Author

Jordan A. Lay

California Institute of Technology

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· 1 Genomics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Organism:mouse· 2 Research Focus:cell type annotation· 1 Assay:ChIP-seq· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Animesh RayiD· 2 shared Faisal Bin AshrafiD· 2 shared Karen PacoiD· 2 shared Mariana Paco Mendivil· 2 shared Stefano LonardiiD· 2 shared Zihao ZhangiD· 2 shared Andrew A. PereziD· 1 shared C. DavilaiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersBioinformatics

Animesh RayORCID

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Author profile →

3 papers

Recent·Most cited

Genome-wide chromatin recording resolves dynamic cell state changes

Yodai Takei, Jordan A. Lay, James M. Linton, Duncan M. Chadly, Yoshiki Ochiai, Ron Hadas, Andrew A. Perez, Mario R. Blanco, Paola Laurino, Mitchell Guttman, Michael B. Elowitz

This paper introduces LagTag, a method to recover both earlier and endpoint chromatin states in mammalian cells, and applies it to study dynamic chromatin transitions during stem cell differentiation.

Cell Systems · Sep 1, 2026Peer-reviewedGenomics

Fine-tuned Protein Language Model Identifies Antigen-specific B Cell Receptors from Immune Repertoires

Karen Paco, Mariana Paco Mendivil, Zihao Zhang, Sanaz Zebardast, C. Davila, R.F. Mooney, Peace O. Olatoyinbo, Tristan Yang, Sebastián Bassi, Virginia Gonzalez, Eva Chen, Faisal Bin Ashraf, Isabel Condori Roman, Jonathan R. Felix, Rashid M. Alam, , Animesh Ray

The paper introduces a protein language model fine-tuned to predict antigen-specific B cell receptors from immune repertoires, showing effectiveness across multiple antigens.

bioRxiv · Oct 30, 2025 · PreprintBioinformatics

A Large Language Model Guides the Affinity Maturation of Variant Antibodies Generated by Combinatorial Optimization

Faisal Bin Ashraf, Zihao Zhang, Karen Paco, Mariana Paco Mendivil, Jordan A. Lay, Animesh Ray, Stefano Lonardi

This paper introduces Ab-Affinity, a large language model that generates high-affinity antibodies against SARS-CoV-2 spike protein peptides using combinatorial optimization and AI.

bioRxiv · Dec 19, 2024 · PreprintMolecular Biology