Author

Samuel L. Neff

Dartmouth CollegeORCID 0000-0002-5993-8445Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Assay:bulk RNA-seq· 3 Research Focus:differential expression· 3 Organism:bacteria (other)· 2 Research Focus:benchmarking· 2 Research Focus:database / resource· 2 Research Focus:software / tool· 2 Approach:benchmark study· 1

Frequent Co-Authors

Bruce A. StantoniD· 3 shared Georgia DoingiD· 3 shared Thomas H. HamptoniD· 3 shared Alexandra J. LeeiD· 2 shared Deborah A. HoganiD· 2 shared Katja KoeppeniD· 2 shared Sharanya SarkariD· 2 shared Ambrose L. CheungiD· 1 shared

Activity by Year

2022-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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3 shared papersBioinformatics

Bruce A. StantonORCID

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Author profile →

4 papers

Recent·Most cited

E.PathDash, pathway activation analysis of publicly available pathogen gene expression data

Lily D. Taub, Thomas H. Hampton, Sharanya Sarkar, Georgia Doing, Samuel L. Neff, Carson E. Finger, Kiyoshi F. Fukutani, Bruce A. Stanton

E.PathDash provides a tool for analyzing gene expression data from pathogens, enabling rapid pathway activation analysis and reproducibility assessment across multiple studies.

mSystems · Oct 18, 2024Peer-reviewedBioinformatics

Rocket-miR, a Translational Launchpad for miRNA-based Antimicrobial Drug Development

Samuel L. Neff, Thomas H. Hampton, Katja Koeppen, Sharanya Sarkar, Casey J. Latario, Benjamin D. Ross, Bruce A. Stanton

Rocket-miR predicts human miRNA interactions with pathogens to identify potential antimicrobial candidates against antibiotic-resistant infections.

mSystems · Nov 17, 2023Peer-reviewedBioinformatics

CF-Seq, An Accessible Web Application for Rapid Re-Analysis of Cystic Fibrosis Pathogen RNA Sequencing Studies

Samuel L. Neff, Thomas H. Hampton, Charles T.S. Puerner, Liviu Cengher, Georgia Doing, Alexandra J. Lee, Katja Koeppen, Ambrose L. Cheung, Deborah A. Hogan, Robert A. Cramer, Bruce A. Stanton

CF-Seq provides a web tool for re-analyzing CF pathogen RNA-seq data, enabling efficient filtering, visualization, and hypothesis generation across multiple studies.

Scientific Data · Jun 16, 2022Peer-reviewedBioinformatics

Compendium-wide analysis of P. aeruginosa core and accessory genes reveal more nuanced transcriptional patterns

Alexandra J. Lee, Georgia Doing, Samuel L. Neff, Taylor E. Reiter, Deborah A. Hogan, Casey S. Greene

The paper analyzes transcriptional patterns of core and accessory genes in P. aeruginosa strains using a transcriptome compendium, revealing stable core gene expression patterns across strains.

bioRxiv · Apr 14, 2022 · PreprintBioinformatics