Author

Bruce Parrello

University of Chicago

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 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Research Focus:database / resource· 2 Assay:metagenomics· 2 Approach:statistical model· 2 Assay:whole-genome sequencing· 2 Organism:bacteria (other)· 1 Assay:bulk RNA-seq· 1 Organism:E. coli· 1

Frequent Co-Authors

Aaron A. BestiD· 2 shared James J. DavisiD· 2 shared Adam D. Slater· 1 shared Adam P. ArkiniD· 1 shared Annette GreineriD· 1 shared Ben P. Bowen· 1 shared Benjamin H. AlleniD· 1 shared Benjamin N. Turner· 1 shared

Activity by Year

2018-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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2 shared papersBioinformatics

Aaron A. BestORCID

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Author profile →

3 papers

Recent·Most cited

Predicting Protein-encoding Gene Content in Escherichia coli Genomes

Marcus Nguyen, Zachary C. Elmore, Clay Ihle, Francesco S. Moen, Adam D. Slater, Benjamin N. Turner, Bruce Parrello, Aaron A. Best, James J. Davis

This study builds machine learning classifiers to predict variable gene presence in E. coli genomes, achieving high accuracy for most gene families, including poorly annotated and horizontally transferred genes.

bioRxiv · Jan 17, 2023 · PreprintBioinformatics

Extraction of near-complete genomes from metagenomic samples: a new service in PATRIC

Bruce Parrello, Rory Butler, Philippe Chlenski, Gordon D. Pusch, Ross Overbeek

The paper introduces a new metagenomic binning service in PATRIC that assigns contigs to reference genomes using marker proteins and provides annotated draft genomes.

PLoS ONE · Apr 15, 2021Peer-reviewedGenomics

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