Browsing by Author "Notredame, Cedric"

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  • A comparative encyclopedia of DNA elements in the mouse genome
    Yue, Feng; Breschi, Alessandra, 1988-; Pervouchine, Dmitri D.; Djebali, Sarah; Prieto Barja, Pablo, 1986-; Lagarde, Julien; Bussotti, Giovanni, 1983-; Tanzer, Andrea; Notredame, Cedric; Guigó Serra, Roderic; Ren, Bing; The Mouse Encyclopedia of DNA Elements (ENCODE) Consortium (Nature Publishing Group, 2014)
    The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into ...
  • A field guide for the compositional analysis of any-omics data
    Quinn, Thomas P.; Erb, Ionas; Gloor, Greg; Notredame, Cedric; Richardson, Mark F.; Crowley, Tamsyn M. (Oxford University Press, 2019)
    Background: Next-generation sequencing (NGS) has made it possible to determine the sequence and relative abundance of all nucleotides in a biological or environmental sample. A cornerstone of NGS is the quantification of ...
  • A long noncoding RNA promotes parasite differentiation in African trypanosomes
    Guegan, Fabien; Rajan, K. Shanmugha; Bento, Fábio; Pinto-Neves, Daniel; Sequeira, Mariana; Gumińska, Natalia; Mroczek, Seweryn; Dziembowski, Andrzej; Cohen-Chalamish, Smadar; Doniger, Tirza; Galili, Beathrice; Estévez, Antonio M.; Notredame, Cedric; Michaeli, Shulamit; Figueiredo, Luisa M. (American Association for the Advancement of Science (AAAS), 2022)
    The parasite Trypanosoma brucei causes African sleeping sickness that is fatal to patients if untreated. Parasite differentiation from a replicative slender form into a quiescent stumpy form promotes host survival and ...
  • An intrinsically disordered proteins community for ELIXIR
    Davey, Norman E.; Notredame, Cedric; Tosatto, Silvio C.E. (F1000Research, 2019)
    Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments ...
  • Big behavioral data analysis : computational methods for the study of continuous recordings behavior
    Espinosa-Carrasco, José (Universitat Pompeu Fabra, 2016-11-08)
    New high-throughput behavioral systems enable the recording of continuous behavioral sequences with an unprecedented richness of signals and a deep temporal resolution. Automated systems offer neuroscience the opportunity ...
  • CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis
    Ounzain, Samir; Micheletti, Rudi; Arnan Ros, Carme; Plaisance, Isabelle; Cecchi, Dario; Schroen, Blanche; Reverter, Ferran; Alexanian, Michael; Gonzales, Christine; Ng, Shi Yan; Bussotti, Giovanni, 1983-; Pezzuto, Iole; Notredame, Cedric; Heymans, Stephane; Guigó Serra, Roderic; Johnson, Rory; Pedrazzini, Thierry (Elsevier, 2015)
    Long noncoding RNAs (lncRNAs) are emerging as important regulators of developmental pathways. However, their roles in human cardiac precursor cell (CPC) remain unexplored. To characterize the long noncoding transcriptome ...
  • Combined Treatment With Environmental Enrichment and (-)-Epigallocatechin-3-Gallate Ameliorates Learning Deficits and Hippocampal Alterations in a Mouse Model of Down Syndrome
    Catuara Solarz, Silvina, 1986-; Espinosa-Carrasco, José; Erb, Ionas; Langohr, Klaus; Gonzalez, Juan Ramon; Notredame, Cedric; Dierssen, Mara (Society for Neuroscience, 2016)
    Intellectual disability in Down syndrome (DS) is accompanied by altered neuro-architecture, deficient synaptic plasticity, and excitation-inhibition imbalance in critical brain regions for learning and memory. Recently, ...
  • Detecting and comparing non-coding RNAs
    Bussotti, Giovanni, 1983- (Universitat Pompeu Fabra, 2013-01-23)
    In recent years there has been a growing interest in the field of non-coding RNA. This surge is a direct consequence of the discovery of a huge number of new non-coding genes, and of the finding that many of these transcripts ...
  • Editorial: NAR Genomics and Bioinformatics: a new journal for reproducible genomics in the Big Data era
    Notredame, Cedric (Oxford University Press, 2019)
  • Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
    Pervouchine, Dmitri D.; Djebali, Sarah; Breschi, Alessandra, 1988-; Prieto Barja, Pablo, 1986-; Lagarde, Julien; Bussotti, Giovanni, 1983-; Monlong, Jean; Notredame, Cedric; Guigó Serra, Roderic; Gingeras, Thomas R. (Nature Pub. Group, 2015)
    Mice have been a long-standing model for human biology and disease. Here we characterize, by RNA sequencing, the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse ...
  • Expression divergence of chemosensory genes between drosophila sechellia and its sibling species and its implications for host shift
    Shiao, Meng-Shin; Chang, Jia-Ming, 1978-; Fan, Wen-Lang; Jade Lu, Mei-Yeh; Notredame, Cedric; Fang, Shu; Kondo, Rumi; Li, Wen-Hsiung (Oxford University Press, 2015)
    Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species Drosophila melanogaster and Drosophila simulans. Although several odorant binding ...
  • Extinction and reinstatement of an operant responding maintained by food in different models of obesity
    Burokas, Aurelijus, 1982-; Martín García, Elena, 1975-; Espinosa-Carrasco, José; Erb, Ionas; McDonald, Jerome; Notredame, Cedric; Dierssen, Mara; Maldonado, Rafael, 1961- (Wiley-Blackwell, 2018)
    A major problem in treating obesity is the high rate of relapse to abnormal food-taking habits after maintaining an energy balanced diet. Alterations of eating behavior such as compulsive-like behavior and lack of self-control ...
  • Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania
    Cuypers, Bart; Meysman, Pieter; Erb, Ionas; Bittremieux, Wout; Valkenborg, Dirk; Baggerman, Geert; Mertens, Inge; Sundar, Shyam; Khanal, Basudha; Notredame, Cedric; Dujardin, Jean-Claude; Domagalska, Malgorzata A.; Laukens, Kris (Public Library of Science (PLoS), 2022)
    Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually ...
  • Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
    Vlasova, Anna; Capella Gutiérrez, Salvador Jesús, 1985-; Erb, Ionas; Cámara, Francisco; Prieto Barja, Pablo, 1986-; Kedra, Darek; González Navarrete, Irene, 1983-; Cozzuto, Luca; Gómez Garrido, Jèssica; Aguilar Morón, María Asunción; Andreu Somavilla, Núria; Zehnsdorf, Maik; Alioto, Tyler; Notredame, Cedric; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic (BioMed Central, 2016)
    Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million ...
  • High performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools
    Orobitg, Miquel; Guirado, Fernando; Cores, Fernando; Lladós, Jordi; Notredame, Cedric (Elsevier, 2015)
    Multiple Sequence Alignment (MSA) is essential for a wide range of applications in Bioinformatics. Traditionally, the alignment accuracy was the main metric used to evaluate the goodness of MSA tools. However, with the ...
  • Highly significant improvement of protein sequence alignments with AlphaFold2
    Baltzis, Athanasios; Mansouri, Leila; Jin, Suzanne; Langer, Björn E.; Erb, Ionas; Notredame, Cedric (Oxford University Press, 2022)
    Motivation: Protein sequence alignments are essential to structural, evolutionary and functional analysis, but their accuracy is often limited by sequence similarity unless molecular structures are available. Protein ...
  • How should we measure proportionality on relative gene expression data?
    Erb, Ionas; Notredame, Cedric (Springer, 2016)
    Correlation is ubiquitously used in gene expression analysis although its validity as an objective criterion is often questionable. If no normalization reflecting the original mRNA counts in the cells is available, correlation ...
  • Impact of recent protein structure prediction methods on homology, evolutionary and functional inference
    Baltzis, Athanasios (Universitat Pompeu Fabra, 2023-03-28)
    Recent advances in deep learning techniques have revolutionised protein structure modelling. Since AlphaFold2’s release, a set of tools have now become available to predict native-like structures at near-experimental ...
  • Improved definition of the mouse transcriptome via targeted RNA sequencing
    Bussotti, Giovanni, 1983-; Leonardi, Tommaso; Clark, Michael B.; Mercer, Tim R.; Crawford, Joanna; Malquori, Lorenzo; Notredame, Cedric; Dinger, Marcel E.; Mattick, John S.; Enright, Anton J. (Cold Spring Harbor Laboratory Press (CSHL Press), 2016)
    Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied ...
  • Improving the accuracy and the efficiency of multiple sequence alignment methods
    Kemena, Carsten, 1983- (Universitat Pompeu Fabra, 2012-12-12)
    Sequence alignment is one of the basic methods to compare biological sequences and the cornerstone of a wide range of different analyses. Due to this privileged position at the beginning of many studies its accuracy is of ...