Author

Gerstein Mark

Yale University

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

Signature Assays, Organisms & Methods

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Assay:ATAC-seq· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Organism:human· 1 Approach:optimal transport· 1 Assay:scRNA-seq· 1 Assay:spatial transcriptomics· 1 Research Focus:trajectory inference· 1

Frequent Co-Authors

Aarti JajooiD· 1 shared Ahituv NadaviD· 1 shared Ahyeon HwangiD· 1 shared Alex A. PolleniD· 1 shared Alex Kozlenkov· 1 shared Alexandre JourdoniD· 1 shared Alexej Abyzov· 1 shared Alistair Wilkinson· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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1 shared paperGenomics

Aarti JajooORCID

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2 papers

Recent·Most cited

GeoSinkhorn Flow: Geometry-Aware Flow Matching for Perturbation-Conditioned Dynamics in Single cell Data Phenoscapes

Ke Xu, Alistair Wilkinson, Ni Shuang, Guillaume Huguet, Gerstein Mark, Guy Wolf, Christopher J. Tape, Smita Krishnaswamy

GeoSinkhorn Flow converts static phenoscapes into dynamic ones by learning perturbation-conditioned transport trajectories that respect the phenoscape's geometry and generalize to unseen conditions.

bioRxiv · Oct 22, 2026 · PreprintBioinformatics

Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex

Chengyu Deng, Sean Whalen, Marilyn Steyert, Ryan Ziffra, Pawel F. Przytycki, Fumitaka Inoue, Daniela A. Pereira, Davide Capauto, Scott Norton, Flora M. Vaccarino, Alex A. Pollen, Tomasz Jan Nowakowski, Ahituv Nadav, Katherine S. Pollard, Schahram Akbarian, , Alex Kozlenkov

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

Science · May 23, 2024Peer-reviewedGenomics