligence, University of Duisburg-Essen
Co-authored papers 3
Adam P Arkin
Lawrence Berkeley National Laboratory
Co-authored papers 3
Elizabeth M Glass
Argonne National Laboratory
Co-authored papers 3
Sean R McCorkle
Brookhaven National Laboratory
Co-authored papers 2
Andrei L Osterman
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 2
Kevin P Keegan
Argonne National Laboratory
Co-authored papers 2
Gary J Olsen
University of Illinois
Co-authored papers 2
Pavel S Novichkov
Lawrence Berkeley National Laboratory
Co-authored papers 2
Fangfang Xia
University of Chicago
Co-authored papers 2
Elisha M Wood-Charlson
Lawrence Berkeley National Laboratory
Co-authored papers 2
James J Davis
University of Chicago
Co-authored papers 2
Patrik D'haeseleer
Lawrence Livermore National Laboratory
Co-authored papers 2
Vivek Kumar
Co-authored papers 1
Christopher Bun
Argonne National Laboratory
Co-authored papers 1
Neal Conrad
University of Chicago
Co-authored papers 1
Sunita Kumari
Manav Rachna International Institute of Research and Studies
Co-authored papers 1
Release 1.2