| The RAST Server: rapid annotations using subsystems technology RK Aziz, D Bartels, AA Best, M DeJongh, T Disz, RA Edwards, K Formsma, ... BMC genomics 9, 1-15, 2008 | 12031 | 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 | 1206 | 2010 |
| 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 | 1159 | 2018 |
| 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 | 189 | 2021 |
| 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, 1-17, 2007 | 176 | 2007 |
| 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: methods and protocols, 17-45, 2013 | 169 | 2013 |
| The DOE systems biology knowledgebase (KBase) AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ... BioRxiv, 096354, 2016 | 78 | 2016 |
| 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 | 60 | 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 | 44 | 2011 |
| 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, 1-14, 2008 | 19 | 2008 |
| Constructing and analyzing metabolic flux models of microbial communities JP Faria, T Khazaei, JN Edirisinghe, P Weisenhorn, SMD Seaver, ... Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System …, 2017 | 15 | 2017 |
| 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 | 15 | 2012 |
| 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 | 14 | 2015 |
| 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, 1-12, 2012 | 10 | 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 | 9 | 2011 |
| 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 | 8 | 2016 |
| Linking molecular function and biological process terms in the ontology for gene expression data analysis M DeJongh, P Van Dort, B Ramsay The 26th Annual International Conference of the IEEE Engineering in Medicine …, 2004 | 8 | 2004 |
| ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction JP Faria, F Liu, JN Edirisinghe, N Gupta, SMD Seaver, AP Freiburger, ... bioRxiv, 2023.10. 04.556561, 2023 | 5 | 2023 |
| 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 | 4 | 2016 |
| 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 | 4 | 2007 |
