Matthew DeJongh
Matthew DeJongh
Professor of Computer Science, Hope College
Verified email at - Homepage
Cited by
Cited by
The RAST Server: rapid annotations using subsystems technology
R Aziz, D Bartels, A Best, M DeJongh, T Disz, R Edwards, K Formsma, ...
BMC genomics 9 (1), 75, 2008
High-throughput generation, optimization and analysis of genome-scale metabolic models
CS Henry, M DeJongh, AA Best, PM Frybarger, B Linsay, RL Stevens
Nature biotechnology 28 (9), 977-982, 2010
Toward the automated generation of genome-scale metabolic networks in the SEED
M DeJongh, K Formsma, P Boillot, J Gould, M Rycenga, A Best
BMC bioinformatics 8 (1), 139, 2007
KBase: the United States department of energy systems biology knowledgebase
AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ...
Nature biotechnology 36 (7), 566, 2018
Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED
S Devoid, R Overbeek, M DeJongh, V Vonstein, AA Best, C Henry
Systems Metabolic Engineering, 17-45, 2013
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence
DA Ravcheev, AA Best, N Tintle, M DeJongh, AL Osterman, PS Novichkov, ...
Journal of bacteriology 193 (13), 3228-3240, 2011
Connecting genotype to phenotype in the era of high-throughput sequencing
CS Henry, R Overbeek, F Xia, AA Best, E Glass, J Gilbert, P Larsen, ...
Biochimica et Biophysica Acta (BBA)-General Subjects 1810 (10), 967-977, 2011
The DOE systems biology knowledgebase (KBase)
AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ...
BioRxiv, 096354, 2016
Gene set analyses for interpreting microarray experiments on prokaryotic organisms
NL Tintle, AA Best, M DeJongh, D Van Bruggen, F Heffron, S Porwollik, ...
BMC bioinformatics 9 (1), 1-14, 2008
CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
M DeJongh, B Bockstege, P Frybarger, N Hazekamp, J Kammeraad, ...
Bioinformatics 28 (6), 891-892, 2012
Increasing engagement and enrollment in breadth-first introductory courses using authentic computing tasks
RL McFall, M DeJongh
Proceedings of the 42nd ACM technical symposium on Computer science …, 2011
Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data
NL Tintle, A Sitarik, B Boerema, K Young, AA Best, M DeJongh
BMC bioinformatics 13 (1), 193, 2012
Cautions about the reliability of pairwise gene correlations based on expression data
S Powers, M DeJongh, AA Best, N Tintle
Frontiers in microbiology 6, 650, 2015
Computing and applying atomic regulons to understand gene expression and regulation
JP Faria, JJ Davis, JN Edirisinghe, RC Taylor, P Weisenhorn, RD Olson, ...
Frontiers in microbiology 7, 1819, 2016
Linking molecular function and biological process terms in the ontology for gene expression data analysis
M DeJongh, P Van Dort, B Ramsay
Engineering in Medicine and Biology Society, 2004. IEMBS'04. 26th Annual …, 2004
Constructing and analyzing metabolic flux models of microbial communities
JP Faria, T Khazaei, JN Edirisinghe, P Weisenhorn, SMD Seaver, ...
Hydrocarbon and Lipid Microbiology Protocols, 247-273, 2016
A Bayesian framework for the classification of microbial gene activity states
C Disselkoen, B Greco, K Cook, K Koch, R Lerebours, C Viss, J Cape, ...
Frontiers in microbiology 7, 1191, 2016
Identification and Analysis of Bacterial Genomic Metabolic Signatures
N Bowerman, N TINTLE, M DeJongh, AA Best
Models of Interdisciplinary Research and Service Learning at Hope College
AA Best, M DeJongh, AJ Barton, JR Brown, CC Barney
CUR Quarterly 28 (2), 18, 2007
Implementing and evaluating a Gaussian mixture framework for identifying gene function from TnSeq data.
K Li, R Chen, W Lindsey, AA Best, M DeJongh, C Henry, NL Tintle
PSB, 172-183, 2019
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