Browsing by Author "Notredame, Cedric"

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  • 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 ...
  • 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 ...
  • 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 ...
  • Earl, Dent; Kemena, Carsten, 1983-; Chang, Jia-Ming, 1978-; Erb, Ionas; Notredame, Cedric; Paten, Benedict (Cold Spring Harbor Laboratory Press (CSHL Press), 2014)
    Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, ...
  • Floden, Evan (Universitat Pompeu Fabra, 2019-01-31)
    A multiple sequence alignment (MSA) provides a description of the relationship between biological sequences where columns represent a shared ancestry through an implied set of evolutionary events. The majority of research ...
  • 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 ...
  • Espinosa-Carrasco, José (Universitat Pompeu Fabra, 2018-05-14)
    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 ...
  • 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 ...
  • 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, ...
  • Bussotti, Giovanni (Universitat Pompeu Fabra, 2014-01-22)
    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 ...
  • Chang, Jia-Ming, 1978-; Taly, Jean-Francois; Erb, Ionas; Sung, Ting-Yi; Hsu, Wen-Lian; Tang, Chuan Yi; Notredame, Cedric; Su, Emily Chia-Yu (Public Library of Science (PLoS), 2013)
    Predicting protein functional classes such as localization sites and modifications plays a crucial role in function annotation. Given a tremendous amount of sequence data yielded from high-throughput sequencing experiments, ...
  • 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 ...
  • Villanueva Cañas, José Luis, 1984-; Fernández Fuentes, Narcís; Saul, Dominik; Kosinsky, Robyn Laura; Teyssier, Catherine; Rogalska, Malgorzata; Pegenaute Pérez, Ferran; Oliva Miguel, Baldomero; Notredame, Cedric; Beato, Miguel; Sharma, Priyanka (Elsevier, 2024)
    Peptidyl arginine deiminases (PADIs) catalyze protein citrullination, a post-translational conversion of arginine to citrulline. The most widely expressed member of this family, PADI2, regulates cellular processes that ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...

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