Author

Matthew DeJongh

Hope CollegeORCID 0000-0002-1582-4614Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 3 Research Focus:database / resource· 3 Approach:statistical model· 3 Organism:plant (other)· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Approach:experimental assay· 1

Frequent Co-Authors

Aaron A. BestiD· 3 shared Adam P. ArkiniD· 3 shared Christopher S. HenryiD· 3 shared Janaka N. EdirisingheiD· 3 shared José P. FariaiD· 3 shared Robert W. CottinghamiD· 3 shared Samuel M. D. SeaveriD· 3 shared Erik PearsoniD· 2 shared

Activity by Year

2018-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersSystems Biology

Aaron A. BestORCID

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3 papers

Recent·Most cited

Systems BiologybioRxivPreprintOct 4, 2023

ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction

José P. Faria, Filipe Liu, Janaka N. Edirisinghe…·Christopher S. Henry

ModelSEED v2 improves genome-scale metabolic model reconstruction with enhanced energy metabolism and better pathway curation, leading to more accurate and comprehensive models.

24 citations

bacteria (other)virus

𝕏 PostBluesky

Systems BiologyNucleic Acids ResearchPeer-reviewedSep 24, 2020

The ModelSEED 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…·Christopher S. Henry

The paper introduces the ModelSEED biochemistry database, which integrates metabolic annotations and supports the reconstruction and analysis of metabolic models for plants, fungi, and microbes.

279 citationstop 1%

plant (other)fungi (other)

𝕏 PostBluesky

BioinformaticsNature BiotechnologyPeer-reviewedJul 1, 2018

✦ In-depth digest

The DOE Systems Biology Knowledgebase (KBase)

Adam P. Arkin, Robert W. Cottingham, Christopher S. Henry…·Dantong Yu

Open-source KBase platform unites reference genomes and biochemistry, over 70 apps, Jupyter-based Narratives with provenance, and a Docker SDK for reproducible plant and microbial systems biology.

1,624 citationstop 1%

multiple speciesbacteria (other)

𝕏 PostBluesky