Author

William J. Riehl

Lawrence Berkeley National LaboratoryORCID 0000-0002-3405-2744Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 3 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Research Focus:genome assembly· 2 Assay:metagenomics· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Adam P. ArkiniD· 3 shared Christopher S. HenryiD· 3 shared Paramvir DehaliD· 3 shared Robert W. CottinghamiD· 3 shared Christopher J. NeelyiD· 2 shared Dylan C. ChivianiD· 2 shared Janaka N. EdirisingheiD· 2 shared José P. FariaiD· 2 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Adam P. ArkinORCID

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Author profile →

3 papers

Recent·Most cited

Data coherence over data volume drives generalisable genome-based prediction of microbial carbon utilisation

Dileep Kishore, Priya Ranjan, Christopher J. Neely, Mikaela Cashman, Zahmeeth Sakkaff, William J. Riehl, Marcin P. Joachimiak, Janaka N. Edirisinghe, José P. Faria, Pamela B. Weisenhorn, Myra B. Cohen, Dale A. Pelletier, Robert W. Cottingham, Christopher S. Henry, Mitchel J. Doktycz, , Paramvir Dehal

This study shows that filtering genomes based on coherent genotype-phenotype relationships improves cross-dataset prediction of microbial carbon utilisation, outperforming larger but less coherent datasets.

bioRxiv · Aug 12, 2026 · PreprintBioinformatics

KBase Research Agent: Automated Multi-Agent Workflow Construction for Reproducible Genome Analysis

Prachi Gupta, William J. Riehl, Mikaela Cashman, Dylan C. Chivian, Christopher J. Neely, Richard Shane Canon, Robert Cottingham, Christopher Henry, Adam P. Arkin, Paramvir Dehal

The KBase Research Agent automates genome analysis workflows, producing reproducible results and annotated genomes without human intervention.

bioRxiv · Jun 4, 2026 · PreprintBioinformatics

The DOE Systems Biology Knowledgebase (KBase)

Adam P. Arkin, Robert W. Cottingham, Christopher S. Henry, Nomi L. Harris, Rick L. Stevens, Sergei Maslov, Paramvir Dehal, Doreen Ware, Fernando Pérez, Richard Shane Canon, Michael W. Sneddon, Matthew L Henderson, William J. Riehl, Dan Murphy-Olson, Stephen Y. Chan, , 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.

Nature Biotechnology · Jul 1, 2018Peer-reviewedBioinformatics✦ In-depth digest