Author

Richard Bonneau

Primary ORCID profile (0000-0003-4354-7906 · 63 papers)Unclaimed ORCID profile · follow to get notified of new preprints

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Richard BonneauiD63 papers · Genentech

Biology Disciplines

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Bioinformatics· 1 Ecology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:gene regulatory network inference· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Approach:deep learning· 1 Organism:human· 1 Assay:metagenomics· 1

Frequent Co-Authors

Tarmo Aijo· 2 shared Addrienne B. Nicotra· 1 shared Anne Plessis· 1 shared Christian Lorenz Mueller· 1 shared Christoph Hafemiester· 1 shared Endang M. Septiningsih· 1 shared Gina M Pham· 1 shared Glenn B. Gregorio· 1 shared

Activity by Year

2016-2016 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersEcology

Tarmo Aijo

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Author profile →

3 papers

Recent·Most cited

Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing

Tarmo Aijo, Christian Lorenz Mueller, Richard Bonneau

The paper introduces a probabilistic model to analyze 16S rRNA sequencing data by accounting for overdispersion and sampling zeros using Gaussian Processes, showing improved performance over existing methods.

bioRxiv · Sep 22, 2016Ecology

Environmental gene regulatory influence networks in rice (Oryza sativa): response to water deficit, high temperature and agricultural environments

Olivia Wilkins, Christoph Hafemiester, Anne Plessis, Meisha-Marika Holloway-Phillips, Gina M Pham, Addrienne B. Nicotra, Glenn B. Gregorio, S. V. Krishna Jagadish, Endang M. Septiningsih, Richard Bonneau, Michael Purugganan

The paper infers Environmental Gene Regulatory Influence Networks (EGRINs) in rice under environmental stresses by integrating transcriptome, chromatin, and cis-regulatory data.

bioRxiv · Jul 5, 2016Systems Biology

Biophysically motivated regulatory network inference: progress and prospects

Richard Bonneau, Tarmo Aijo

This paper discusses progress and future directions in biophysically motivated regulatory network inference, emphasizing the need for improved computational strategies and experimental designs.

bioRxiv · May 4, 2016Bioinformatics