Browsing by Author "Martí Renom, Marc A."

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  • Trussart, Marie, 1985-; Serra, François; Baù, Davide; Junier, Ivan; Serrano Pubull, Luis, 1982-; Martí Renom, Marc A. (Oxford University Press, 2015)
    Restraint-based modeling of genomes has been recently explored with the advent of Chromosome Conformation Capture (3C-based) experiments. We previously developed a reconstruction method to resolve the 3D architecture of ...
  • Serra, François; Baù, Davide; Goodstadt, Michael; Castillo Andreo, David; Filion, Guillaume; Martí Renom, Marc A. (Public Library of Science (PLoS), 2017)
    The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies ...
  • Baeza Delgado, Carlos; von Heijne, Gunnar; Martí Renom, Marc A.; Mingarro, Ismael (Nature Publishing Group, 2016)
    The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix ...
  • Mendieta Esteban, Julen (Universitat Pompeu Fabra, 2021-01-11)
    Genome spatial organisation and transcriptional activity are tightly coordinated to ensure the correct function of the cell. Thus, proper understanding of the chromatin organisation is needed to deepen into the processes ...
  • Galan Martínez, Silvia (Universitat Pompeu Fabra, 2020-12-21)
    El desenvolupament de tècniques experimentals basades en la captura de la conformació genòmica (3C), han aportat informació rellevant sobre l’estructura del genoma. En particular el Hi-C, un derivat del 3C, el qual s’ha ...
  • Goodstadt, Mike N.; Martí Renom, Marc A. (Elsevier, 2019)
    Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the ...
  • Sparavier, Aleksandra (2022-06-10)
    Chromosomal translocation are large-scale genome rearrangements found in several cancers. They are formed when two (or more) non-homologous chromosomes interchange large parts as a result of erroneous DNA repair after ...
  • Stik, Grégoire; Vidal, Enrique; Barrero, Mercedes; Cuartero, Sergi; Vila-Casadesús, Maria; Mendieta Esteban, Julen, 1992-; Tian, Tian V.; Choi, Jinmi; Berenguer, Clara; Abad, Amaya; Borsari, Beatrice, 1992-; Le Dily, François; Cramer, Patrick; Martí Renom, Marc A.; Stadhouders, Ralph; Graf, T. (Thomas) (Nature Research, 2020)
    Three-dimensional organization of the genome is important for transcriptional regulation1-7. In mammals, CTCF and the cohesin complex create submegabase structures with elevated internal chromatin contact frequencies, ...
  • Trussart, Marie, 1985-; Yus, Eva; Martínez, Sira; Baù, Davide; Tahara, Yuhei O.; Pengo, Thomas; Widjaja, Michael; Kretschmer, Simon; Swoger, Jim; Djordjevic, Steven P.; Turnbull, Lynne; Whitchurch, Cynthia B.; Miyata, Makoto; Martí Renom, Marc A.; Lluch-Senar, Maria 1982-; Serrano Pubull, Luis, 1982- (Nature Publishing Group, 2017)
    DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional ...
  • Sandoval Velasco, Marcela; Rodríguez, Juan Antonio; Pérez Estrada, Cynthia; Zhang, Guojie; Lieberman Aiden, Erez; Martí Renom, Marc A.; Gilbert, M Thomas; Smith, Oliver (Oxford University Press, 2020)
    Background: Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the ...
  • Soler-Vila, Paula; Cuscó Pons, Pol, 1987-; Farabella, Irene; Di Stefano, Marco; Martí Renom, Marc A. (Oxford University Press, 2020)
    The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called ...
  • Rajewsky, Nicolaus; Bertero, Michela G.; Martí Renom, Marc A.; LifeTime Community (Nature Research, 2020)
    LifeTime aims to track, understand and target human cells during the onset and progression of complex diseases and their response to therapy at single-cell resolution. This mission will be implemented through the development ...
  • Martínez Jiménez, Francisco; Martí Renom, Marc A. (Public Library of Science (PLoS), 2015)
    Target identification is essential for drug design, drug-drug interaction prediction, dosage adjustment and side effect anticipation. Specifically, the knowledge of structural details is essential for understanding the ...
  • Soler Vila, Paula (Universitat Pompeu Fabra, 2020-01-10)
    High-throughput Chromosome Conformation Capture (3C) techniques have provided a comprehensive overview of the genome architecture. Hi-C, a derivative of 3C, has become a reference technique to study the 3D chromatin structure ...
  • Vidal Ocabo, Enrique; Le Dily, François; Quilez Oliete, Javier; Stadhouders, Ralph; Cuartero, Yasmina; Graf, T. (Thomas); Martí Renom, Marc A.; Beato, Miguel; Filion, Guillaume (Oxford University Press, 2018)
    The three-dimensional conformation of genomes is an essential component of their biological activity. The advent of the Hi-C technology enabled an unprecedented progress in our understanding of genome structures. However, ...
  • Sali, Andrej; Martí Renom, Marc A.; Westbrook, John D. (Elsevier, 2015)
    Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the ...
  • Espadaler, Jordi; Eswar, Narayanan; Querol, Enrique; Avilés, Francesc Xavier; Sali, Andrej; Martí Renom, Marc A.; Oliva Miguel, Baldomero (BioMed Central, 2008)
    Background: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein ...
  • Álvarez-González, Lucía; Arias-Sardá, Cristina; Montes-Espuña, Laia; Marín-Gual, Laia; Vara, Covadonga; Lister, Nicholas C.; Cuartero, Yasmina; Garcia, Francisca; Deakin, Janine; Renfree, Marilyn B.; Robinson, Terence J.; Martí Renom, Marc A.; Waters, Paul D.; Farré, Marta; Ruiz Herrera, Aurora (Elsevier, 2022)
    Studying the similarities and differences in genomic interactions between species provides fertile grounds for determining the evolutionary dynamics underpinning genome function and speciation. Here, we describe the ...
  • Martínez-Jiménez, Francisco, 1988-; Overington, John P.; Al-Lazikani, Bissan; Martí Renom, Marc A. (Nature Publishing Group, 2017)
    Drug resistance is one of the major problems in targeted cancer therapy. A major cause of resistance is changes in the amino acids that form the drug-target binding site. Despite of the numerous efforts made to individually ...

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