Barry Slaff

I am a PhD student at the University of Pennsylvania (CIS Program) supervised by Yoseph Barash (Biociphers Lab).

The focus of my PhD work has been developing algorithms to detect and quantify RNA processing events such as splicing from RNA sequencing. Current and somewhat recent projects include:

• MAJIQ-CLIN (Aicher et al, medRxiv preprint, 2025), a novel tool for the identification of Mendelian disease-causing variants from RNA-Seq data
• MAJIQ V3 (Aicher et al, BioRxiv preprint, 2024), a major update to the MAJIQ software for discovering, quantifying, and comparing RNA splicing from RNA sequencing experiments.
• MOCCASIN (Slaff et al, Nat Comm. 2021), a method for correcting for known and unknown confounders in RNA splicing analysis

My external research presentations include:

• Poster at ASHG Denver 2024
• MAJIQ V3 – Poster at RNADay@Penn 2025, ISCB/ISMB Montreal 2024
• MOCCASIN – Short talk at ISCB/ISMB Basel 2019

My past projects in the analysis of language associations in psychology and epidemiology include:

• The language of character strengths: Predicting morally valued traits on social media (Pang et al, J Pers 2020)
• Association Between HIV-Related Tweets and HIV Incidence in the United States: Infodemiology Study (Stevens et al, JMIR 2020)
• Modeling Empathy and Distress in Reaction to News Stories (Buechel et al, ACL 2018)

My past projects in the analysis of metabolomic variations in disease and circadian biology include:

• Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines (Smith et al, JCI 2020)
• NMR Spectroscopy of Urine (Slaff et al, chapter in NMR-based Metabolomics, H. Keun ed., RSC 2018)
• Deciphering the Duality of Clock and Growth Metabolism in a Cell Autonomous System Using NMR Profiling of the Secretome (Sengupta et al, Metabolites 2016)

I have worked as a Teaching Assistant for graduate courses at the University of Pennsylvania:

• Machine Learning (CIS 520)
• Advanced Computational Biology (GCB 537)

I have reviewed submissions to

• Conferences: ICLR, ICML, NeurIPS
• Journals: NAR, Nature Communications

I worked as a Software Development Engineer at Amazon from 2019 – 2024. My work there included designing, building, testing, and maintaining:

• Major components of a recommender system for an Amazon Devices product.
• Microservices in support of AWS region expansion and Prime Video availability monitoring.
• A new console for internal users of a fleet-monitoring service.
• Various company-internal websites.

I have a BA in Mathematics and Master’s degrees in Mathematics and Computer Science from the University of Pennsylvania.

Recent non-science activities include:

• Paddler on the United States Dragon Boat Federation Premier national team (2025)
  • Media: UPenn post about me on Linkedin
• Board member of the Philadelphia Dragon Boat Association
• Trombonist in the Penn Wind Ensemble

Contact: bslaff at seas dot upenn dot edu