Publications
2025
Generative modeling for RNA splicing predictions and design
Wu D, Maus N, Jha A., Yang K, Wales-McGrath B,
Jewell S, Tangiyan A, Choi P.S, Gardner J.R., Barash Y
under review
MAJIQ-CLIN: A novel tool for the identification of Mendelian disease-causing variants from RNA-Seq data
Aicher J.K., Issakova D, Slaff B.M., Jewell S., Lahanes N.F, Grant G.R, Baralle D., Rosenfeld J.A, Daryl S.A, Bhoj E.,Barash, Y
under review
2024
A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants that Explain Neurodegenerative Disease
Wang D, Gazzara M.R, Jewell S, Wales-McGrath B,
Brown C.D, Choi P.S ,Barash Y
under review
Trametinib Sensitivity is Defined by a Myeloid Differentiation Profile in Acute Myeloid Leukemia
Quesnel-Vallières et al
G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data
Zhuang F, Gutman D, Islas N, Guzman B.B,
Jimenez A, Jewell S, Hand N.J, Nathanson K., Dominguez D, Barash Y
under review
Neuronal cell adhesion molecule (NRCAM) variant defined by microexon skipping is an essential, antigenically distinct, and targetable proteoform in high-grade glioma
Priyanka S. et al
under review
Machine learning-optimized targeted detection of alternative splicing
Yang K., Islas N., Jewell S., Jha A., Radens C.M, Pleiss J.A, Lynch K.W, Barash Y., Choi P.S
BioRXiv
A Novel Aberrantly Spliced Gain-of-Function NT5C2 Isoform Contributes to Thiopurine Resistance in Acute Lymphoblastic Leukemia
Torres-Diz et al
Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads
BioRXiv
MAJIQ V3 offers improvements in accuracy, performance, and usability for splicing analysis from RNA sequencing
Aicher J.K., Slaff B.M., Jewell S., Bhoj E.,
Barash, Y
Under review
2023
An anciently diverged family of RNA binding proteins maintain correct splicing of ultra-long exons through cryptic splice site repression
Siachisumo et al
eLife
The Tumor Suppressor Adenomatous Polyposis Coli (apc) Is Required for Neural Crest-Dependent Craniofacial Development in Zebrafish
Liu X. et al.
J. of Developmental Biology Vol 11 Issue 3
Parkin deficiency suppresses antigen presentation to promote tumor immune evasion and immunotherapy resistance
Renzo P. et al.
Cancer Discovery in press
URL
2022
The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice
Peart N. et al.
Plos Genetics. Vol 18 Issue 9
Identification and characterization of RBM12 as a novel regulator of fetal hemoglobin expression
Wakabayashi A. et al.
Blood Advances. Vol 6 Issue 23
The global Protein-RNA interaction map of ESRP1 defines a post-transcriptional program that is essential for epithelial cell function
Peart N. et al.
iScience. Vol 25 Issue 10
2021
Modulation of CD22 protein expression in childhood leukemia by pervasive splicing aberrations: implications for CD22-directed immunotherapies
Zheng S. et al.
Blood Cancer Discovery
CAMPAREE: a robust and configurable RNA expression simulator
Lahens N. F. et al
BMC Genomoics Vol 22 Issue 1
CYP11B1 Variants Influence Skeletal Maturation Via Alternative Splicing
Grgic O.*, Gazzara R. M.* et al
Nature Comm. Bio. Vol 4, Issue 1
RNA-Binding Proteins PCBP1 and PCBP2 Are Critical Determinants of Murine Erythropoiesis
Ji, X., Jha, A., Humenik, J., Ghanem, L.R., Kromer, A., Duncan-Lewis, C., Traxler, E., Weiss, M.J., Barash, Y., Liebhaber, S.A.
Mol Cell Biol 41
The Global Protein-RNA Interaction map of Epithelial Splicing Regulatory Protein 1 defines a post-transcriptional program that is essential for epithelial cell function
Peart, N.J., Hwang, J.Y., Vallières, M.Q.-, Sears, M.J., Yang, Y., Stoilov, P., Barash, Y., Park, J.W., Carstens, R.P
Cell Reports, in press
Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
Schulz, L., Torres-Diz, M., Cortés-López, M., Hayer, K.E., Asnani, M., Tasian, S.K., Barash, Y., Sotillo, E., Zarnack, K., König, J., Thomas-Tikhonenko, A
Genome Biology 22, 190
2020
Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases
Nurnberg ST, Guerraty MA, Rao HS, Pjanic M, Norton S, Serrano F, Perisic L, Elwyn S, Pluta J, Zhao W, Testa S, Park Y, Wang T, Hedin U, Sinha S, Barash Y, Brown CD, Quertermous T, and Rader DJ.
PLoS Genet 16(1): e1008538.
2019
An ancient germ cell-specific RNA binding protein protects the germline from cryptic splice site poisoning
Ehrmann I., Crichton J.H., Gazzara M.R. 3,4, James K., Liu Y., Grellscheid S., Curk T., de Rooij D.G., Steyn J., Cockell S.J., Adams I.R, Barash Y. and Elliott D.J
ELife, 2019;8:e39304
URLGoogle Scholar | URL
Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19
Asnani, M., Hayer, K.E., Naqvi, A.S. et al.
Leukemia (2019)
2018
RNA-binding protein A1CF modulates plasma triglyceride levels through posttranscriptional regulation of stress-induced VLDL secretion
Lin, J., Conlon, D.M., Wang, X., Nostrand, E.V., Robano, I., Park, Y., Strong, A., Radmanesh, B., Barash, Y., Rader, D.J., Yeo, W. Y, Musunuru K.
Submitted
Poly(C)-Binding Protein Pcbp2 Enables Differentiation of Definitive Erythropoiesis by Directing Functional Splicing of the Runx1 Transcript
Ghanem LR, Kromer A, Silverman IM, Ji X, Gazzara M, Nguyen N, Aguilar G, Martinelli M, Barash Y, Liebhaber SA.
Mol Cell Biol. 2018 Jul 30;38(16).
LeafCutter vs. MAJIQ and comparing software in the fast-moving field of genomics
Vaquero-Garcia J., Norton S , Barash Y.
Google Scholar | BioRxiv
2017
PRiMeUM: a model for predicting risk of metastasis in Uveal Melanoma
Vaquero-Garcia J., Lalonde E., Ewens K.G, Ebrahimzadeh J., Richard-Yutz J., Shields C.L., Barrera A., Green C.J. Barash Y.*, Ganguly A.*
Investigative Ophthalmology & Visual Science, Vol.58, p4096-4105. 2017
ESRP1 mutations cause hearing loss due to defects in alternative splicing that disrupt cochlear development
Rohacek A.M., Bebee T.W., Tilton R.K., Radens C.M., McDermott-Roe C., Peart N., Kaur M., Zaykaner M., Cieply B., Musunuru K., Barash Y., Germille J.A., Krantz I.D., Carstens R.P., Epstein D.J.
Developmental Cell, accepted
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
Norton S., Vaquero-Garcia J., Barash Y.
Submitted
Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing
Shinde M. Y., Sidoli S., Kulej K., Mallory M.J., Radens C.M., Reicherter A., Myers R., Barash Y., Lynch K.W., Garcia B.A., Klein P.S.
JBC, in press
Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation
Brady L.K., Wang H., Radens C.M., Bi Y., Radovich M., Maity A., Ivan C., Ivan M., Barash Y., Koumenis C.
Plos Biology, in press
2016
A new view of transcriptome complexity and regulation through the lens of local splicing variations
Vaquero-Garcia J., Barrera A., Gazzara, M. González-Vallinas J., Lahens N., Hogenesch J., Lynch K., Barash Y.
ELife 2016;10.7554/eLife.11752
A SLM2 feedback pathway controls cortical network activity and mouse behavior
Ingrid Ehrmann, Matthew R. Gazzara, Vittoria Pagliarini, Caroline Dalgliesh, Mahsa Kheirollahi-Chadegani, Yaobo Xu, Eleonora Cesari, Marina Danilenko, Marie Maclennan, Kate Lowdon, Tanja Vogel, Piia Keskivali-Bond, Sara Wells, Heather Cater, Philippe Fort, Mauro Santibanez-Koref, Silvia Middei, Claudio Sette, Gavin J. Clowry*, Yoseph Barash*, Mark O. Cunningham*, David J. Elliott*
Cell Reports, Volume 17, Issue 12
2015
Convergence of acquired mutations and alternative splicing of CD19 enables resistance to CART-19 immunotherapy
Sotillo E., Barrett D., Black K., Bagashev A., Oldridge D., Wu G., Sussman R., Lanauze C., Gazzara M, Martinez N., Ruella M., Harrington C., Chung E., Perazzelli J., Hofmann T., Maude S., Raman P., Barrera A., Gill S., Lacey S., Melenhorst J., Allman D., Jacoby E., Fry T., Mackall C., Barash Y., Lynch K., Maris J, Grupp S.,Thomas-Tikhonenko A.
Cancer Discovery, In press
Hui Y. Xiong, Babak Alipanahi, Leo J. Lee, Hannes Bretschneider, Daniele Merico, Ryan K. C. Yuen, Yimin Hua, Serge Gueroussov, Hamed S. Najafabadi, Timothy R. Hughes, Quaid Morris, Yoseph Barash, Adrian R. Krainer, Nebojsa Jojic, Stephen W. Scherer, Benjamin J. Blencowe, Brendan J. Frey
Science. Vol. 347 no. 6218
Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation
Martinez N, Agosto L., Qiu J., Mallory M., Gazarra M., Barash Y., Fu X., Lynch K.
Genes & Development Vol. 29 Issue 19
2014
In silico to in vivo splicing analysis using splicing code models
Gazzara, M., Vaquero-Garcia, J., Lynch, K., Barash, Y.
Methods
Splicing Code Modeling
Barash Y. Vaquero-Garcia J.
Systems Biology of RNA Binding Proteins, Editor Yeo G. W., Springer
Predicting alternative splicing
Barash Y., Vaquero-Garcia J.
Spliceosomal Pre-mRNA Splicing, Hertel K. J. Editor, Springer
2013
ESRP1 mutations cause hearing loss due to defects in alternative splicing that disrupt cochlear development
Rohacek A.M., Bebee T.W., Tilton R.K., Radens C.M., McDermott-Roe C., Peart N., Kaur M., Zaykaner M., Cieply B., Musunuru K., Barash Y., Germille J.A., Krantz I.D., Carstens R.P., Epstein D.J.
Developmental Cell, accepted
2011
Bayesian prediction of
tissue-regulated splicing using RNA sequence and cellular context
Xiong H.Y., Barash Y., Frey B.J.
Bioinformatics. 27:2554–2562
2010
An illuminated view of molecular biology
Barash Y., Wang X.
Genome Biology. 11:307
Deciphering the splicing code
Barash Y., Calarco J.A., Gao W., Pan Q., Wang X., Shai O., Blencowe B.J. Frey B.J.
Nature. 465:53–9
Model-based detection of
alternative splicing signals
Barash Y., Blencowe B.J., Frey B.J.
Bioinformatics. 26:i325–i333
2008
A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative
Aznarez I., Barash Y., Shai O.
Genome Research. 18(8):1247–1258
2007
Functional coordination of alternative splicing in the mammalian central nervous system
Fagnani M., Barash Y., Ip J.Y.
Genome Biology. 8:R108
2005
CIS: compound importance sampling method for protein–DNA binding site p-value estimation
Barash Y., Elidan G., Kaplan T. Friedman N.
Bioinformatics. 21:596–600
2004
Comparative analysis of algorithms
for signal quantitation from oligonucleotide microarrays
Barash Y., Dehan E., Krupsky M., Franklin W., Geraci M., Kaminski N.
Bioinformatics. 20:839–846
Sfp1 is a stressand nutrient-sensitive regulator of ribosomal protein gene expression
Marion R.M., Regev A., Segal E.
Barash Y., Koller D., Friedman N. O'Shea E.K.
Proceedings of the National Academy
of Sciences of the United States of America. 101:14315–14322
2003
Modeling dependencies in
Protein-DNA binding sites
Barash Y., Elidan G., Friedman N.
Kaplan T.
Proc. of the 7th Annual International Conference on Research in Computational Molecular Biology (RECOMB)
2002
Context-Specific Bayesian clustering
for Gene Expression Data
Barash Y., Friedman N.
Journal of Computational Biology: 169-191
From Promoter Sequence to Expression: A Probabilistic Framework
Segal E., Barash Y., Simon I., Friedman N. Keller D.
Proc. of the 6th Annual International Conference on Research in Computational Molecular Biology (RECOMB). :263–272
2001
Context-Specific Bayesian clustering
for Gene Expression Data
Barash Y., Friedman N.
Proc. of the 5th Annual International Conference on Research in Computational Molecular Biology (RECOMB)
A Simple Hyper-Geometric Approach
for Discovering Putative Transcription Factor Binding Sites
Barash Y., Bejerano G., Friedman N.
Algorithms in Bioinformatics:
Proc. First International Workshop
(WABI). :278–293