Author

Benjamin L. Oakes

Innovative Genomics Institute

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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Molecular Biology· 2 Synthetic Biology· 2

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Assay:CRISPR screen· 2 Organism:yeast· 2 Research Focus:drug response / drug discovery· 1 Organism:E. coli· 1 Organism:human· 1 Organism:mouse· 1 Research Focus:perturbation response prediction· 1

Frequent Co-Authors

Christof FellmanniD· 2 shared David F. SavageiD· 2 shared Jennifer A. DoudnaiD· 2 shared Amanda MokiD· 1 shared Andrew H. NgiD· 1 shared Anna MrakiD· 1 shared Arik ShamsiD· 1 shared Ashley T WongiD· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersMolecular Biology

Christof FellmannORCID

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Author profile →

4 papers

Recent·Most cited

Sequential Proofreading Enhances Specificity and Potency of CRISPR-CasX-based Epigenetic Repressors

Emeric J. Charles, Ross White, Ryan V. Tran, Amanda Mok, Lea Alice Kiefer, Kirsten A. Reimer, Ashley T Wong, Sterling Ripley-Phipps, Natalie Goh, T.C. Stevenson Keller, Carlos Santamaría, Christopher Duncan-Lewis, Beatriz Alvarado, Heather M. Kozy, Zoi Kyrkou, , Jason D. Fernandes

This paper introduces ELXRs, CRISPR-CasX-based epigenetic repressors that use sequential proofreading to enhance specificity and potency by reading chromatin state before DNA methylation.

bioRxiv · Aug 31, 2026 · PreprintMolecular Biology

Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules

Arik Shams, Sean A. Higgins, Christof Fellmann, Thomas G. Laughlin, Benjamin L. Oakes, Rachel Lew, Shineui Kim, Maria Lukarska, Madeline L. Arnold, Brett T. Staahl, Jennifer A. Doudna, David F. Savage

The paper uses a genetic minimization technique to identify minimal DNA-binding modules in Cas9, showing that large domain deletions can retain function.

Nature Communications · Sep 27, 2021Peer-reviewedMolecular Biology

A yeast optogenetic toolkit (yOTK) for gene expression control in Saccharomyces cerevisiae

Jidapas An‐adirekkun, Cameron J. Stewart, Stephanie H. Geller, Michael T. Patel, Justin Melendez, Benjamin L. Oakes, Marcus B. Noyes, Megan N. McClean

The paper develops an optogenetic toolkit for controlling gene expression in yeast by using light to modulate synthetic transcription factors.

Biotechnology and Bioengineering · Dec 2, 2019Peer-reviewedSynthetic Biology

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

Kale Kundert, James E. Lucas, Kyle E. Watters, Christof Fellmann, Andrew H. Ng, Benjamin Murray Heineike, Christina M. Fitzsimmons, Benjamin L. Oakes, Jiuxin Qu, Neha K. Prasad, Oren S. Rosenberg, David F. Savage, Hana El‐Samad, Jennifer A. Doudna, Tanja Kortemme

Inserting theophylline aptamers into the sgRNA yields ligand-activated and ligand-deactivated guides that tune CRISPRi in E. coli over 11x to 13x dynamic ranges, enabling two-ligand multiplexing.

Nature Communications · May 9, 2019Peer-reviewedSynthetic Biology✦ In-depth digest