List of works - Yoseph Barash

A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior.

scientific article

A new view of transcriptome complexity and regulation through the lens of local splicing variations

scientific article published on February 2016

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 splicing regulation

scientific article

AVISPA: a web tool for the prediction and analysis of alternative splicing

scientific article

Aberrant splicing in B-cell acute lymphoblastic leukemia

scientific article published on 01 November 2018

Aberrant splicing in B-cell acute lymphoblastic leukemia

An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning

scientific article published on 24 January 2019

An illuminated view of molecular biology

scientific article published on 26 August 2010

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes

scientific article published on 16 May 2017

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context ⬇️

scientific article published on July 29, 2011

Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays

scientific article published on 29 January 2004

Context-specific Bayesian clustering for gene expression data

scientific article

Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy

scientific article

Deciphering the splicing code

scientific article

ESRP1 Mutations Cause Hearing Loss due to Defects in Alternative Splicing that Disrupt Cochlear Development

scientific article

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

scientific article published on 19 June 2020

From promoter sequence to expression

Functional coordination of alternative splicing in the mammalian central nervous system

scientific article published on January 2007

Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases

scientific article published on 09 January 2020

In silico to in vivo splicing analysis using splicing code models

scientific article published on 07 December 2013

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

scientific article published on 27 January 2020

Integrative deep models for alternative splicing

scientific article published in July 2017

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

scientific article

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

scientific article published on 07 June 2021

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

scientific article published on 30 March 2020

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

scientific article published on 17 June 2020

Missense Mutations in NKAP Cause a Disorder of Transcriptional Regulation Characterized by Marfanoid Habitus and Cognitive Impairment

scientific article published on 03 October 2019

Model-based detection of alternative splicing signals

scientific article

Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.

scientific article published on 11 December 2017

PRiMeUM: A Model for Predicting Risk of Metastasis in Uveal Melanoma.

scientific article published in August 2017

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing

scientific article published on 15 September 2017

Poly(C)-Binding Protein Pcbp2 Enables Differentiation of Definitive Erythropoiesis by Directing Functional Splicing of the Runx1 Transcript

scientific article published on 30 July 2018

Predicting alternative splicing.

scientific article published in January 2014

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease

scientific article published on 18 December 2014

Rapid and Scalable Profiling of Nascent RNA with fastGRO

scientific article published on 01 November 2020

Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

scientific article published on 07 October 2019

Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression

scientific article

Splicing code modeling

scientific article published on January 2014

Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation

scientific article published on 29 September 2017

Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation

scientific article

List of works by Yoseph Barash

A SLM2 Feedback Pathway Controls Cortical Network Activity and Mouse Behavior.

A new view of transcriptome complexity and regulation through the lens of local splicing variations

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 splicing regulation

AVISPA: a web tool for the prediction and analysis of alternative splicing

Aberrant splicing in B-cell acute lymphoblastic leukemia

Aberrant splicing in B-cell acute lymphoblastic leukemia

An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning

An illuminated view of molecular biology

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context ⬇️

Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays

Context-specific Bayesian clustering for gene expression data

Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy

Deciphering the splicing code

ESRP1 Mutations Cause Hearing Loss due to Defects in Alternative Splicing that Disrupt Cochlear Development

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

From promoter sequence to expression

Functional coordination of alternative splicing in the mammalian central nervous system

Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases

In silico to in vivo splicing analysis using splicing code models

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

Integrative deep models for alternative splicing

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

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

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

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

Missense Mutations in NKAP Cause a Disorder of Transcriptional Regulation Characterized by Marfanoid Habitus and Cognitive Impairment

Model-based detection of alternative splicing signals

Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.

PRiMeUM: A Model for Predicting Risk of Metastasis in Uveal Melanoma.

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing

Poly(C)-Binding Protein Pcbp2 Enables Differentiation of Definitive Erythropoiesis by Directing Functional Splicing of the Runx1 Transcript

Predicting alternative splicing.

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease

Rapid and Scalable Profiling of Nascent RNA with fastGRO

Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression

Splicing code modeling

Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation

Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation