Author

Jason F. Perera

Chan Zuckerberg Biohub 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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Genomics· 2 Bioinformatics· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Assay:proteomics· 3 Approach:deep learning· 2 Research Focus:drug response / drug discovery· 2 Approach:benchmark study· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Approach:contrastive learning· 1

Frequent Co-Authors

Aly Azeem KhaniD· 3 shared Abdalla M. AbdrabouiD· 1 shared Alanur Tutar· 1 shared Ali DavariashtiyaniiD· 1 shared Ali ElSheikh· 1 shared Amber C. LennoniD· 1 shared Andrew KangiD· 1 shared Ben LaiiD· 1 shared

Activity by Year

2024-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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Curved chords = mutual co-authorship

3 shared papersGenomics

Aly Azeem KhanORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

AI-Guided CRISPR Screen Accelerates Discovery of New Drug Targets

Chenlin Zhao, Mushaine Shih, Sharif Ahmed, Steven Song, Amber C. Lennon, Julia M. Mayes, Mengqi Jonathan Fan, Pei-Ying Lo, Jason F. Perera, Alanur Tutar, Andrew Kang, Elizabeth Warren, Ryan A. McClure, Aly Azeem Khan, Shana O. Kelley, Abdalla M. Abdrabou

This study uses a CRISPR screen and AI to identify new drug targets for psoriasis, finding ALOX5 and OXTR as promising candidates with validated therapeutic effects.

bioRxiv · Feb 28, 2026 · PreprintGenomics

Virtual Cells Need Context, Not Just Scale

Payam Dibaeinia, Sudarshan Babu, Mei K. Knudson, Ali ElSheikh, Yibo Wen, Han Liu, Jason F. Perera, Aly Azeem Khan

The paper argues that scaling model capacity alone is insufficient for Virtual Cells, emphasizing the need for contextual diversity and causal representation learning over data volume.

bioRxiv · Feb 9, 2026 · PreprintGenomics

DecoderTCR: Compositional Pretraining and Entropy-Guided Decoding for TCR-pMHC Interactions

Ben Lai, Melissa Englund, Ramit Bharanikumar, Isabel Nocedal, Ali Davariashtiyani, Jason F. Perera, Aly Azeem Khan

DecoderTCR improves TCR-pMHC interaction prediction using pretraining and entropy-guided decoding, achieving high AUROC scores without epitope-specific training.

bioRxiv · Feb 6, 2026 · PreprintBioinformatics

Pep2Vec: An Interpretable Model for Peptide-MHC Presentation Prediction and Contaminant Identification in Ligandome Datasets

William John Thrift, Quade Broadwell, Jason F. Perera, Nicolas Lounsbury, Jieming Chen, Suchit Jhunjhunwala

bioRxiv · Oct 14, 2024 · PreprintImmunology