Faculty

Yoseph Barash, Ph.D.

Professor of Genetics

Department: Genetics

Graduate Group Affiliations

Contact information

Richards Building D205
3700 Hamilton Walk
Philadelphia, PA 19104

Office: 215-746-8683
Fax: 215-573-3111

Email:
yosephb@upenn.edu

Education:
B.Sc. (Computer Science and Physics)
Hebrew University, Jerusalem, Israel., 1998.
Ph.D. (Machine learning, computational biology)
School of Computer Science & Engineering Hebrew University, Jerusalem, Israel, 2006.

Links
Lab webpage

Permanent link

> Perelman School of Medicine > Faculty > Details

Description of Research Expertise

Research Interests:
The lab develops machine learning algorithms that integrate high-throughput data (RNASeq, CLIPSeq , PIPSeq, etc.) to infer RNA biogenesis and function, followed by experimental verifications of inferred mechanisms.

Keywords:
Machine learning, probabilistic graphical models, computational biology, RNA splicing, post-transcriptional regulation, genomics, high-throughput sequencing analysis.

Selected Publications

Yu S, Chen WC, Wang L, Jewell S, Mammedova A, Han SW, Wickramasinghe J, Barash Y, Tian B.: PolyA_DB v4: systematic polyA site identification and isoform annotation in human and mouse genomes using 3' end and long-read sequencing data. Nucleic Acids Res 54: D247-D254, Jan 2026.

Bergfort A, Gordon JM, Gazzara MR, Hung CT, Lee B, Barash Y, Neugebauer KM.: The exon junction complex coordinates the cotranscriptional inclusion of blocks of neighboring exons. Genes Dev 40: 94-109, Jan 2026.

Wang D, Gazzara MR, Jewell S, Wales-McGrath BD, Yang K, Brown CD, Choi PS, Barash Y.: A deep dive into statistical modeling of RNA splicing QTLs reveals variants that explain neurodegenerative disease. Am J Hum Genet 112: 3010-3029, Dec 2025.

Zhuang F, Gutman D, Islas N, Guzman BB, Jimenez A, Jewell S, Hand NJ, Nathanson K, Dominguez D, Barash Y.: G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data. Nat Commun 16: 10221, Nov 2025.

Gazzara MR, Cater T, Mallory MJ, Barash Y, Lynch KW.: Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity. Genome Biol 26: 386, Nov 2025.

Sehgal P, Naqvi AS, Higgins M, Liu J, Harvey K, Jarroux J, Kim T, Mankaliye B, Mishra P, Watterson G, Fine J, Davis J, Hayer KE, Castro A, Mogbo A, Drummer C 4th, Martinez D, Koptyra MP, Ang Z, Wang K, Farrel A, Quesnel-Vallieres M, Barash Y, Spangler JB, Rokita JL, Resnick AC, Tilgner HU, De Raedt T, Powell DJ Jr, Thomas-Tikhonenko A.: NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas. Cell Rep 44: 116099, Aug 2025.

Aicher JK, Issakova D, Slaff B, Jewell S, Lahens NF, Grant GR, Baralle D, Rosenfeld JA, Scott DA; Undiagnosed Diseases Network; Bhoj EJ, Barash Y.: MAJIQ-CLIN: A novel tool for the identification of Mendelian disease-causing variants from RNA-Seq data. medRxiv Feb 2025.

Sehgal P, Naqvi AS, Higgins M, Liu J, Harvey K, Jarroux J, Kim T, Mankaliye B, Mishra P, Watterson G, Fine J, Davis J, Hayer KE, Castro A, Mogbo A, Drummer C, Martinez D, Koptyra MP, Ang Z, Wang K, Farrel A, Quesnel-Vallieres M, Barash Y, Spangler JB, Rokita JL, Resnick AC, Tilgner HU, DeRaedt T, Powell DJ, Thomas-Tikhonenko A.: Neuronal cell adhesion molecule (NRCAM) variant defined by microexon skipping is an essential, antigenically distinct, and targetable proteoform in high-grade glioma. eLife Jan 2025.

Yang K, Islas N, Jewell S, Jha A, Radens CM, Pleiss JA, Lynch KW, Barash Y, Choi PS.: Machine learning-optimized targeted detection of alternative splicing. Nucleic Acids Res 53(3): gkae1260, Jan 2025 Notes: Co-corresponding.

Wu D, Maus N, Jha A, Yang K, Wales-McGrath BD, Jewell S, Tangiyan A, Choi P, Gardner JR, Barash Y.: Generative modeling for RNA splicing predictions and design. bioRxiv Jan 2025.