Author

John St. John

Nvidia (United Kingdom)

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 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Assay:whole-genome sequencing· 2 Research Focus:cancer & tumor microenvironment· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Organism:human· 1

Frequent Co-Authors

Aditi T. MerchantiD· 1 shared Alden Deran· 1 shared Aleah F. Caulin· 1 shared Ali Taghibakshi· 1 shared Amy X. LuiD· 1 shared Anibal R. Cordero· 1 shared Anthony Beardsworth CostaiD· 1 shared Anton Vorontsov· 1 shared

Activity by Year

2017-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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1 shared paperGenomics

Aditi T. MerchantORCID

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Author profile →

3 papers

Recent·Most cited

Genome modeling and design across all domains of life with Evo 2

Garyk Brixi, Matthew G. Durrant, Jerome Ku, Michael Poli, Greg Brockman, Daniel Chang, Gabriel A. Gonzalez, S. B. King, David B. Li, Aditi T. Merchant, Mohsen Naghipourfar, Eric Nguyen, Chiara Ricci-Tam, David W. Romero, Gwanggyu Sun, , Brian Hie

A 40B-parameter DNA model trained on 9.3 trillion tokens scores coding and noncoding variants zero-shot, exposes interpretable sequence features, and writes chromosome-scale sequences.

bioRxiv · Feb 18, 2025 · PreprintGenomics✦ In-depth digest

Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers

Collin M. Blakely, Thomas B.K. Watkins, Wei Wu, Beatrice Gini, Jacob J. Chabon, Caroline E. McCoach, Nicholas McGranahan, Gareth A. Wilson, Nicolai J. Birkbak, Victor R. Olivas, Julia Rotow, Ashley Maynard, Victoria Wang, Matthew A. Gubens, Kimberly C. Banks, , Trever G. Bivona

The paper investigates genetic epistasis in EGFR-mutant lung cancers using over 2,000 cases, showing that genetic combinations, not single drivers, dominate tumor progression and clinical outcomes.

bioRxiv · Mar 16, 2017 · PreprintCancer Biology

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

Edward Stallknecht Rice, Satomi Kohno, John St. John, Son Pham, Jonathan Howard, Liana Lareau, Brendan O'Connell, Glenn Hickey, Joel Armstrong, Alden Deran, Ian Fiddes, Roy N. Platt, Cathy Gresham, Fiona McCarthy, Colin Kern, , Richard E Green

The paper improves the American alligator genome assembly and identifies estrogen-responsive regions linked to female-biased gene expression in post-temperature-sensitive gonads.

Genome Research · Jan 30, 2017Peer-reviewedGenomics