Browsing by Author "Valencia, Alfonso"

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  • Automatic identification of informative regions with epigenomic changes associated to hematopoiesis
    Carrillo-de-Santa Pau, Enrique; Juan, David; Pancaldi, Vera; Were, Felipe; Martin-Subero, José Ignacio; Rico, Daniel; Valencia, Alfonso; BLUEPRINT Consortium (Oxford University Press, 2017)
    Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate ...
  • Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts
    Frenkel-Morgenstern, Milana; Lacroix, Vincent; Ezkurdia, Iakes; Levin, Yishai; Gabashvili, Alexandra; Prilusky, Jaime; Pozo, Angela del; Tress, Michael; Johnson, Rory; Guigó Serra, Roderic; Valencia, Alfonso (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Chimeric RNAs comprise exons from two or more different genes and have the potential to encode novel proteins that alter cellular phenotypes. To date, numerous putative chimeric transcripts have been identified among the ...
  • Comparison of algorithms for the detection of cancer drivers at subgene resolution
    Porta-Pardo, Eduard; Kamburov, Atanas; Tamborero Noguera, David; Pons, Tirso; Grases, Daniela; Valencia, Alfonso; López Bigas, Núria; Getz, Gad; Godzik, Adam (Nature Publishing Group, 2017)
    Understanding genetic events that lead to cancer initiation and progression remains one of the biggest challenges in cancer biology. Traditionally, most algorithms for cancer-driver identification look for genes that have ...
  • Erratum to: The UBC-40 urothelial bladder cancer cell line index: a genomic resource for functional studies
    Earl, Julie; Rico, Daniel; Carrillo, Enrique; Rodríguez Santiago, Benjamín; Méndez Pertuz, Marinela; Auer, Herbert; Gómez, Gonzalo; Barton Grossman, Herbert; Pisano, David G.; Schulz, Wolfgang; Pérez Jurado, Luis Alberto; Carrato, Alfredo; Theodorescu, Dan; Chanock, Stephen J.; Valencia, Alfonso; Real, Francisco X. (BioMed Central, 2015)
    Following the publication of our recent article in BMC Genomics [1] a number of aspects were called to our attention. We have carefully reviewed the experiments reported in this manuscript, as well as additional data from ...
  • Intronic CNVs and gene expression variation in human populations
    Rigau, Maria; Juan Sopeña, David Alejandro, 1975-; Valencia, Alfonso; Rico, Daniel (Public Library of Science (PLoS), 2019)
    Introns can be extraordinarily large and they account for the majority of the DNA sequence in human genes. However, little is known about their population patterns of structural variation and their functional implication. ...
  • LimTox: A web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
    Cañada, Andrés; Capella Gutiérrez, Salvador Jesús, 1985-; Rabal, Obdulia; Oyarzábal, Julen; Valencia, Alfonso; Krallinger, Martin (Oxford University Press, 2017)
    A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in ...
  • Look-alike humans identified by facial recognition algorithms show genetic similarities
    Joshi, Ricky S.; Rigau, Maria; García-Prieto, Carlos A.; Castro de Moura, Manuel; Piñeyro, David; Moran, Sebastian; Davalos, Veronica; Carrión, Pablo; Ferrando-Bernal, Manuel, 1990-; Olalde Marquínez, Íñigo, 1987-; Lalueza Fox, Carles, 1965-; Navarro i Cuartiellas, Arcadi, 1969-; Fernández-Tena, Carles; Aspandi, Decky; Sukno, Federico Mateo; Binefa i Valls, Xavier; Valencia, Alfonso; Esteller, Manel (Elsevier, 2022)
    The human face is one of the most visible features of our unique identity as individuals. Interestingly, monozygotic twins share almost identical facial traits and the same DNA sequence but could exhibit differences in ...
  • Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome
    Rodríguez Santiago, Benjamín; Malats i Riera, Núria; Rothman, Nathaniel; Armengol i Dulcet, Lluís; García Closas, Montserrat; Kogevinas, Manolis; Villa, Olaya; Hutchinson, Amy; Earl, Julie; Marenne, Gaëlle; Jacobs, Kevin; Rico, Daniel; Tardón, Adonina; Carrato, Alfredo; Thomas, Gilles; Valencia, Alfonso; Silverman, Debra T.; Real, Francisco X.; Chanock, Stephen J.; Pérez Jurado, Luis Alberto (Elsevier, 2010)
    Mosaicism is defined as the coexistence of cells with different genetic composition within an individual, caused by postzygotic somatic mutation. Although somatic mosaicism for chromosomal abnormalities is a well-established ...
  • Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm
    Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália (Springer, 2019)
    Background: Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such ...
  • STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells
    Richart, Laia; Lapi, Eleonora; Pancaldi, Vera; Cuenca-Ardura, Mirabai; Carrillo-de-Santa Pau, Enrique; Madrid-Mencía, Miguel; Neyret-Kahn, Hélène; Radvanyi, François; Rodríguez, Juan Antonio; Cuartero, Yasmina; Serra, François; Le Dily, François; Valencia, Alfonso; Martí Renom, Marc A.; Real, Francisco X. (Oxford University Press, 2021)
    Cohesin exists in two variants containing STAG1 or STAG2. STAG2 is one of the most mutated genes in cancer and a major bladder tumor suppressor. Little is known about how its inactivation contributes to tumorigenesis. Here, ...
  • The UBC-40 urothelial bladder cancer cell line index: a genomic resource for functional studies
    Earl, Julie; Rico, Daniel; Carrillo, Enrique; Rodríguez Santiago, Benjamín; Méndez Pertuz, Marinela; Auer, Herbert; Gómez, Gonzalo; Barton Grossman, Herbert; Pisano, David G.; Schulz, Wolfgang; Pérez Jurado, Luis Alberto; Carrato, Alfredo; Theodorescu, Dan; Chanock, Stephen J.; Valencia, Alfonso; Real, Francisco X. (BioMed Central, 2015)
    Background. Urothelial bladder cancer is a highly heterogeneous disease. Cancer cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines ...

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