Author

S. Whalen

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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Evolutionary Biology· 2 Microbiology· 1

Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 3 Research Focus:chromatin & epigenetic regulation· 3 Research Focus:gene regulatory network inference· 3 Organism:human· 3 Organism:chicken / avian· 2 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Assay:DNA methylation· 1

Frequent Co-Authors

K. S. Pollard· 3 shared F. Inoue· 2 shared H. Ryu· 2 shared S. Thomas· 2 shared T. Fair· 2 shared A. A. McBride· 1 shared A. A. Pollen· 1 shared A. Kriegstein· 1 shared

Activity by Year

2017-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 30 mutual co-author links

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3 shared papersEvolutionary Biology

K. S. Pollard

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Author profile →

3 papers

Recent·Most cited

Three-dimensional genome re-wiring in loci with Human Accelerated Regions

K. C. Keough, S. Whalen, F. Inoue, P. F. Przytycki, T. Fair, C. Deng, M. Steyert, H. Ryu, K. Lindblad-Toh, E. Karlsson, Zoonomia Consortium, T. J. Nowakowski, N. J. Ahituv, A. A. Pollen, K. S. Pollard

The paper identifies human-specific 3D genome re-wiring in conserved loci, linking accelerated evolution to regulatory rewiring in neural progenitor cells.

bioRxiv · Oct 4, 2022Evolutionary Biology

Machine-learning dissection of Human Accelerated Regions in primate neurodevelopment

S. Whalen, F. Inoue, H. Ryu, T. Fair, E. Markenscoff-Papadimitriou, K. Keough, M. Kircher, B. Martin, B. Alvarado, O. Elor, D. L. Cintron, A. Williams, M. A. H. Samee, S. Thomas, R. Krencik, , K. S. Pollard

The paper uses machine learning to analyze human-chimpanzee variants in HARs, finding 43% affect chromatin state and 14% affect neurodevelopmental enhancer activity, with species-specific activity predicted by transcription factor footprints.

bioRxiv · Sep 28, 2022Evolutionary Biology

The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation

S. A. Moquin, S. Thomas, S. Whalen, A. Warburton, S. G. Fernanadez, A. A. McBride, K. S. Pollard, J. L. Miranda

This paper shows that the Epstein-Barr virus episome shifts between repressive and active nuclear compartments during latency and reactivation, using interchromosomal interactions to regulate transcription.

bioRxiv · Aug 17, 2017Microbiology