Author

John J. Desmarais

Cold Spring Harbor LaboratoryORCID 0000-0002-7739-2079Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Assay:whole-genome sequencing· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Research Focus:cell-cell communication· 1 Assay:CRISPR screen· 1 Approach:deep learning· 1 Research Focus:differential expression· 1

Frequent Co-Authors

David F. SavageiD· 2 shared Justin B. KinneyiD· 2 shared Allen W CheniD· 1 shared Andrea J. SchorniD· 1 shared Avi I. FlamholziD· 1 shared Brian M. SchilderiD· 1 shared Brittney W. ThorntoniD· 1 shared Carmelle Catamura· 1 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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2 shared papersMolecular Biology

David F. SavageORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Reprogramming Cas9 PAM Recognition for Allele-Specific Editing

Julia Amber Tartaglia, Vivian Nguyen, John J. Desmarais, Rachel F. Weissman, Brittney W. Thornton, Marena I. Trinidad, Kevin Briseno, Taylor R. Hudson, Carmelle Catamura, Liana F. Lareau, Fyodor D. Urnov, Jennifer A. Doudna, David F. Savage

This paper develops yeast-selected SpCas9 variants with re-specified PAM recognition to enable allele-specific editing, demonstrating improved specificity and catalytic efficiency compared to PAM-broadened variants.

bioRxiv · Aug 11, 2026 · PreprintMolecular Biology

Genetic background shapes AI-predicted variant effects

Brian M. Schilder, Zhihan Liu, John J. Desmarais, David Laub, Fahimeh Rahimi, Palash Sethi, Lucas A. Pereira, Mengyi Sun, Justin B. Kinney, David M. McCandlish, Juannan Zhou, Peter K. Koo

This study introduces pVEP, a framework showing how genetic background affects AI predictions of variant effects, revealing variant effects vary across haplotypes.

bioRxiv · Apr 7, 2026 · PreprintGenomics

HENMT1 restricts endogenous retrovirus activity by methylation of 3'-tRNA fragments

Joshua I. Steinberg, Helene Sertznig, John J. Desmarais, Jenna Wilken, Daisy Rubio, Matthew Peacey, Justin B. Kinney, Andrea J. Schorn

This study identifies HENMT1 as a methyltransferase that protects 3'-tRNA fragments from degradation, enhancing their ability to silence endogenous retroviruses.

bioRxiv · May 12, 2025 · PreprintMolecular Biology

Genome-wide screening reveals a novel class of carbonic anhydrase-like inorganic carbon transporters in chemoautotrophic bacteria

John J. Desmarais, Avi I. Flamholz, Cecilia Blikstad, Eli J. Dugan, Thomas G. Laughlin, Luke M. Oltrogge, Allen W Chen, Kelly M. Wetmore, Spencer Diamond, Joy Y. Wang, David F. Savage

The paper identifies a novel class of inorganic carbon transporters in chemoautotrophic bacteria through a genome-wide screen and characterizes their function as energy-coupled bicarbonate pumps.

bioRxiv · Dec 7, 2018 · PreprintMolecular Biology