Author

Matthew A. Richards

Institute for Systems Biology

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:database / resource· 2 Assay:DNA methylation· 2 Organism:human· 2 Approach:benchmark study· 1 Assay:ChIP-seq· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Nathan D. PriceiD· 3 shared Ben HeavneriD· 2 shared Carl KesselmaniD· 2 shared Cory C. FunkiD· 2 shared Gustavo GlusmaniD· 2 shared Ian T FosteriD· 2 shared Kyle ChardiD· 2 shared Paul T. ShannoniD· 2 shared

Activity by Year

2017-2020 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Nathan D. PriceORCID

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Author profile →

3 papers

Recent·Most cited

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data Across 27 Tissue Types

Cory C. Funk, Alex M. Casella, Segun C. Jung, Matthew A. Richards, Alex Rodriguez, Paul T. Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilüfer Ertekin‐Taner, Todd Eliot Golde, Arthur W. Toga, Leroy Hood, , Seth A. Ament

The paper develops a workflow to identify transcription factor binding sites across 27 human tissues using DNase-seq data, resulting in a comprehensive footprint atlas with high-quality predictions.

Cell Reports · Aug 1, 2020Peer-reviewedBioinformatics

Reproducible big data science: A case study in continuous FAIRness

Ravi Madduri, Kyle Chard, Mike D’Arcy, Segun C. Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W. Deutsch, Cory C. Funk, Ben Heavner, Matthew A. Richards, Paul T. Shannon, Gustavo Glusman, Nathan D. Price, Carl Kesselman, Ian T Foster

The paper presents tools for ensuring FAIRness in big biomedical data analysis through a case study on creating a transcription factor binding site atlas from ENCODE data.

PLoS ONE · Apr 11, 2019Peer-reviewedBioinformatics

ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions

Brendan King, Terry Farrah, Matthew A. Richards, Michael B. Mundy, Evangelos Simeonidis, Nathan D. Price

ProbAnnoWeb and ProbAnnoPy fill gaps in metabolic reconstructions by using probabilistic annotations specific to the target organism.

Bioinformatics · Dec 15, 2017Peer-reviewedSystems Biology