Author

Gaspar A. Pacheco

Broad InstitutePrimary ORCID profile (0000-0001-5748-5027 · 1 paper)Unclaimed ORCID profile · follow to get notified of new preprints

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Gaspar A. PachecoiD1 paper · Broad Institute

Biology Disciplines

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Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Research Focus:gene regulatory network inference· 2 Research Focus:benchmarking· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Approach:machine learning (classical)· 1 Organism:mouse· 1

Frequent Co-Authors

Duane R. WesemanniD· 2 shared Shahab SaghaeiiD· 2 shared Alexander PernissiD· 1 shared Caitlin WongiD· 1 shared Chunli FengiD· 1 shared Ersin GüliD· 1 shared Hildreth Robert FrostiD· 1 shared Hiroaki Hayashi· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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2 shared papersImmunology

Duane R. WesemannORCID

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2 papers

Recent·Most cited

Progenitor T cells drive chronic pulmonary type 2 inflammation

Radomir Kratchmarov, Xiaojiong Jia, Jun Nagai, Gaspar A. Pacheco, Alexander Perniss, M. A. Bell, Ersin Gül, Thornton W. Thompson, Hiroaki Hayashi, Shahab Saghaei, Caitlin Wong, Madeline Hastings, Kinan Alhallak, Juying Lai, Chunli Feng, , Patrick J. Brennan

The paper identifies tissue Th2 progenitors as a distinct cellular state that sustains chronic type 2 inflammation by self-renewal and effector differentiation.

Nature Immunology · Aug 20, 2026Peer-reviewedImmunology

Biological foundation models illuminate annotation blind spots in evolutionarily divergent genomes

Toby B. Lanser, Sydney K. Caldwell, Gaspar A. Pacheco, Jessica W. Chen, Shahab Saghaei, Mariah Hassan, Meydan Kronrod, Duane R. Wesemann, Hildreth Robert Frost

The paper introduces a hybrid annotation framework that improves cross-species protein similarity assignment and gene annotation in evolutionarily divergent genomes, expanding structural catalogs and improving single-cell immune cell state annotation in sea lamprey.

bioRxiv · May 16, 2026 · PreprintBioinformatics