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Matthew DeJongh
Matthew DeJongh
Professor of Computer Science, Hope College
Verified email at hope.edu - Homepage
Title
Cited by
Cited by
Year
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
100312008
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
10452010
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), 566-569, 2018
6122018
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), 1-17, 2007
1622007
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
1412013
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
SMD Seaver, F Liu, Q Zhang, J Jeffryes, JP Faria, JN Edirisinghe, ...
Nucleic acids research 49 (D1), D575-D588, 2021
622021
The DOE systems biology knowledgebase (KBase)
AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ...
BioRxiv, 096354, 2016
622016
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
492011
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
432011
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
192008
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
152012
Cautions about the reliability of pairwise gene correlations based on expression data
S Powers, M DeJongh, AA Best, NL Tintle
Frontiers in microbiology 6, 650, 2015
112015
Constructing and analyzing metabolic flux models of microbial communities
JP Faria, T Khazaei, JN Edirisinghe, P Weisenhorn, S Seaver, N Conrad, ...
Hydrocarbon and Lipid Microbiology Protocols, 247-273, 2016
92016
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), 1-12, 2012
92012
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
92011
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
82016
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
82004
The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes
SMD Seaver, F Liu, Q Zhang, J Jeffryes, JP Faria, JN Edirisinghe, ...
bioRxiv, 2020
52020
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
42016
Models of interdisciplinary research and service learning at Hope College
A Best, M DeJongh, A Barton, JR Brown, CC Barney
CUR Focus 28 (2), 18, 2007
42007
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Articles 1–20