Received Invitations

Event Node Id Invitation Id Invitation Event date Organizer Id Last Update time Email Address Response Invitation
Selected publications
Qui som
Quiénes somos
AStalavista
sgp2
geneid
AcE
gff2ps
meta
mmeta
project
SECISaln
Projects
Publications
Publications
Publications
PhylomeDB
The Flux Capacitor
Nna1-like proteins are active metallocarboxypeptidases of a new and diverse M14 subfamily.
Publications - Evolutionary Genomics
A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells.
Sulfatases and sulfatase modifying factors: an exclusive and promiscuous relationship.
Active poly(ADPribose) metabolism in DNAase- and salt-resistant rat testis chromatin with high transcriptional activity/competence.
The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones.
T-Coffee
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics
gff2aplot
TrSDB: a proteome database of transcription factors.
Ecological Genomics Summer School in Bologna
Sample collection trip and a conference in Russia
Annual Group Photo 2008 - Bioinformatics and Genomics
Annual Group Photo 2009 - Bioinformatics and Genomics
gff2ps shirts in a group meeting
PRBB building
Parc de Recerca Biomèdica de Barcelona
groma
Research in our lab
Selection and mutation on the DNA level
Colleague in the field in Chukotka
Picture gallery
Prova de continguts amb biblio
Samovar
Field work in Chukotka
Pàgina de prova de group
Compensatory evolution
Fixing tanks in the field
Classification of common functional loops of kinase super-families.
ArchDB: automated protein loop classification as a tool for structural genomics.
A novel subfamily of mouse cytosolic carboxypeptidases.
Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm.
Experimental projects
Gene dosage and gene duplication
Selection and mutation on the DNA level
Evolutionary genomics
Metazoan mt-tRNAs
Theory
Environment for Tree Exploration (ETE)
Fastal - Fast alignment program
trimAl
Services and software
Margarita Meer
Fyodor Kondrashov
How much does it cost? Optimization of costs in sequence analysis of social science data
R-Coffee: a method for multiple alignment of non-coding RNA
R-Coffee: a web server for accurately aligning noncoding RNA sequences
Segment-based multiple sequence alignment
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods
Recent evolutions of multiple sequence alignment algorithms
Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time
M-Coffee: combining multiple sequence alignment methods with T-Coffee
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
The iRMSD: a local measure of sequence alignment accuracy using structural information
SAGA: sequence alignment by genetic algorithm
RAGA: RNA sequence alignment by genetic algorithm
COFFEE: an objective function for multiple sequence alignments
Optimization of ribosomal RNA profile alignments
T-Coffee: A novel method for fast and accurate multiple sequence alignment
Mocca: semi-automatic method for domain hunting
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
Recent progress in multiple sequence alignment: a survey
Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments
Computing multiple sequence/structure alignments with the T-coffee package
CaspR: a web server for automated molecular replacement using homology modelling
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment
3DCoffee: combining protein sequences and structures within multiple sequence alignments
APDB: a web server to evaluate the accuracy of sequence alignments using structural information
Tyler Alioto
Rainbow and PRBB building
Lab Members
Events
In the lab - November 2009
The histone variant macroH2A is an epigenetic regulator of key developmental genes.
Identifying protein-coding genes in genomic sequences.
Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins.
Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency.
The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells.
CROC: finding chromosomal clusters in eukaryotic genomes.
Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver.
Functional targets of the monogenic diabetes transcription factors HNF-1alpha and HNF-4alpha are highly conserved between mice and humans.
The genome sequence of taurine cattle: a window to ruminant biology and evolution.
A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins.
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.
ASTD: The Alternative Splicing and Transcript Diversity database.
The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome.
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.
Prediction of gene structure.
Sequence and analysis of chromosome 2 of Dictyostelium discoideum.
The genome sequence of the malaria mosquito Anopheles gambiae.
Comparative gene prediction in human and mouse.
Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster.
Characterization of mammalian selenoproteomes.
Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome.
Recent advances in gene structure prediction.
gff2aplot: Plotting sequence comparisons.
An assessment of gene prediction accuracy in large DNA sequences.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
The ENCODE (ENCyclopedia Of DNA Elements) Project.
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.
Gene organization features in A/T-rich organisms.
Comparison of splice sites in mammals and chicken.
Splice site identification by idlBNs.
Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition.
EGASP: collaboration through competition to find human genes.
Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.
Are splicing mutations the most frequent cause of hereditary disease?
Transcription factor map alignment of promoter regions.
Mutation patterns of amino acid tandem repeats in the human proteome.
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.
Tandem chimerism as a means to increase protein complexity in the human genome.
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family.
Unweaving the meanings of messenger RNA sequences.
EGASP: Introduction.
EGASP: the human ENCODE Genome Annotation Assessment Project.
GENCODE: producing a reference annotation for ENCODE.
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
Improving gene annotation using peptide mass spectrometry.
The implications of alternative splicing in the ENCODE protein complement.
Multiple non-collinear TF-map alignments of promoter regions.
Using geneid to identify genes.
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
Structured RNAs in the ENCODE selected regions of the human genome.
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations.
Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.
Evolution of genes and genomes on the Drosophila phylogeny.
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.
In silico meets in vivo.
SNP and haplotype mapping for genetic analysis in the rat.
Interoperability with Moby 1.0–it's better than sharing your toothbrush!
Efficient targeted transcript discovery via array-based normalization of RACE libraries.
A general definition and nomenclature for alternative splicing events.
Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes.
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.
Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila.
Initial sequencing and comparative analysis of the mouse genome.
The sequence of the human genome.
Evaluation of gene structure prediction programs.
Large-scale assignment of orthology: back to phylogenetics?
A combinatorial code for CPE-mediated translational control.
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.
Reconstruction of the proto-mitochondrial metabolism.
The human phylome.
An anaerobic mitochondrion that produces hydrogen.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
PhylomeDB: a database for genome-wide collections of gene phylogenies.
Michael Sammeth
Ionas Erb
Emanuele Raineri
Perceptions about postdocs
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome
Dmitry Ivankov
DeathBase
PATRONUS
Paolo Ribeca
Acquisition of prokaryotic genes by fungal genomes
Joining forces in the quest for orthologs
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.
PhylomeDB: a database for genome-wide collections of gene phylogenies.
Variation and evolution of biomolecular systems: searching for functional relevance.
Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin.
Computational approaches for the prediction of protein function in the mitochondrion.
Evolution of proteins and proteomes: a phylogenetics approach.
Shaping the mitochondrial proteome.
Prediction of protein function and pathways in the genome era.
Perceptions about postdocs.
Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence.
Mitochondria and peroxisomes and their role in disease
Phylogenomics and genome evolution through large-scale phylogenetics
Structural analyses of a hypothetical minimal metabolism.
Comparative genomics of fungal pathogens
Theories on gene duplication are classified
Meritxell Oliva Pavia
Thomas Lingner
dkormes
Inna Povolotskaya
Javier Diez
Presentation
Angelika - Status Update Group Meeting
Tyler - Status Update Group Meeting
Micha - Status Update Group Meeting
David Martin - Status Update Group Meeting
Thomas - Status Update Group Meeting
Hagen - Status Update Group Meeting
Colin - Status Update Group Meeting
Marco - Status Update Group Meeting
David González - Status Update Group Meeting
Annia - Status Update Group Meeting
Julien - Status Update Group Meeting
Paolo - Status Update Group Meeting
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
Origin and evolution of the peroxisomal proteome.
Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I).
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.
Comparative Bioinformatics
About us
Annotations for all by all - the BioSapiens network.
Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls.
ETE: A python Environment for Tree Exploration, published
trimAl 1.2 has been released
Project pictures
Project pictures
Project pictures
Project pictures
Peroxisome diversity and evolution.
gff2ps of the human genome
2X genomes - depth does matter.
ETE: a python Environment for Tree Exploration.
Artur Tymanyan
Shingo Suzuki
Oriol Pich Rosello
Peter Vlasov
Peter Vlasov
Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.
Evolution of spliceosomal introns following endosymbiotic gene transfer.
Immunity and other defenses in pea aphids, Acyrthosiphon pisum.
The pea aphid genome fully-sequenced.
Compensatory evolution and fitness valleys
Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression.
Nucleic Acids Research (2005): Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes
Human molecular genetics research at the International Centre for Genetic Engineering and Biotechnology.
TACC3-TSC2 maintains nuclear envelope structure and controls cell division.
DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death.
DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death.
David Gonzalez - Status Update Group Meeting
Sarah- Status Update Group Meeting
Julien - Status Update Group Meeting
Rory- Status Update Group Meeting
Andrea- Status Update Group Meeting
Spatial Clustering of Molecular Dynamics Trajectories in Protein Unfolding Simulations
Pedro Ferreira - Status Update Group Meeting
Joao Curado - Status Update Group Meeting
Analysis and manipulation of phylogenomic data using ETE
2007 group retreat
Group retreat 2010 (Vic)
Retreat 2008 (Nàquera)
CRG 2009
The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes.
Evolution of cell death pathways
Evolution of the eukaryotic cell: mitochondria and peroxisomes
Transcriptome genetics using second generation sequencing in a Caucasian population
From chromatin to splicing: RNA-processing as a total artwork
International network of cancer genome projects
Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
Nucleosome positioning as a determinant of exon recognition
Complete alternative splicing events are bubbles in splicing graphs
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
Filipe G. Vieira
keywordcloud
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB).
Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes.
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes (2010) Bioinformatics (Oxford, England)
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
From Saccharomyces cerevisiae to Candida glabrata in a few easy steps: important adaptations for an opportunistic pathogen.
Impact of the mitochondrial genetic background in complex III deficiency.
YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNALeu isoacceptors.
CRG Web Administrator
People
Re:
alicethomas
Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae
SymCurv
Joint CRG-CRM Meeting on Mathematics in Genomics and Systems Biology
New trends in protein sequence divergence
PhylomeDB v3.0 released
People
Software Engineer
Master student
MetaPhOrs
Publications - Gene Function and Evolution
The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates.
Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences.
Organism complexity anti-correlates with proteomic beta-aggregation propensity.
Similarities in the thermodynamics and kinetics of aggregation of disease-related Abeta(1-40) peptides.
Systematic in vivo analysis of the intrinsic determinants of amyloid Beta pathogenicity.
Characterisation of amyloid fibril formation by small heat-shock chaperone proteins human alphaA-, alphaB- and R120G alphaB-crystallins.
Life on the edge: a link between gene expression levels and aggregation rates of human proteins.
The distribution of residues in a polypeptide sequence is a determinant of aggregation optimized by evolution.
Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins.
Prediction of local structural stabilities of proteins from their amino acid sequences.
Towards quantitative predictions in cell biology using chemical properties of proteins.
The Zyggregator method for predicting protein aggregation propensities.
Molecular determinants of the aggregation behavior of alpha- and beta-synuclein.
Amyloid-like Aggregates Sequester Numerous Metastable Proteins with Essential Cellular Functions.
Translationally optimal codons associate with aggregation-prone sites in proteins.
Interactions in the native state of monellin, which play a protective role against aggregation.
Proteome-level interplay between folding and aggregation propensities of proteins.
Intrinsic determinants of neurotoxic aggregate formation by the amyloid beta peptide.
Physicochemical determinants of chaperone requirements.
Competition between folding, native-state dimerisation and amyloid aggregation in beta-lactoglobulin.
Mutational analysis of the aggregation-prone and disaggregation-prone regions of acylphosphatase.
Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins.
A relationship between mRNA expression levels and protein solubility in E. coli.
Amyloid formation by the pro-inflammatory S100A8/A9 proteins in the ageing prostate.
Competition between intramolecular and intermolecular interactions in an amyloid-forming protein.
Correlation between mRNA expression levels and protein aggregation propensities in subcellular localisations.
Position-dependent electrostatic protection against protein aggregation.
Predictor of Interactions with Molecular Chaperones
Predictor of Protein Amyloidogenicity
Predictor of Protein Folding Propensities
Predictor of Soluble Expression
A note on minimum variance theory and beyond.
BioMoby Web Services and Workflows
Judith Flo Gaya
Jørgen Skancke
priscilla
RGASP3/dnGASP
Assigning duplication events to relative temporal scales in genome-wide studies.
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.
Regulation of Candida glabrata oxidative stress resistance is adapted to host environment.
TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.
MetaPhOrs: orthologs and paralogs accross 829 genomes, based on multiple phylogenetic evidence
Alexandros Pittis
Services and software
[Long non-coding RNAs with enhancerlike function in human cells.]
Long Noncoding RNAs as Enhancers of Gene Expression
The origins, evolution and functional potential of alternative splicing in vertebrates
Group in 2009
Databases and Tools
treeKO
Detection of Early Locomotor Abnormalities in a Drosophila Model of Alzheimer's Disease.
Effects of the known pathogenic mutations on the aggregation pathway of the amyloidogenic peptide of Apolipoprotein A-I
Predicting protein associations with long noncoding RNAs
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia
Maik Röder
Romain Derelle
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gene finding in the chicken genome.
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
Publications
ionas erb
Thomas Derrien
France Denoeud
Micha Sammeth
Genis Parra
Enrique Blanco
Josep Francesc April
Xavier Fustero
Christoforos Nikolaou
Jan-Jaap Wesselink
Arnaud Kerhornou
Paolo Ribeca
Tyler Alioto
The catRAPID method
A user's guide to the encyclopedia of DNA elements (ENCODE).
CycADS: an annotation database system to ease the development and update of BioCyc databases.
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
A midzone-based ruler adjusts chromosome compaction to anaphase spindle length.
Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions.
MULTICHANNEL SEQUENCE ANALYSIS APPLIED TO SOCIAL SCIENCE DATA
{How Much Does it Cost? Optimization of Costs in Sequence Analysis of Social Science Data}
Exploiting parallelism on progressive alignment methods
Disulfide bonds reduce the toxicity of the amyloid fibrils formed by an extracellular protein
Metastability of Native Proteins and the Phenomenon of Amyloid Formation.
SPIn: model selection for phylogenetic mixtures via linear invariants.
Alexandros
Interplay between BRCA1 and RHAMM Regulates Epithelial Apicobasal Polarization and May Influence Risk of Breast Cancer
Carla
ALS mutations in FUS cause neuronal dysfunction and death in Caenorhabditis elegans by a dominant gain-of-function mechanism
Evolutionary histories of expanded peptidase families in Schistosoma mansoni.
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.
A user's guide to the encyclopedia of DNA elements (ENCODE).
Project pictures
Jørgen Skancke
Angelika Merkel
Project pictures
CLL
RGASP-ENCODE
Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells
schadterhode1985
Federico Agostini
Matteo Bellucci
Priscilla De Rosa
Sequence-based prediction of protein solubility
fagostini
Fast computation and applications of genome mappability.
Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors.
The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter"
Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode.
Evolution of the ferritin family in vertebrates
overlap
People
Group and tree (March 2012)
compmerge
Composition and evolution of the vertebrate and Mammalian selenoproteomes
Selection of marker genes using whole-genome DNA polymorphism analysis.
Toward community standards in the quest for orthologs.
Expression in Drosophila of Tandem Aβ Peptides Provides Insights Into the Link Between Aggregation and Neurotoxicity
DnaK Functions as a Central Hub in the E. coli Chaperone Network
Group picture (March 2012, Vic)
biotechnology
Multiple sequence alignment based on dynamic weighted guidance tree.
Use of ChIP-Seq data for the design of a multiple promoter-alignment method.
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.
AMPA: an automated web server for prediction of protein antimicrobial regions.
BlastR–fast and accurate database searches for non-coding RNAs.
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.
The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences.
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.
Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.
A user-friendly web portal for T-Coffee on supercomputers.
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.
A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis.
T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.
Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite proliferation and viability.
Computing multiple sequence/structure alignments with the T-coffee package.
Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
Predicting phenotypic traits of prokaryotes from protein domain frequencies.
Upcoming challenges for multiple sequence alignment methods in the high-throughput era.
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences
Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast
The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion
Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters
Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions.
STRIKE: evaluation of protein MSAs using a single 3D structure.
Long Noncoding RNAs with Enhancer-like Function in Human Cells
A genome-wide screen for genetic variants that modify the recruitment of REST to its target genes
kullye
Comparative Genomics
Toni Hermoso Pulido
The tomato genome sequence provides insights into fleshy fruit evolution
Charles (Karolos) Chapple
An encyclopedia of mouse DNA elements (Mouse ENCODE)
Landscape of transcription in human cells
An integrated encyclopedia of DNA elements in the human genome
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
kevyin
The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties.
Mitochondrial genome variability within the Candida parapsilosis species complex.
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi.
The kinomes of apicomplexan parasites.
vicky
Adina
esaus
Modeling gene expression using chromatin features in various cellular contexts.
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.
Measurements of spontaneous rates of mutations in the recent past and the near future
Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
Sequence space and the ongoing expansion of the protein universe
Stop codons in bacteria are not selectively equivalent
Acrocephalus orinus: a case of mistaken identity
Gene duplication as a mechanism of genomic adaptation to a changing environment
Epistasis as the primary factor in molecular evolution
The evolution of gene duplications: classifying and distinguishing between models
Rate of sequence divergence under constant selection
Gene Dosage and Duplication
Translation termination in pyrrolysine-utilizing archaea.
Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene.
Hypermutable non-synonymous sites are under stronger negative selection.
Nested genes and increasing organizational complexity of metazoan genomes.
Birds of the Krasnoye Lake area (South Chukotka)
Selection for Functional Uniformity of tuf Duplicates in Gamma-proteobacteria
A Manually Curated Database of Tetrapod Mitochondrially Encoded tRNA Sequences and Secondary Structures
Extensive Parallelism in Protein Evolution
Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites
Conversion and Compensatory Evolution of the Gamma-crystallin Genes and Identification of a Cataractogenic Mutation that Reverses the Sequence of the Human CRYGD gene to an Ancestral State
Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius
Role of Selection in Fixation of gene Duplications
Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis
Evolution of Glyoxylate Cycle Enzymes in Metazoa: Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation
In Search of the Limits of Evolution
Prediction of Pathogenic Mutations in Mitochondrially Encoded Human tRNAs
A Universal Trend of Amino acid gain and loss in Protein Evolution
[The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine tRNA in the Nine-banded Armadillo Dasypus Novemcinctus]
Distribution of the Strength of Selection Against Amino acid Replacements in Human Proteins
[The Analysis of Monomer Sequences in Protein and tRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution]
The Functional Genomic Distribution of Protein Divergence in two Animal Phyla: Coevolution, Genomic Conflict, and Constraint
A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of gene Duplications
Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial tRNAs
Prediction of Functional Sites by Analysis of Sequence and Structure Conservation
Positive Selection at Sites of Multiple Amino acid Replacements Since Rat-mouse Divergence
Bioinformatical Assay of Human gene Morbidity
Impact of Selection, Mutation rate and Genetic Drift on Human Genetic Variation
Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences
Evolution of the Mouse polyubiquitin-C gene
Selection for Short Introns in Highly Expressed Genes
Selection in the Evolution of gene Duplications
Dobzhansky-Muller Incompatibilities in Protein Evolution
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.
Multidimensional Epistasis and the Disadvantage of sex
Use of Mutation Spectra Analysis Software
Presence of ATG Triplets in 5' Untranslated Regions of Eukaryotic cDNAs Correlates with a 'weak' Context of the Start Codon
Footprints of Primordial Introns on the Eukaryotic Genome: Still no Clear Traces
Origin of Alternative Splicing by Tandem exon Duplication
No Footprints of Primordial Introns in a Eukaryotic Genome
Interactions Among Quantitative Traits in the Course of Sympatric Speciation
The importance of epistasis
Evolutionary Genomics
Resumé
My research interests
angelakswan
The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology.
Bioinformatician
A rationally designed six-residue swap generates comparability in the aggregation behavior of α-synuclein and β-synuclein
Predictions of protein–RNA interactions
Neurodegeneration as an RNA disorder
X-inactivation: quantitative predictions of protein interactions in the Xist network
weight loss
Grape RNA-Seq analysis pipeline environment
Intron-Centric Estimation of Alternative Splicing from RNA-seq data
The GEM mapper: fast, accurate and versatile alignment by filtration
Modelling and simulating generic RNA-Seq experiments with the flux simulator
Estimation of alternative splicing variability in human populations
veralmdias
james2012
Home
Compensatory evolution and epistasis
Long non-coding RNAs in Huntington's disease neurodegeneration.
Join our lab
Marianela Masin
People
Gene Function and Evolution
X-inactivation
Neurodegenerative diseases: Quantitative predictions of protein-RNA interactions
Predictor of protein-RNA interactions
CPEB1 coordinates alternative 3'-UTR formation with translational regulation
Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes
The Protein-RNA world
Selenoprofiles2
Learn a trade for a rainy day
Autogenous Interactions
Neurodegenerative diseases: Quantitative predictions of protein-RNA interactions
Fermi's way
Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus.
The genome of melon (Cucumis melo L.).
Jean François Taly
Andrea Tanzer
David González
Anna Magdalena Kedzierska
Hagen Ulrich Tilgner
Pedro Gabriel Ferreira
David Martin
collaborator
Chiara Medoro
jmonlong
maikroeder
Michael Breen
Carsten Kemena
Roderic Guigó Serra
abreschi
Lab Technician
Didac Santesmasses
Oscar Gonzalez
Julien Lagarde
Giovanni Bussoti
Sarah Djebali
dkedra
Romina Garrido Enamorado
João Curado
Cedric Notredame
Jamming Chang
Toni Gabaldón
apittis
Fran Supek
Gabriela Aguileta
mmarcet
Salvador Capella Gutierrez
Gian Gaetano Tartaglia
Rory Johnson
ijunier
Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates.
Comparative transcriptomics of early dipteran development.
Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes.
Functional and evolutionary implications of gene orthology.
Measuring guide-tree dependency of inferred gaps in progressive aligners.
Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.
FUNGALOXPHOS: An integrated database for oxidative phosphorylation in fungi.
The Genotype-Tissue Expression (GTEx) project.
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location
SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins
Yun Yan
Group retreat (Vic) 2013
Group at CRG, 2013
Xavier Estivill
Geòrgia Escaramis
Kelly Rabionet
Open positions in Gabaldon's lab
People
Services and software
PeSV-Fisher
Francisco Câmara Ferreira
Improving data and knowledge management to better integrate health care and research
Topoisomerase II regulates yeast genes with singular chromatin architectures
Genomics and Disease
Transcriptome and genome sequencing uncovers functional variation in humans
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
Damien de Vienne
catRAPID omics: a web server for large-scale prediction of protein-RNA interactions
Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein
Tobias Warnecke
Grape
LncRNA Data Page - Gencode Version 7 Annotations
Gene Prediction/Genome Annotation
Rectangular cladogram tree-of-life built using geneid-trained species
Long Noncoding RNAs with Enhancer-like Function in Human Cells
Development of methods to analyze the relationship between chromatin and splicing
Long Non-Coding RNA (lncRNA) page
Project: Investigating the function of new long non-coding RNAs from the human genome
High throughput transcript discovery via array based normalisation of RACE libraries
Multiple-species conservation vs evolvability: case study of splicing regulators
Evaluation of Gene Prediction Programs
Gene Prediction Software: geneid
Characterization of the Eukaryotic Selenoproteome
Gene Prediction based on Comparative Genomics
Computational Analysis of Splicing
Simple Sequences in Proteins and DNA
Visualization Tools: gff2ps and gff2aplot
Comparative Analysis of Virus Sequences
Knowledge Extraction from Biological Databases
Other Research at Our Lab
Gene Predictions
Publications
U12DB: a database of orthologous U12-type spliceosomal introns
Genome Research (2005): Comparison of Splice Sites in Mammals and Chicken
Bioinformatics (2004): Splice site identification by idlBNs
Science (2003): Selenoprotein gene prediction in Human
PNAS (2003): Comparison of human and mouse genomes followed by experimental validation
Genome Research (2003): Comparative Gene Prediction in Human and Mouse
Genome Research (2000): Gene Prediction Programs Evaluation in Large DNA Sequences
Genome Research (2000): geneid in Drosophila melanogaster
Genomics (1996): Evaluation of gene structure prediction programs
EMBO reports (2001): Selenoprotein gene prediction in the Fly
BMC Bioinformatics: Multiple Non-Collinear TF-map Alignments of Promoter Regions
PLoS Computational Biology (2006): Transcription Factor Map Alignment of Promoter Regions
Genome Biology (2006): EGASP: The human ENCODE GENOME ANNOTATION ASSESSMENT PROJECT
Services and software
Events
Gallery
Model fitting for mixture models
Homepage
SymCurv
SusieYu
PhylomeDB V4 released
Assessment of transcript reconstruction methods for RNA-seq
Systematic evaluation of spliced alignment programs for RNA-seq data
SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
Transcriptome characterization by RNA sequencing (The CLL project)
The Group 2012
The group 2011
The group 2013
The group 2010 B
epalumbo
Lateral Block
Constitutive patterns of gene expression regulated by RNA-binding proteins
postdoc
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fernandosiddins
ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection
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jonellealbritton
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Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
Gabaldon group in 2014
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Comparative analysis of the transcriptome across distant species.
Identification of genetic variants associated with alternative splicing using sQTLseekeR.
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sQTLseekeR
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Computational Biology of RNA Processing
Methods for RNAseq (NGS) data analysis
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minervalanglands
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IRBIS: a systematic search for conserved complementarity.
Transcriptional diversity during lineage commitment of human blood progenitors.
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
elda
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The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima.
Principles of regulatory information conservation between mouse and human.
A comparative encyclopedia of DNA elements in the mouse genome.
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bernadettearedy
Leszek Pryszcz
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eulaliaaphzozseq
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RNA. Prescribing splicing
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jacelyncollings
BLUEPRINT to decode the epigenetic signature written in blood
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
GENCODE: The reference human genome annotation for The ENCODE Project
Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs
Domains of genome-wide gene expression dysregulation in Down's syndrome
Transcriptional Signatures of Viral Control in HIV-1 Infected South African Women.
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quentinvalasquez
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Defining functional DNA elements in the human genome
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Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
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