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List of works by Roderic Guigó i Serra

A combinatorial code for CPE-mediated translational control

scientific article

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

scientific article

A general definition and nomenclature for alternative splicing events

scientific article

A limited set of transcriptional programs define major cell types

scientific article published on 29 July 2020

A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins

scientific article published on 17 February 2009

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

scientific article

ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection

scientific article published on 7 November 2013

ASTD: The Alternative Splicing and Transcript Diversity database

scientific article

Absence of canonical marks of active chromatin in developmentally regulated genes

scientific article

Active transcription without histone modifications

scientific article published on 30 November 2015

An encyclopedia of mouse DNA elements (Mouse ENCODE).

scientific article

Are splicing mutations the most frequent cause of hereditary disease?

scientific article

Assessment of transcript reconstruction methods for RNA-seq

scientific article

BLUEPRINT to decode the epigenetic signature written in blood.

scientific article

BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations

scientific article published on 12 May 2007

Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease

scientific article

CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis.

scientific article published on 27 September 2015

CPEB1 coordinates alternative 3′-UTR formation with translational regulation

scientific article published in Nature

CROC: finding chromosomal clusters in eukaryotic genomes

scientific article

Cell type-specific genetic regulation of gene expression across human tissues

scientific article published on 01 September 2020

Characterization of mammalian selenoproteomes.

scientific article

ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

scientific article

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts

scientific article

Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome

scientific article published on July 2004

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

scientific article

Comparative analysis of amino acid repeats in rodents and humans

scientific article published on April 2004

Comparative analysis of neutrophil and monocyte epigenomes

Comparative analysis of the transcriptome across distant species

scientific article

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

scientific article

Comparative gene prediction in human and mouse

scientific article published on January 2003

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity.

scientific article published on 19 April 2018

Comparative transcriptomics in human and mouse.

scientific article published on 8 May 2017

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

scientific article published on 18 June 2015

Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes

scientific article

Comparison of splice sites in mammals and chicken

scientific article

Composition and evolution of the vertebrate and mammalian selenoproteomes

scientific article published in 2012

Computational gene identification ⬇️

scientific article published on 01 June 1997

Computational gene identification: an open problem ⬇️

scientific article published on 01 January 1997

Computational identification of the selenocysteine tRNA (tRNASec) in genomes

scientific article

Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila

scientific article published on 10 September 2008

Conserved long-range base pairings are associated with pre-mRNA processing of human genes

scientific article published on 16 April 2021

Correction to: The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest ⬇️

scientific article published on 11 September 2020

Correction: Relaxation of Selective Constraints Causes Independent Selenoprotein Extinction in Insect Genomes

article by Charles E. Chapple & Roderic Guigó published 10 July 2009 in PLOS One

Corrigendum: Domains of genome-wide gene expression dysregulation in Down’s syndrome

scientific article published in Nature

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

scientific article published on 18 April 2016

DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs

scientific article published on 23 October 2015

Damage-responsive elements in regeneration

scientific article published on 20 November 2018

Data Resources for Human Functional Genomics.

scientific article published on 22 February 2017

De longs ARN non codants activateurs de la transcription des gènes

article

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

scientific article

Defining functional DNA elements in the human genome

scientific article

Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features

scientific article published on 27 January 2017

Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family

scientific article

Domains of genome-wide gene expression dysregulation in Down's syndrome.

scientific article published in April 2014

Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development

scientific article published on 01 February 2020

Dynamics of microRNA expression during mouse prenatal development

scientific article published on 23 October 2019

EGASP: Introduction

scientific article published on 7 August 2006

EGASP: collaboration through competition to find human genes

scientific article published in August 2005

EGASP: the human ENCODE Genome Annotation Assessment Project

scientific article

Effect of BDNF Val66Met on hippocampal subfields volumes and compensatory interaction with APOE-ε4 in middle-age cognitively unimpaired individuals from the ALFA study

scientific article published on 17 August 2020

Efficient targeted transcript discovery via array-based normalization of RACE libraries

scientific article

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

scientific article

Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes

scientific article published on 17 January 2020

Erratum to: 'DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs'.

scientific article published on 9 March 2016

Erratum to: Promoter-like epigenetic signatures in exons displaying cell type-specific splicing

scientific article published on 18 March 2016

Estimation of alternative splicing variability in human populations

scientific article published on 23 November 2011

Evidence for transcript networks composed of chimeric RNAs in human cells

scientific article

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization

scientific article

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Expression of the transcribed ultraconserved region 70 and the related long non-coding RNA AC092652.2-202 has prognostic value in Chronic Lymphocytic Leukaemia

scientific article published on 24 April 2018

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

scientific article

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

scientific article

FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow

scientific article

Fast computation and applications of genome mappability

scientific article

Finding the missing honey bee genes: lessons learned from a genome upgrade

scientific article

From chromatin to splicing: RNA-processing as a total artwork

scientific article published on 01 April 2010

From identification to validation to gene count.

scientific article

Functional annotation of human long noncoding RNAs via molecular phenotyping

scientific article published on 27 July 2020

Functional targets of the monogenic diabetes transcription factors HNF-1alpha and HNF-4alpha are highly conserved between mice and humans

scientific article published on 02 February 2009

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

GENCODE 2021 ⬇️

scientific article published on 03 December 2020

GENCODE reference annotation for the human and mouse genomes

scientific article published on 01 January 2019

GENCODE: producing a reference annotation for ENCODE

scientific article

GENCODE: the reference human genome annotation for The ENCODE Project

scientific article

Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite, Gyrodactylus bullatarudis

scientific article published on 28 March 2020

Gene finding in the chicken genome

scientific article

Gene organization features in A/T-rich organisms

scientific article published in January 2005

Gene-specific patterns of expression variation across organs and species

scientific article published on 08 July 2016

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

scientific article

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

scientific article

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

scientific article

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

scientific article

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

scientific article

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

scientific article

Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs

scientific article

Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

scientific article published on 03 April 2015

Genomic history of the origin and domestication of common bean unveils its closest sister species

scientific article published on 29 March 2017

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

scientific article

Grape RNA-Seq analysis pipeline environment.

scientific article published on 17 January 2013

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

scientific article

Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver.

scientific article published on 16 March 2009

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome

scientific article

Human genomics. The human transcriptome across tissues and individuals

scientific article

Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements

scientific article

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

scientific article published in June 2007

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome

scientific article published in 2021

Identification of a selenium-dependent glutathione peroxidase in the blood-sucking insect Rhodnius prolixus

scientific article published on 18 September 2015

Identification of genetic variants associated with alternative splicing using sQTLseekeR.

scientific article

Identifying protein-coding genes in genomic sequences

scientific article published on 30 January 2009

Improving gene annotation using peptide mass spectrometry

scientific article published on 22 December 2006

In silico meets in vivo

scientific article published on 25 February 2008

Initial sequencing and comparative analysis of the mouse genome

scientific article

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

scientific article

Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay.

scientific article published in June 2019

International network of cancer genome projects

scientific article

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

scientific article

Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer

scientific article

Intron-centric estimation of alternative splicing from RNA-seq data

scientific article

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

scientific article

Landscape of transcription in human cells

scientific article (publication date: 6 September 2012)

List of Contributors

LncATLAS database for subcellular localization of long noncoding RNAs

scientific article published on 06 April 2017

Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems

scientific article

Long noncoding RNAs with enhancer-like function in human cells

scientific article (publication date: October 2010)

Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins

scientific article published on June 2009

Modeling gene expression using chromatin features in various cellular contexts

scientific article (publication date: 13 June 2012)

Modelling and simulating generic RNA-Seq experiments with the flux simulator

scientific article

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

scientific article published on 20 August 2018

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

scientific article

Multiple non-collinear TF-map alignments of promoter regions

scientific article

Mutation patterns of amino acid tandem repeats in the human proteome

scientific article

NEAT1 Long Isoform Is Highly Expressed in Chronic Lymphocytic Leukemia Irrespectively of Cytogenetic Groups or Clinical Outcome

scientific article published on 13 March 2020

Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?

scientific article

Nucleosome positioning as a determinant of exon recognition

scientific article

Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages

scientific article published on 26 May 2022

Processive Recoding and Metazoan Evolution of Selenoprotein P: Up to 132 UGAs in Molluscs

scientific article published on 20 August 2019

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions

scientific article

Promoter-like epigenetic signatures in exons displaying cell type-specific splicing

scientific article published on 23 October 2015

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

scientific article

Publisher Correction: The tuatara genome reveals ancient features of amniote evolution

scientific article published on 18 August 2020

PyHIST: A Histological Image Segmentation Tool

scientific article published on 19 October 2020

RNA. Prescribing splicing

scientific article published on January 2015

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

scientific article published on 02 December 2019

Recent advances in functional genome analysis

scientific article published on 21 December 2018

Recent advances in gene structure prediction

scientific article published on June 2004

Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution

scientific article

Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition

scientific article

Relaxation of Selective Constraints Causes Independent Selenoprotein Extinction in Insect Genomes

scientific article (publication date: 13 August 2008)

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

scientific article published on 15 September 2013

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

scientific article

Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing

scientific article published on 22 April 2015

SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements

scientific article published on 29 January 2009

SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins

scientific article published on 19 June 2013

SNP and haplotype mapping for genetic analysis in the rat.

scientific article

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

scientific article

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

scientific article

SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans

scientific article

Selenoprofiles: A Computational Pipeline for Annotation of Selenoproteins

scientific article published in January 2018

Selenoprotein Gene Nomenclature

scientific article published on 19 September 2016

Sequence and analysis of chromosome 2 of Dictyostelium discoideum

scientific article published in Nature

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

scientific article

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

scientific article published on 12 September 2016

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

scientific article

Spatiotemporal Control of Forkhead Binding to DNA Regulates the Meiotic Gene Expression Program.

scientific article published on 19 January 2016

Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae

scientific article published on 12 November 2010

Structured RNAs in the ENCODE selected regions of the human genome

scientific article

Systematic evaluation of spliced alignment programs for RNA-seq data

scientific article

Tandem chimerism as a means to increase protein complexity in the human genome

scientific article

Ten Simple Rules on How to Organize a Scientific Retreat

scientific article (publication date: February 2017)

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

scientific article

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

scientific article

The European Genome-phenome Archive in 2021

scientific article published on 01 January 2022

The GEM mapper: fast, accurate and versatile alignment by filtration

scientific article

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

scientific article

The GTEx Consortium atlas of genetic regulatory effects across human tissues

scientific article

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

scientific article

The Long Non-Coding RNAs: A New (P)layer in the “Dark Matter” ⬇️

scientific article published on January 9, 2012

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

scientific article

The abundance of the long intergenic non-coding RNA 01087 differentiates between luminal and triple-negative breast cancers and predicts patient outcome

scientific article published on 14 October 2020

The discovery potential of RNA processing profiles

The discovery potential of RNA processing profiles.

scientific article

The effects of death and post-mortem cold ischemia on human tissue transcriptomes.

scientific article published on 13 February 2018

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima ⬇️

scientific article

The genome of melon (Cucumis melo L.).

scientific article

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

scientific article

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

scientific article published on 23 July 2020

The genomes of two key bumblebee species with primitive eusocial organization ⬇️

scientific article

The genomic basis of evolutionary differentiation among honey bees

scientific article published on 04 May 2021

The histone variant macroH2A is an epigenetic regulator of key developmental genes

scientific article

The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells.

scientific article

The impact of sex on gene expression across human tissues

scientific article

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The origins, evolution, and functional potential of alternative splicing in vertebrates

scientific article

The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues

scientific article published on 27 May 2020

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

scientific article published on 21 May 2018

The tuatara genome reveals ancient features of amniote evolution

scientific article published on 5 August 2020

Topoisomerase II regulates yeast genes with singular chromatin architectures

scientific article published on 09 August 2013

Towards a complete map of the human long non-coding RNA transcriptome

scientific article published on 01 September 2018

Transcription factor map alignment of promoter regions

scientific article

Transcriptional diversity during lineage commitment of human blood progenitors

scientific article

Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster

scholarly article

Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes

scientific article (publication date: 26 February 2013)

Transcriptome and genome sequencing uncovers functional variation in humans

scientific article

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

scientific article

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

scientific article

Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC)

Unravelling the hidden DNA structural/physical code provides novel insights on promoter location

scientific article published on 12 June 2013

Unweaving the meanings of messenger RNA sequences

scientific article published on July 2006

Using geneid to Identify Genes

article

Using geneid to identify genes

scientific article

Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls

scientific article published on September 2009

Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life

scientific article published on 06 March 2016

bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage

scientific article published on 28 December 2020

gff2aplot: Plotting sequence comparisons

scientific article published on 01 December 2003

ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization

scientific article published on 17 August 2018

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