Browsing by Author "Vazquez, Miguel"

Now showing items 1-11 of 11

    • A user guide for the online exploration and visualization of PCAWG data 

      Goldman, Mary J.; Zhang, Junjun; Fonseca, Nuno A.; Cortés-Ciriano, Isidro; Xiang, Qian; Craft, Brian; Piñeiro-Yáñez, Elena; O'connor, Brian D.; Bazant, Wojciech; Barrera, Elisabet; Muñoz-Pomer, Alfonso; Petryszak, Robert; Füllgrabe, Anja; Al-Shahrour, Fatima; Keays, Maria; Haussler, David; Weinstein, John N; Huber, Wolfgang; Park, Peter J.; Papatheodorou, Elena; Valencia, Alfonso; Zhu, Jingchun; Ferretti, Vincent; Vazquez, Miguel (Springer Nature, 2020)
      Article
      Open Access
      The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which ...

    • Annotating Cancer-Related Variants at Protein–Protein Interface with Structure-PPi 

      Vazquez, Miguel; Pons, Tirso (Springer US, 2022)
      Part of book or chapter of book
      Open Access
      A comprehensive analysis of germline and somatic variants requires complex computational approaches that combine next-generation sequencing (NGS)-based omics data with curated annotations from public repositories. Here, ...

    • ChiPPI: a novel method for mapping chimeric protein–protein interactions uncovers selection principles of protein fusion events in cancer 

      Frenkel-Morgenstern, Milana; Gorohovski, Alessandro; Tagore, Somnath; Sekar, Vaishnovi; Vazquez, Miguel; Valencia, Alfonso (Oxford University Press, 2017-05-26)
      Article
      Open Access
      Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using ...

    • COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms 

      Ostaszewski, Marek; Niarakis, Anna; Mazein, Alexander; Kuperstein, Inna; Phair, Robert; Montagud, Arnau; Ponce De Leon, Miguel; Vazquez, Miguel; Valencia, Alfonso (Wiley Open Access, 2021-10-21)
      Article
      Open Access
      We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. ...

    • ExTRI: Extraction of transcription regulation interactions from literature 

      Vazquez, Miguel; Krallinger, Martin; Leitner, Florian; Kuiper, Martin; Valencia, Alfonso; Laegreid, Astrid (Elsevier, 2022)
      Article
      Open Access
      The regulation of gene transcription by transcription factors is a fundamental biological process, yet the relations between transcription factors (TF) and their target genes (TG) are still only sparsely covered in databases. ...

    • Fine tuning a logical model of cancer cells to predict drug synergies: combining manual curation and automated parameterization 

      Flobak, Åsmund; Zobolas, John; Vazquez, Miguel; Steigedal, Tonje S.; Thommesen, Liv; Grislingås, Asle; Niederdorfer, Barbara; Folkesson, Evelina; Kuiper, Martin (Frontiers Media, 2023)
      Article
      Open Access
      Treatment with combinations of drugs carries great promise for personalized therapy for a variety of diseases. We have previously shown that synergistic combinations of cancer signaling inhibitors can be identified based ...

    • Immune analysis of lymph nodes in relation to the presence or absence of tumor infiltrating lymphocytes in triple-negative breast cancer 

      Quintana, Ángela; Peg, Vicente; Prat, Aleix; Moliné, Teresa; Vazquez, Miguel (Elsevier, 2021)
      Article
      Open Access
      Triple-negative breast cancer (TNBC) is a subtype of breast cancer with unmet medical needs. Several studies have proved that high levels of tumor infiltrating lymphocytes (TILs) at diagnosis of TNBC confer better prognosis ...

    • Pan-cancer analysis of whole genomes 

      The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium; Royo, Romina; Vazquez, Miguel; Bosio, Mattia; Valencia, Alfonso; Torrents, David; Gelpi, Josep; Milovanovic, Ana; Puiggròs, Montserrat; Bartolome, Javier; Vicente, David; Fink, J. Lynn; Dueso Barroso, Ana; Villasante, Izar; Bartolomé Rodriguez, Javier (Nature Research, 2020)
      Article
      Open Access
      Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 ...

    • Patient dossier: healthcare queries over distributed resources 

      Vazquez, Miguel; Valencia, Alfonso (PLOS, 2019-10-17)
      Article
      Open Access
      As with many other aspects of the modern world, in healthcare, the explosion of data and resources opens new opportunities for the development of added-value services. Still, a number of specific conditions on this domain ...

    • Strategies to enhance logic modeling-based cell line-specific drug synergy prediction 

      Niederdorfer, Barbara; Touré, Vasundra; Vazquez, Miguel; Thommesen, Liv; Kuiper, Martin; Lægreid, Astrid; Flobak, Åsmund (Frontiers Media, 2020-07)
      Article
      Open Access
      Discrete dynamical modeling shows promise in prioritizing drug combinations for screening efforts by reducing the experimental workload inherent to the vast numbers of possible drug combinations. We have investigated ...

    • TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat 

      Acencio, Marcio L; Vazquez, Miguel; Chawla, Konika; Lægreid, Astrid; Kuiper, Martin (Oxford University Press, 2023-11)
      Article
      Open Access
      Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. ...