Author

Sawal Acharya

Brigham and Women's Hospital

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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Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Approach:statistical model· 2 Approach:Bayesian inference· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Bonnie BergeriD· 2 shared Georg Kurt GerberiD· 2 shared Travis E. GibsoniD· 2 shared Younhun KimiD· 2 shared Ashlee M. EarliD· 1 shared Colin J. WorbyiD· 1 shared Daniel Alfonsetti· 1 shared David E. Kaplan· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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2 shared papersSystems Biology

Bonnie BergerORCID

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2 papers

Recent·Most cited

Microbial dynamics inference at ecosystem-scale

Travis E. Gibson, Younhun Kim, Sawal Acharya, David E. Kaplan, Nicholas DiBenedetto, Richard Lavin, Bonnie Berger, Jessica Ravikoff Allegretti, Lynn Bry, Georg Kurt Gerber

The paper introduces MDSINE2, a Bayesian method for inferring microbial dynamics from time-series data, and shows it outperforms existing methods in identifying ecosystem-scale interactions.

Nature Microbiology · Sep 9, 2025Peer-reviewedSystems Biology

Strain Tracking with Uncertainty Quantification

Younhun Kim, Colin J. Worby, Sawal Acharya, Lucas R. van Dijk, Daniel Alfonsetti, Zackary Gromko, Philippe N. Azimzadeh, Karen Dodson, Georg Kurt Gerber, Scott J. Hultgren, Ashlee M. Earl, Bonnie Berger, Travis E. Gibson

ChronoStrain tracks low-abundance microbial strains over time with uncertainty quantification, outperforming existing methods on real and synthetic data.

Nature Microbiology · May 6, 2025Peer-reviewedBioinformatics