List of works - Eduardo Eyras

A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing

scientific article

A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins

scientific article published on 2 May 2015

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

scientific article published on 11 September 2014

A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells

scientific article published on 14 July 2015

ASTD: The Alternative Splicing and Transcript Diversity database

scientific article

An overview of Ensembl

scientific article (publication date: May 2004)

Approaches to link RNA secondary structures with splicing regulation

scientific article published in January 2014

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

scientific article

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

scientific article published on 25 June 2015

CD133-directed CAR T-cells for MLL leukemia: on-target, off-tumor myeloablative toxicity

article

Chromatin and Alternative Splicing

scientific article published on 01 January 2010

Co-evolution of the branch site and SR proteins in eukaryotes

article published in 2008

Combined analysis of genome sequencing and RNA-motifs reveals novel damaging non-coding mutations in human tumors

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes

scientific article

Control of alternative splicing through siRNA-mediated transcriptional gene silencing.

scientific article published on 21 June 2009

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor

scientific article

Databases and resources for human small non-coding RNAs ⬇️

scientific article published on March 1, 2011

Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing

scientific article published in September 2011

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

scientific article published on 10 January 2015

Differentiated evolutionary rates in alternative exons and the implications for splicing regulation

scientific article published on 22 June 2006

Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression

scientific article published on 31 August 2011

Drosha regulates gene expression independently of RNA cleavage function.

scientific article published on 19 December 2013

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing

scientific article published on 8 March 2016

EGASP: the human ENCODE Genome Annotation Assessment Project

scientific article

ESTGenes: alternative splicing from ESTs in Ensembl

scientific article published on May 2004

Ensembl 2002: accommodating comparative genomics

scientific article published on January 2003

Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

scientific article

Exon creation and establishment in human genes

scientific article published on January 2008

Gene finding in the chicken genome

scientific article

Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors.

scientific article published on 28 March 2018

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome-wide association between branch point properties and alternative splicing

scientific article published in 2010

Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling

scientific article

ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer

scientific article published on 16 September 2021

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Initial sequencing and comparative analysis of the mouse genome

scientific article

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

Intersections involving monopoles and waves in eleven dimensions

article

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

scientific article

Key contribution of CPEB4-mediated translational control to cancer progression

scientific article

Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

scientific article

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes

scientific article

Leveraging transcript quantification for fast computation of alternative splicing profiles

scientific article published on 15 July 2015

Methods to study splicing from high-throughput RNA sequencing data

scientific article

Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB.

scientific article published on 19 January 2015

Nucleosome-driven transcription factor binding and gene regulation

scientific article published on 21 November 2012

Predictive models of gene regulation from high-throughput epigenomics data

scientific article

Pyicos: A Flexible Tool Library for Analyzing Protein-Nucleotide Interactions with Mapped Reads from Deep Sequencing

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

scientific article

RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation

scientific article published on December 2013

RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae

scientific article

Regulation of FAS exon definition and apoptosis by the Ewing sarcoma protein

scientific article published on 10 May 2014

ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning

scientific article published on 29 November 2019

Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome

scientific article published on 14 April 2020

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.

scientific article published on 29 March 2018

SUPPA2 provides fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

scientific article published on 23 March 2018

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation.

scientific article published on 8 July 2011

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

scientific article published in April 2018

Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing

scientific article published on 08 June 2021

Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1.

scientific article published on 21 December 2017

The 5' untranslated region of the serotonin receptor 2C pre-mRNA generates miRNAs and is expressed in non-neuronal cells

scientific article

The BioMart community portal: an innovative alternative to large, centralized data repositories

scientific article (publication date: July 2015)

The Ensembl genome database project

scientific article

The Functional Impact of Alternative Splicing in Cancer

scientific article published in August 2017

The Microprocessor controls the activity of mammalian retrotransposons

scientific article (publication date: October 2013)

The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development.

scientific article published on 20 October 2016

The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

scientific article published on 17 June 2016

The discovery potential of RNA processing profiles

The discovery potential of RNA processing profiles.

scientific article

The functional impact of alternative splicing in cancer

The genome sequence of taurine cattle: a window to ruminant biology and evolution

scientific article

The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution

scientific article (publication date: November 2009)

The prognostic potential of alternative transcript isoforms across human tumors

scientific article published on 17 August 2016

The prognostic potential of alternative transcript isoforms across human tumors

The translational landscape of the splicing factor SRSF1 and its role in mitosis.

scientific article published on 6 May 2014

Use of ChIP-Seq data for the design of a multiple promoter-alignment method

scientific article

List of works by Eduardo Eyras

A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing

A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins

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

A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells

ASTD: The Alternative Splicing and Transcript Diversity database

An overview of Ensembl

Approaches to link RNA secondary structures with splicing regulation

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

CD133-directed CAR T-cells for MLL leukemia: on-target, off-tumor myeloablative toxicity

Chromatin and Alternative Splicing

Co-evolution of the branch site and SR proteins in eukaryotes

Combined analysis of genome sequencing and RNA-motifs reveals novel damaging non-coding mutations in human tumors

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes

Control of alternative splicing through siRNA-mediated transcriptional gene silencing.

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor

Databases and resources for human small non-coding RNAs ⬇️

Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

Differentiated evolutionary rates in alternative exons and the implications for splicing regulation

Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression

Drosha regulates gene expression independently of RNA cleavage function.

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing

EGASP: the human ENCODE Genome Annotation Assessment Project

ESTGenes: alternative splicing from ESTs in Ensembl

Ensembl 2002: accommodating comparative genomics

Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

Exon creation and establishment in human genes

Gene finding in the chicken genome

Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Genome-wide association between branch point properties and alternative splicing

Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling

ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Initial sequencing and comparative analysis of the mouse genome

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

Intersections involving monopoles and waves in eleven dimensions

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

Key contribution of CPEB4-mediated translational control to cancer progression

Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes

Leveraging transcript quantification for fast computation of alternative splicing profiles

Methods to study splicing from high-throughput RNA sequencing data

Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB.

Nucleosome-driven transcription factor binding and gene regulation

Predictive models of gene regulation from high-throughput epigenomics data

Pyicos: A Flexible Tool Library for Analyzing Protein-Nucleotide Interactions with Mapped Reads from Deep Sequencing

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation

RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae

Regulation of FAS exon definition and apoptosis by the Ewing sarcoma protein

ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning

Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.

SUPPA2 provides fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing

Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1.

The 5' untranslated region of the serotonin receptor 2C pre-mRNA generates miRNAs and is expressed in non-neuronal cells

The BioMart community portal: an innovative alternative to large, centralized data repositories

The Ensembl genome database project

The Functional Impact of Alternative Splicing in Cancer

The Microprocessor controls the activity of mammalian retrotransposons

The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development.

The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

The discovery potential of RNA processing profiles

The discovery potential of RNA processing profiles.

The functional impact of alternative splicing in cancer

The genome sequence of taurine cattle: a window to ruminant biology and evolution

The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution

The prognostic potential of alternative transcript isoforms across human tumors

The prognostic potential of alternative transcript isoforms across human tumors

The translational landscape of the splicing factor SRSF1 and its role in mitosis.

Use of ChIP-Seq data for the design of a multiple promoter-alignment method