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​   Publications

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2023

Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads

Han S.W, Jewell S., Lynch K.W., Thomas-Tikhonenko A., Barash Y.

Under review

BioRXiv

An anciently diverged family of RNA binding proteins maintain correct splicing of ultra-long exons through cryptic splice site repression

Siachisumo et al

eLife

URL

MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer

Quesnel-Vallières M., Jewell S., Lynch K.W., Thomas-Tikhonenko A., Barash Y.

NAR

In press

A Novel Aberrantly Spliced Gain-of-Function NT5C2 Isoform Contributes to Thiopurine Resistance in Acute Lymphoblastic Leukemia

Torres-Diz et al

Under review

BioRxiv  | URL

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

The APAeval Community effort

RNA

BioRxiv  | URL

Alternative splicing of its 5’ untranslated region controls CD20 mRNA translation and enables resistance to CD20-directed immunotherapies

Ang Z. et al

Blood

BioRxiv  | URL

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

URL

Parkin deficiency suppresses antigen presentation to promote tumor immune evasion and immunotherapy resistance

Renzo P. et al.

Cancer Discovery in press

URL

A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers

Wang D., Quesnel-Vallières M., Jewell S., Elzubier M., Lynch K.W., Thomas-Tikhonenko A., Barash Y.

Nature Comm. Vol 14 Issue 1

URL

RNA splicing analysis using heterogeneous and large RNA-seq datasets

Vaquero-Garcie J.*, Aicher J.K.*, Jewell S.*, Gazzara M.R.*, Radens, C.M.^, Jha, A.^, Green C.J., Norton S., Lahens N.F., Grant, G.R., Barash Y.

Nature Comm, Vol 14 Issue 1

BioRxiv  | 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

URL

Identification and characterization of RBM12 as a novel regulator of fetal hemoglobin expression

Wakabayashi A. et al.

Blood Advances. Vol 6 Issue 23

URL

FBXW7β isoform drives transcriptional activation of a proinflammatory TNF cluster in normal and malignant pro-B cells

Yang SY, Hayer KE, Fazelinia H, Spruce LA, Asnani M, Black KL, Naqvi AS, Pillai V, Barash Y, Elenitoba-Johnson KSJ, Thomas-Tikhonenko A

Blood Advances,

BioRxiv | URL

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

URL

Identifying common transcriptome signatures of cancer by interpreting deep learning models

Jha A.*, Quesnel-Vallières M.*, Wang D., Thomas-Tikhonenko A., Lynch K.W., Barash Y.

Genome Biology

BioRxiv | URL

High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance

Cortés-López M. et al.

Nature Comm. Vol 13 Issue 1

BioRxiv |  URL

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

URL

Alternative splicing redefines landscape of commonly mutated genes in acute myeloid leukemia

Rivera, O.D., Mallory, M.J., Quesnel-Vallières, M., Chatrikhi, R., Schultz, D.C., Carroll, M., Barash, Y., Cherry, S., Lynch, K.W.

Proc Natl Acad Sci USA 118, e2014967118

BioRxiv | URL

CAMPAREE: a robust and configurable RNA expression simulator

Lahens N. F. et al

BMC Genomoics Vol 22 Issue 1

URL

Disrupting upstream translation in mRNAs is associated with human disease

Lee, D.S.M., Park, J., Kromer, A., Baras, A., Rader, D.J., Ritchie, M.D., Ghanem, L.R., Barash, Y

Nature Comm. 12, 1515

BioRxiv | URL

CYP11B1 Variants Influence Skeletal Maturation Via Alternative Splicing

Grgic O.*, Gazzara R. M.* et al

Nature Comm. Bio. Vol 4, Issue 1

URL

MOCCASIN: A method for correcting for known and unknown confounders in RNA splicing analysis

Slaff, B., Radens, C.M., Jewell, P., Jha, A., Lahens, N.F., Grant, G.R., Thomas-Tikhonenko, A., Lynch, K.W., Barash, Y.

Nature Comm. Vol 12 Issue 1

BioRxiv | URL

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

URL

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

BioRxiv

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

URL

2020

Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq.

Aicher J.K , Jewell P., Vaquero-Garcia J., Barash Y., and Bhoj E.J

Genet Med (2020)

BioRxiv | URL

Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations.

Lee, D.S.M., Ghanem, L.R. & Barash, Y.

Nature Com. 11, 527 (2020).

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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.

URL

Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study

Jha A., Aicher J.K, Singh D. and Barash Y.

Genome Biology, 21, 149 (2020)

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Rapid and scalable profiling of nascent RNA with fastGRO

Barbieri E., Hill C., Quesnel-Vallieres M., Barash Y., Gardini A.

Cell Reports, Vol 33, Issue 6

BioRxiv | URL

Meta-Analysis of Transcriptomic Variation in T cell Populations Reveals Novel Signatures of Gene Expression and Splicing

Radens C.M, Blake D., Jewell P., Barash Y.* and Lynch K.W.*

RNA 10.1261 2020

BioRxiv | URL

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

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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)

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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

Aberrant splicing in B-cell acute lymphoblastic leukemia

Black, K.L., Naqvi, A.S., Hayer, K.E., Yang, S.Y., Gillespie, E., Bagashev, A., Pillai, V., Tasian, S., Gazzara, M.R., Carroll, M., Taylor D., Lynch K. W., Barash Y., Thomas-Tikhonenko A.

Nucleic Acids Res 46, 11357–11369

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).

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LeafCutter vs. MAJIQ and comparing software in the fast-moving field of genomics

Vaquero-Garcia J., Norton S , Barash Y.

Google Scholar | BioRxiv

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2017

Integrative Deep Models for Alternative Splicing

Jha A., Gazzara M., Barash Y.

Bioinformatics, 33 (14): i274-i282 (selected for ISMB2017 proceedings)

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes

Gazzara, M., Mallory M., Roytenberg R., Lindberg J., Jha A., Lynch K.*, Barash Y.*

Genome Research, 10.1101/gr.220517.117

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

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MAJIQ-SPEL: Web-tool to interrogate classical and complex splicing variations from RNA-Seq data

Green CJ, Gazzara M.R., Barash Y.

Bioinformatics, doi/10.1093

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

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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

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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

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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

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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

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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

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Predicting alternative splicing

Barash Y., Vaquero-Garcia J.

Spliceosomal Pre-mRNA Splicing, Hertel K. J. Editor, Springer

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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

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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

Google Scholar​ | URL

2010

An illuminated view of molecular biology

Barash Y., Wang X.



Genome Biology. 11:307

Google Scholar​ | URL

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

​Google Scholar​​​​​ | URL

Model-based detection of

alternative splicing signals

Barash Y., Blencowe B.J., Frey B.J.

 

Bioinformatics. 26:i325–i333

Google Scholar​ | URL

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

Google Scholar​ | URL

2007

Functional coordination of alternative splicing in the mammalian central nervous system

Fagnani M., Barash Y., Ip J.Y.



Genome Biology. 8:R108

Google Scholar​ | URL

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

Google Scholar​ ​| URL

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

Google Scholar​ | URL

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

Google Scholar​ | URL

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

Google Scholar​ | PDF​

Google Scholar​ | PDF​

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)

Google Scholar | PDF

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

Google Scholar​ | PDF​

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