Yoseph Barash, Ph.D.
Professor of Genetics
Department: Genetics
Graduate Group Affiliations
Contact information
Richards Building D205
3700 Hamilton Walk
Philadelphia, PA 19104
3700 Hamilton Walk
Philadelphia, PA 19104
Office: 215-746-8683
Fax: 215-573-3111
Fax: 215-573-3111
Email:
yosephb@upenn.edu
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.
Permanent linkB.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.
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
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. bioRxiv 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.
Siachisumo C, Luzzi S, Aldalaqan S, Hysenaj G, Dalgliesh C, Cheung K, Gazzara MR, Yonchev ID, James K, Kheirollahi Chadegani M, Ehrmann IE, Smith GR, Cockell SJ, Munkley J, Wilson SA, Barash Y, Elliott DJ.: An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression. Elife 12: RP89705, Oct 2024.
Torres-Diz M, Reglero C, Falkenstein CD, Castro A, Hayer KE, Radens CM, Quesnel-Vallières M, Ang Z, Sehgal P, Li MM, Barash Y, Tasian SK, Ferrando A, Thomas-Tikhonenko A.: An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia. Cancer Res 84(20): 3327-3336, Oct 2024.
Han SW, Jewell S, Thomas-Tikhonenko A, Barash Y.: Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads. Genome Res 34(10): 1624-1635, Oct 2024.
Quesnel-Vallières M, Schultz DC, Orlenko A, Lo Y, Moore J, Ritchie M, Roth D, Carroll M, Barash Y, Lynch KW, Cherry S.: Trametinib Sensitivity is Defined by a Myeloid Differentiation Profile in Acute Myeloid Leukemia. Drugs R D 24(3): 489-499, Sep 2024.
Wang D, Gazzara MR, Jewell S, Wales-McGrath B, Brown CD, Choi PS, Barash Y.: A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants that Explain Neurodegenerative Disease. bioRxiv Sep 2024 Notes: corresponding.
Renzo Perales-Linares, Nektaria Maria Leli, Hesham Mohei, Silvia Beghi, Osvaldo Rivera, Nektarios Kostopoulos, Andrea Giglio, Subin George, Mireia Uribe-Herranz, Francesca Costabile, Stefano Pierini, Sergei Pustylnikov, Giorgos Skoufos, Yoseph Barash, Artemis Hatzigeorgiou, Constantinos Koumenis, Amit Maity, Michael Lotze, and Andrea Facciabene : Parkin regulates tumor evasion by modulating antigen processing and presentation through the PTEN/Akt network. Cancer Research 83(21): 3562-3576, Nov 2023 Notes: My student, Osvaldo Rivera, performed the cancer genomics/survival analysis for this paper (Fig 4).