Author

Molly Stephenson

Pacific Northwest National Laboratory

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Microbiology· 1 Synthetic Biology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:bacteria (other)· 3 Approach:deep learning· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Approach:genetic perturbation / CRISPR· 1 Assay:metabolomics· 1 Research Focus:protein design· 1 Assay:proteomics· 1

Frequent Co-Authors

Joshua R. ElmoreiD· 3 shared Andrew Frank· 2 shared Elise M. Van FosseniD· 2 shared Robert G. EgbertiD· 2 shared Abby JergeriD· 1 shared Alex Beliaev· 1 shared Allan ScottiD· 1 shared Andrew J. WilsoniD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersSystems Biology

Joshua R. ElmoreORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

ChatGEM: An Agentic Architecture Enabling Interactive Simulation of Genome-Scale Metabolic Models

Niaz Bahar Chowdhury, August George, Sumit Purohit, Angela Contolesi, Erin Bredeweg, Jeffrey J. Czajka, Kelly G. Stratton, Yuqian Gao, Molly Stephenson, Joshua R. Elmore, Allan Scott, Damon T. Leach, Abby Jerger, Teresa Lemmon, Paul Piehowski, , Jaydeep P. Bardhan

ChatGEM enables interactive simulation of genome-scale metabolic models via natural language, improving performance and reducing execution time for complex tasks.

bioRxiv · Jul 21, 2026 · PreprintSystems Biology

Efficient genetic code expansion tools enable in vivo study of lysine acetylation in non-model bacteria

Elise M. Van Fossen, Molly Stephenson, Andrew Frank, Soujanya Akella, Rowan S. Wooldridge, Andrew J. Wilson, Youngki You, Ernesto Satoshi Nakayasu, Robert G. Egbert, Joshua R. Elmore

This paper develops a genetic code expansion platform for in vivo study of lysine acetylation in non-model bacteria, demonstrating its use in a non-E. coli strain.

bioRxiv · Apr 14, 2025 · PreprintSynthetic Biology

Reinforced CRISPR interference enables reliable multiplex gene repression in phylogenetically distant bacteria

Joshua R. Elmore, Ritu Shrestha, Andrew Wilson, Elise M. Van Fossen, Andrew Frank, Ryan M. Francis, Henri Baldino, Molly Stephenson, Bhavya Gupta, Jeane Rivera, Robert G. Egbert

This paper develops a CRISPRi platform for multiplex gene repression in diverse bacteria, demonstrating its effectiveness in multiple species.

bioRxiv · Apr 14, 2025 · PreprintMicrobiology