Browsing by Author "Filion, Guillaume"

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  • Pokusaeva, Victoria O.; Usmanova, Dinara R.; Putintseva, Ekaterina V.; Espinar, Lorena; Sarkisyan, Karen S.; Mishin, Alexander S.; Bogatyreva, Natalya S.; Ivankov, Dmitry N.; Akopyan, Arseniy V.; Avvakumov, Sergey Ya; Povolotskaya, Inna, 1986-; Filion, Guillaume; Carey, Lucas, 1980-; Kondrashov, Fyodor A., 1979- (Public Library of Science (PLoS), 2019)
    Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the ...
  • Filion, Guillaume (MDPI, 2018)
    Seeding heuristics are the most widely used strategies to speed up sequence alignment in bioinformatics. Such strategies are most successful if they are calibrated, so that the speed-versus-accuracy trade-off can be ...
  • 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 ...
  • Filion, Guillaume; Cortini, Ruggero; Zorita, Eduard (Frontiers, 2020)
    The increasing throughput of DNA sequencing technologies creates a need for faster algorithms. The fate of most reads is to be mapped to a reference sequence, typically a genome. Modern mappers rely on heuristics to gain ...
  • Bauer, Moritz, 1987-; Payer, Bernhard; Filion, Guillaume (Wiley, 2022)
    The spatial organization of genomes is becoming increasingly understood. In mammals, where it is most investigated, this organization ties in with transcription, so an important research objective is to understand whether ...
  • Bauer, Moritz, 1987-; Vidal, Enrique; Zorita, Eduard; Üresin, Nil; Pinter, Stefan F.; Filion, Guillaume; Payer, Bernhard (Nature Research, 2021)
    A hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments, and into topologically associating domains (TADs). Both structures were regarded to be absent from the ...
  • Corrales Berjano, Marc, 1984-; Rosado, Aránzazu; Cortini, Ruggero; van Arensbergen, Joris; van Steensel, Bas; Filion, Guillaume (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)
    Housekeeping genes of animal genomes cluster in the same chromosomal regions. It has long been suggested that this organization contributes to their steady expression across all the tissues of the organism. Here, we show ...
  • Le Dily, François; Baù, Davide; Pohl, Andy, 1979-; Vicent, Guillermo Pablo; Serra, François; Soronellas, Daniel; Castellano, Giancarlo; Wright, Roni H.G.; Ballare, Cecilia Julia; Filion, Guillaume; Marti-Renom, Marc A.; Beato, Miguel (Cold Spring Harbor Laboratory Press (CSHL Press), 2014)
    The human genome is segmented into topologically associating domains (TADs), but the role of this conserved organization during transient changes in gene expression is not known. Here we describe the distribution of ...
  • Cuscó Pons, Pol, 1987- (Universitat Pompeu Fabra, 2017-12-13)
    Des de l’aparició de les tecnologies de seqüenciació d’alt rendiment, els conjunts de dades biològiques han esdevingut cada cop més grans i complexes, la qual cosa els fa pràcticament impossibles d’interpretar manualment. ...
  • Corrales, Marc; Cuscó, Pol; Usmanova, Dinara R.; Chen, Heng-Chang; Bogatyreva, Natalya S.; Filion, Guillaume; Ivankov, Dmitry N. (Public Library of Science (PLoS), 2015)
    The prediction of protein folding rates is a necessary step towards understanding the principles of protein folding. Due to the increasing amount of experimental data, numerous protein folding models and predictors of ...
  • 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, ...
  • Chen, Heng-Chang; Martínez Vesga, Javier Pablo; Zorita, Eduard; Meyerhans, Andreas; Filion, Guillaume (Nature Publishing Group, 2017)
    The main obstacle to curing HIV is the presence of latent proviruses in the bodies of infected patients. The partial success of reactivation therapies suggests that the genomic context of integrated proviruses can interfere ...
  • Filion, Guillaume (BioMed Central, 2015)
    The two-sample Kolmogorov-Smirnov (KS) test is often used to decide whether two random samples have the same statistical distribution. A popular modification of the KS test is to use a signed version of the KS statistic ...
  • Lucic, Bojana; Chen, Heng-Chang; Kuzman, Maja; Zorita, Eduard; Wegner, Julia; Minneker, Vera; Wang, Wei; Fronza, Raffaele; Laufs, Stefanie; Schmidt, Manfred; Stadhouders, Ralph; Roukos, Vassilis; Vlahovicek, Kristian; Filion, Guillaume; Lusic, Marina (Nature Research, 2019)
    HIV-1 recurrently targets active genes and integrates in the proximity of the nuclear pore compartment in CD4+ T cells. However, the genomic features of these genes and the relevance of their transcriptional activity for ...
  • Zorita, Eduard; Cuscó Pons, Pol, 1987-; Filion, Guillaume (Oxford University Press, 2015)
    Motivation: The increasing throughput of sequencing technologies offers new applications and challenges for computational biology. In many of those applications, sequencing errors need to be/ncorrected. This is particularly ...
  • Pokusaeva, Victoria O.; Rosado Diez, Aránzuru; Espinar, Lorena; Torelló Pérez, Albert; Filion, Guillaume (BioMed Central, 2022)
    Background: Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the ...
  • Corrales Berjano, Marc, 1984- (Universitat Pompeu Fabra, 2018-01-19)
    This thesis reports the study of chromatin composition and conformation on the expression of integrated reporters at thousands of genomic locations in the Drosophila genome. We have adapted and improved a technology ...
  • Vansant, Gerlinde; Chen, Heng-Chang; Zorita, Eduard; Trejbalová, Katerina; Miklík, Dalibor; Filion, Guillaume; Debyser, Zeger (Oxford University Press, 2020)
    HIV-1 persists lifelong in memory cells of the immune system as latent provirus that rebounds upon treatment interruption. Therefore, the latent reservoir is the main target for an HIV cure. Here, we studied the direct ...
  • Cortini, Ruggero; Filion, Guillaume (Nature Research, 2018)
    All organisms regulate transcription of their genes. To understand this process, a complete understanding of how transcription factors find their targets in cellular nuclei is essential. The DNA sequence and other variables ...
  • Stadhouders, Ralph; Vidal Ocabo, Enrique; Serra, François; Di Stefano, Bruno, 1984-; Le Dily, François; Quilez Oliete, Javier; Gómez, Antonio; Collombet, Samuel; Berenguer, Clara; Cuartero, Yasmina; Hecht, Jochen; Filion, Guillaume; Beato, Miguel; Martí Renom, Marc A.; Graf, T. (Thomas) (Nature Publishing Group, 2018)
    Chromosomal architecture is known to influence gene expression, yet its role in controlling cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem cells (PSCs) by the transcription factors ...

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