Welcome to the UPF Digital Repository

Browsing Documents OpenAIRE (Open Access Infrastructure for Research in Europe) by Document Type "info:eu-repo/semantics/article"

Browsing Documents OpenAIRE (Open Access Infrastructure for Research in Europe) by Document Type "info:eu-repo/semantics/article"

Sort by: Order: Results:

  • 2D zernike polynomial expansion: finding the protein-protein binding regions
    Milanetti, Edoardo; Miotto, Mattia; Di Rienzo, Lorenzo; Monti, Michele; Gosti, Giorgio; Ruocco, Giancarlo (Elsevier, 2020)
    We present a method for efficiently and effectively assessing whether and where two proteins can interact with each other to form a complex. This is still largely an open problem, even for those relatively few cases where ...
  • 3-Deazaadenosine alleviates senescence to promote cellular fitness and cell therapy efficiency in mice
    Guerrero, Ana; Innes, Andrew J.; Roux, Pierre-François; Buisman, Sonja C.; Jung, Johannes; Ortet Cortada, Laura; Moiseeva, Victoria, 1992-; Wagner, Verena; Robinson, Lucas; Ausema, Albertina; Potapova, Anna; Perdiguero, Eusebio, 1968-; Weersing, Ellen; Aarts, Marieke; Martin, Nadine; Wuestefeld, Torsten; Muñoz Cánoves, Pura, 1962-; Haan, Gerald de; Bischof, Oliver; Gil, Jesús (Nature Research, 2022)
    Cellular senescence is a stable type of cell cycle arrest triggered by different stresses. As such, senescence drives age-related diseases and curbs cellular replicative potential. Here, we show that 3-deazaadenosine (3DA), ...
  • 3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: a pilot study
    Cardenes, Rubén; Zhang, Chong; Klementieva, Oxana; Werner, Stephan; Guttmann, Peter; Pratsch, Christoph; Cladera i Cerdà, Josep; Bijnens, Bart (Public Library of Science (PLoS), 2017)
    Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension ...
  • 3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?
    Le Dily, François; Serra, François; Marti-Renom, Marc A. (Wiley, 2017)
    The genome is organized in a hierarchical fashion within the nucleus in interphase. This nonrandom folding of the chromatin fiber is thought to play important roles in the processing of the genetic information. Therefore, ...
  • 3D-printing of transparent bio-microfluidic devices in PEG-DA
    Urrios Garcia, Arturo, 1990-; Parra-Cabrera, Cesar; Bhattacharjee, Nirveek; Gonzalez-Suarez, Alan M.; Rigat-Brugarolas, Luis G.; Nallapatti, Umashree; Samitier, Josep; DeForest, Cole A.; Posas Garriga, Francesc; Garcia-Cordero, José L.; Folch, Albert (Royal Society of Chemistry, 2016)
    The vast majority of microfluidic systems are molded in poly(dimethylsiloxane) (PDMS) by soft lithography due to the favorable properties of PDMS: biocompatible, elastomeric, transparent, gas-permeable, inexpensive, and ...
  • 4D genome rewiring during oncogene-induced and replicative senescence
    Sati, Satish; Serra, François; Castillo Andreo, David; Marti-Renom, Marc A.; Cavalli, Giacomo (Cell Press, 2020)
    To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene ...
  • 4D nucleome modeling
    Marti-Renom, Marc A.; Paulsen, Jonas; Jost, Daniel; Marti-Renom, Marc A. (Elsevier, 2021)
    The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in regulating DNA transcription, replication, and damage-repair among other nuclear functions. With this increased awareness, reinforced ...
  • 4D reconstruction of murine developmental trajectories using spherical harmonics
    Dalmasso, Giovanni; Musy, Marco; Niksic, Martina; Robert Moreno, Alexandre; Badía Careaga, Claudio; Sanz-Ezquerro, Juan José; Sharpe, James (Elsevier, 2022)
    Normal organogenesis cannot be recapitulated in vitro for mammalian organs, unlike in species including Drosophila and zebrafish. Available 3D data in the form of ex vivo images only provide discrete snapshots of the ...
  • 90 YEARS OF PROGESTERONE: Molecular mechanisms of progesterone receptor action on the breast cancer genome
    Beato, Miguel; Wright, Roni H.G.; Le Dily, François (BioScientifica, 2020)
    Gene regulation by steroid hormones has been at the forefront in elucidating the intricacies of transcriptional regulation in eukaryotes ever since the discovery by Karlson and Clever that the insect steroid hormone ecdysone ...
  • A benchmark of transposon insertion detection tools using real data
    Vendrell Mir, Pol; Barteri, Fabio; Merenciano, Miriam; González, Josefa; Casacuberta, Josep M.; Castanera, Raúl (BioMed Central, 2019)
    Background: Transposable elements (TEs) are an important source of genomic variability in eukaryotic genomes. Their activity impacts genome architecture and gene expression and can lead to drastic phenotypic changes. ...
  • A brain atlas of axonal and synaptic delays based on modelling of cortico-cortical evoked potentials
    Lemaréchal, Jean-Didier; Rocamora Zúñiga, Rodrigo Alberto; F-TRACT consortium (Oxford University Press, 2022)
    Epilepsy presurgical investigation may include focal intracortical single-pulse electrical stimulations with depth electrodes, which induce cortico-cortical evoked potentials at distant sites because of white matter ...
  • A burst of segmental duplications in the genome of the African great ape ancestor
    Marquès i Bonet, Tomàs, 1975-; Kidd, Jeffrey M.; Ventura, Mario; Graves, Tina A.; Cheng, Ze; Hillier, LeDeana W.; Jiang, Zhaoshi; Baker, Carl; Malfavon-Borja, Ray; Fulton, Lucinda; Alkan, Can; Aksay, Gozde; Girirajan, Santhosh; Siswara, Priscillia; Chen, Lin; Cardone, Maria Francesca; Navarro i Cuartiellas, Arcadi, 1969-; Mardis, Elaine R.; Wilson, Richard K.; Eichler, Evan E. (Nature Publishing Group, 2009)
    It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there ...
  • A chromatin code for alternative splicing involving a putative association between CTCF and HP1alpha proteins
    Agirre Ortiz de Guzmán, Eneritz, 1983-; Bellora Pereyra, Nicolás; Alló, Mariano; Pagès Pinós, Amadís; Bertucci, Paola; Kornblihtt, Alberto R.; Eyras Jiménez, Eduardo (BioMed Central, 2015)
    BACKGROUND: Alternative splicing is primarily controlled by the activity of splicing factors and by the elongation of the RNA polymerase II (RNAPII). Recent experiments have suggested a new complex network of splicing ...
  • A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis
    de la Herrán, Roberto; Gómez-Garrido, Jèssica; Cruz, Fernando; Alioto, Tyler S; Martínez, Paulino (Wiley, 2023)
    Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and ...
  • A class of nonlocal variational problems on a vector bundle for color image local contrast reduction/enhancement
    Bertalmío, Marcelo; Batard, Thomas (International Press of Boston, 2016)
    We extend two existing variational models from the Euclidean space to a vector bundle over a Riemannian manifold. The Euclidean models, dedicated to regularize or enhance some color image features, are based on the concept ...
  • A closer look at scalar diversity using contextualized semantic similarity
    Westera, Matthijs; Boleda, Gemma (University of Konstanz, 2020)
    We take a closer look at van Tiel et al.’s (2016) experimental results on diversity in scalar inference rates. In contrast to their finding that semantic similarity had no significant effect on scalar inference rates, ...
  • 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 comparative genomics multitool for scientific discovery and conservation
    Zoonomia Consortium; Serres Armero, Aitor, 1992-; Juan, David; Kuderna, Lukas F.K.; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2020)
    The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe ...
  • A comparison of mechanistic signaling pathway activity analysis methods
    Amadoz, Alicia; Hidalgo, Marta R.; Çubut, Cankut; Carbonell-Caballero, Jose; Dopazo, Joaquín (Oxford University Press, 2019)
    Understanding the aspects of cell functionality that account for disease mechanisms or drug modes of action is a main challenge for precision medicine. Classical gene-based approaches ignore the modular nature of most human ...
  • A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
    Alioto, Tyler; Derdak, Sophia; Ribeca, Paolo; Castro Giner, Francesc; Beltran, Sergi; Raineri, Emanuele; Dabad, Marc; Heath, Simon C.; Gut, Marta; Gut, Ivo Glynne (Nature Research, 2015)
    As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different ...

Search DSpace


Advanced Search

Browse

My Account

Compliant to Partaking