Author

José Manuel Villalobos‐Escobedo

Lawrence Berkeley National LaboratoryORCID 0000-0002-8412-6748Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Microbiology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Assay:metagenomics· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Research Focus:database / resource· 1 Assay:DNA methylation· 1 Research Focus:drug response / drug discovery· 1 Approach:experimental assay· 1 Organism:fungi (other)· 1

Frequent Co-Authors

Adam M. DeutschbaueriD· 1 shared Adam P. ArkiniD· 1 shared Adriana M. Rico-RamíreziD· 1 shared Alexander Rosales· 1 shared Alexandra Trejo-GaytaniD· 1 shared Ana Calheiros de CarvalhoiD· 1 shared Andrés Gatica-AriasiD· 1 shared Anna LipzeniD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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1 shared paperSystems Biology

Adam M. DeutschbauerORCID

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3 papers

Recent·Most cited

BioinformaticsbioRxivPreprintJul 26, 2026

Genome-resolved metagenomics of traditional fermented beverages reveals biosynthetic diversity and informs the rational in silico design of probiotic synthetic communities

Alexandra Trejo-Gaytan, Axel Armando Rojero-Hernandez, José T. Otero-Pappatheodorou…·José Manuel Villalobos‐Escobedo

The paper uses metagenomic analysis of fermented beverages to identify microbial producers of beneficial compounds and designs a synthetic microbial community for probiotic applications.

DOI 10.64898/2026.07.22.740150

metagenomicsstatistical model

Systems BiologybioRxivPreprintNov 30, 2025

Construction of a randomly barcoded insertional mutant library in the filamentous fungus Trichoderma atroviride

Lori B. Huberman, José Manuel Villalobos‐Escobedo, Jeffrey M. Skerker…·N. Louise Glass

The paper constructs a barcoded insertional mutant library in Trichoderma atroviride to enable high-throughput functional genomics in filamentous fungi.

1 citation

fungi (other)experimental assay

MicrobiologyNature MicrobiologyPeer-reviewedAug 29, 2024

Multi-omics analysis of a traditional fermented food reveals a byproduct-associated subpopulation of Neurospora intermedia for waste-to-food upcycling

Vayu Maini Rekdal, José Manuel Villalobos‐Escobedo, Nabila Rodríguez Valerón…·Jay D. Keasling

This study uses multi-omics analysis to characterize Neurospora intermedia in oncom, revealing its role in byproduct conversion and potential for waste-to-food upcycling.

85 citationstop 1%

metagenomicsmetabolomics