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List of works by Benjamin J. Blencowe

5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary

scientific article

A Dynamic Splicing Program Ensures Proper Synaptic Connections in the Developing Cerebellum

scientific article published on 01 June 2020

A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals

scientific article published on August 2012

A compendium of RNA-binding motifs for decoding gene regulation.

scientific article

A germline mutation in SRRM2, a splicing factor gene, is implicated in papillary thyroid carcinoma predisposition

scientific article published on 2 July 2015

A global regulatory mechanism for activating an exon network required for neurogenesis

scientific article published on 11 September 2014

A highly conserved program of neuronal microexons is misregulated in autistic brains

scientific article published on December 2014

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

scientific article published on 04 March 2019

A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes

article

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

A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.

scientific article

A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription

scientific article

ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development

scientific article published on 01 April 2019

Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2

scientific article published on 19 November 2020

Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2

scientific article published on 01 January 2021

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

scientific article published on 01 October 2019

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

scientific article published on July 2015

Alternative splicing networks regulated by signaling in human T cells.

scientific article

Alternative splicing of conserved exons is frequently species-specific in human and mouse

scientific article published on 01 February 2005

Alternative splicing: decoding an expansive regulatory layer

scientific article published on 30 March 2012

Alternative splicing: new insights from global analyses

scientific article published on July 2006

An RNA map predicting Nova-dependent splicing regulation

scientific article

An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing

scientific article published on 18 February 2020

An alternative splicing event amplifies evolutionary differences between vertebrates

scientific article

An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming

scientific article

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

scientific article published on 30 August 2017

An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation

scientific article (publication date: 7 November 2003)

An exon-centric perspective

scientific article published on 11 July 2012

An extensive program of periodic alternative splicing linked to cell cycle progression

scientific article published on 25 March 2016

Analysis of the requirement for RNA polymerase II CTD heptapeptide repeats in pre-mRNA splicing and 3'-end cleavage

scientific article

Author Correction: Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism

scientific article published in Nature

Autism spectrum disorder: insights into convergent mechanisms from transcriptomics

scientific article published on 01 January 2019

Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions

scientific article published on 29 January 2020

Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder

scientific article

CDKN1C mutation in Wiedemann-Beckwith syndrome patients reduces RNA splicing efficiency and identifies a splicing enhancer

scientific article published on 01 June 2004

Characterization of disease-associated mutations affecting an exonic splicing enhancer and two cryptic splice sites in exon 13 of the cystic fibrosis transmembrane conductance regulator gene

scientific article published on 01 August 2003

Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing.

scientific article

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians

scientific article published on 09 August 2016

Considerations in the identification of functional RNA structural elements in genomic alignments

scientific article published on 30 January 2007

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

scientific article published on 24 October 2016

Corrigendum: Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming

scientific article published on June 2015

Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis

scientific article published in September 2011

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

scientific article published on June 2009

Deciphering the splicing code

scientific article

Differential contribution of steady-state RNA and active transcription in chromatin organization

scientific article published on 26 August 2019

Distinct types of disorder in the human proteome: functional implications for alternative splicing

scientific article

Dynamic integration of splicing within gene regulatory pathways

scientific article

Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop

scientific article published on 13 September 2018

Epstein-Barr virus EBNA1 protein regulates viral latency through effects on let-7 microRNA and dicer

scientific article

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development

scientific article

Exon skipping through the creation of a putative exonic splicing silencer as a consequence of the cystic fibrosis mutation R553X.

scientific article published in May 2007

Functional coordination of alternative splicing in the mammalian central nervous system

scientific article published on January 2007

Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins

scientific article published on 11 April 2014

Gene Expression: The Close Coupling of Transcription and Splicing

article

Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform

scientific article published on 16 March 2020

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

scientific article published on 01 November 2018

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

scientific article

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs

scientific article published on 28 August 2005

Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism

scientific article published on 5 December 2016

Global Mapping of Human RNA-RNA Interactions

scientific article

Global analysis of alternative splicing differences between humans and chimpanzees

scientific article

Global analysis of alternative splicing during T-cell activation

scientific article published on 16 February 2007

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

scientific article

Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer

scientific article

Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine

scientific article published on 02 June 2016

Highly consistent patterns for inherited human diseases at the molecular level

scientific article published on 15 November 2005

IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC.

scientific article

Identification and characterization of RED120: a conserved PWI domain protein with links to splicing and 3'-end formation.

scientific article

Identification of small molecule modulators of HIV-1 Tat and Rev protein accumulation

scientific article published on 26 January 2017

In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei

scientific article published in April 2004

Inferring global levels of alternative splicing isoforms using a generative model of microarray data

scientific article published on 10 January 2006

LUMIER: A Discovery Tool for Mammalian Protein Interaction Networks

scientific article published on January 2017

Latent regulatory potential of human-specific repetitive elements

scientific article published on 13 December 2012

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.

scientific article published on 05 June 2013

MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs

scientific article published in October 2016

Major Roles for Pyrimidine Dimers, Nucleotide Excision Repair, and ATR in the Alternative Splicing Response to UV Irradiation.

scientific article published in March 2017

Microarray analysis of RNA processing and modification

scientific article published on January 2006

Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder

scientific article published on 11 June 2020

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders

scientific article published in December 2016

Model-based detection of alternative splicing signals

scientific article

Molecular biology: RNA in control

scientific article published in Nature

Most "dark matter" transcripts are associated with known genes

scientific article published in May 2010

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

scientific article published in February 2017

Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming

scientific article

Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts

scientific article

Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100

scientific article published on 27 September 2019

Next-generation RNA Sequencing of Archival Formalin-fixed Paraffin-embedded Urothelial Bladder Cancer

Orchestrating Ribosomal Subunit Coordination to Control Stem Cell Fate

scientific article published on 01 April 2018

Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization.

scientific article published in January 2009

Probabilistic Inference of Alternative Splicing Events in Microarray Data ⬇️

scientific article published in January 2005

Probing microRNAs with microarrays: tissue specificity and functional inference

scientific article

Proteomic Analysis of SRm160-containing Complexes Reveals a Conserved Association with Cohesin

scientific article published on 13 September 2005

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data

scientific article published on 28 March 2018

Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression

scientific article

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

scientific article published on 18 December 2014

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

scientific article

Reflections for the 20th anniversary issue of RNA journal

scientific article published in April 2015

Regulated aggregative multicellularity in a close unicellular relative of metazoa

scientific article published on 24 December 2013

Regulation of alternative splicing by histone modifications

scientific article

Regulation of alternative splicing by the core spliceosomal machinery

scientific article

Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay

scientific article published on 28 April 2008

Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein

scientific journal article

Regulatory Expansion in Mammals of Multivalent hnRNP Assemblies that Globally Control Alternative Splicing.

scientific article published in July 2017

Response to “The Reality of Pervasive Transcription”

scientific article

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform

scientific article

Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo

scientific article

SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and alters gene expression via direct interaction with host mRNAs

scientific article published on 23 October 2020

SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination

scientific journal article

SRm160 Splicing Coactivator Promotes Transcript 3′-End Cleavage ⬇️

scientific article published on January 1, 2002

Sequence evidence for common ancestry of eukaryotic endomembrane coatomers

scientific article

Shifts in Ribosome Engagement Impact Key Gene Sets in Neurodevelopment and Ubiquitination in Rett Syndrome

scientific article published on 01 March 2020

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes

article

Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay

scientific article

SnapShot: High-throughput sequencing applications

scientific article published on 01 September 2011

SnapShot: The splicing regulatory machinery

scientific article published on 01 April 2008

Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD

scientific article

Splicing on the brain

scientific article published on 01 August 2005

Splicing regulation: the cell cycle connection

scientific article

Stromal Fat4 acts non-autonomously with Dchs1/2 to restrict the nephron progenitor pool

scientific journal article

Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing

scientific article

Technologies for the global discovery and analysis of alternative splicing.

scientific article published on January 2007

The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo

scientific article published on 01 May 2019

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation ⬇️

scientific article published on September 24, 2010

The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation

scientific article published on 30 June 2016

The Relationship between Alternative Splicing and Proteomic Complexity

scientific article published on 5 May 2017

The alternative splicing factor Nova2 regulates vascular development and lumen formation

scientific article

The evolutionary landscape of alternative splicing in vertebrate species

scientific article

The functional landscape of mouse gene expression

scientific article

The ribosome-engaged landscape of alternative splicing

scientific article

The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress.

scientific article

Tissue-specific alternative splicing remodels protein-protein interaction networks

scientific article published in June 2012

Toward unrestricted use of public genomic data:

scientific article

Transcription: surprising role for an elusive small nuclear RNA.

scientific article

Transcriptional Profiling of Endocrine Cerebro-Osteodysplasia Using Microarray and Next-Generation Sequencing ⬇️

scientific article published on September 27, 2011

Transcriptional activators control splicing and 3'-end cleavage levels

scientific journal article

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

scientific article (publication date: 25 May 2011)

Using expression profiling data to identify human microRNA targets

scientific article

When chromatin meets splicing

scientific article published on 01 September 2009

Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity

Widespread intron retention in mammals functionally tunes transcriptomes

scientific article

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