Browsing by Author "Singh, Babita, 1986-"

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  • A quality control portal for sequencing data deposited at the European genome-phenome archive
    Fernández-Orth, Dietmar; Rueda, Manuel; Singh, Babita, 1986-; Moldes, Mauricio; Jene, Aina; Ferri, Marta; Vasallo, Claudia; Fromont, Lauren A.; Navarro i Cuartiellas, Arcadi, 1969-; Rambla de Argila, Jordi (Oxford University Press, 2022)
    Since its launch in 2008, the European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data. In this regard, one of the community concerns is the potential usability ...
  • A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells
    González-Vallinas Rostes, Juan, 1983-; Pagès Pinós, Amadís; Singh, Babita, 1986-; Eyras Jiménez, Eduardo (BioMed Central, 2015)
    Background. Transcriptional enhancers are generally known to regulate gene transcription from afar. Their activation involves a series of changes in chromatin marks and recruitment of protein factors. These enhancers may ...
  • Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond
    Rambla de Argila, Jordi; Baudis, Michael; Ariosa, Roberto; Beck, Timothy; Fromont, Lauren A.; Navarro i Cuartiellas, Arcadi, 1969-; Paloots, Rahel; Rueda, Manuel; Saunders, Gary; Singh, Babita, 1986-; Spalding, J. Dylan; Törnoos, Juha; Vasallo, Claudia; Veal, Colin D.; Brookes, Anthony J. (Wiley, 2022)
    Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human ...
  • IRFinder: assessing the impact of intron retention on mammalian gene expression
    Middleton, Robert; Gao, Dadi; Thomas, Aubin; Singh, Babita, 1986-; Au, Amy; Wong, Justin J.-L.; Bomane, Alexandra; Cosson, Bertrand; Eyras Jiménez, Eduardo; Rasko, John E.J.; Ritchie, William (BioMed Central, 2017)
    Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis ...
  • Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks
    Sebestyén, Endre; Singh, Babita, 1986-; Miñana Gómez, Belén; Pagès Pinós, Amadís; Mateo, Francesc; Pujana, Miguel Angel; Valcárcel, J. (Juan); Eyras Jiménez, Eduardo (Cold Spring Harbor Laboratory Press (CSHL Press), 2016)
    Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting ...
  • SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
    Trincado Alonso, Juan Luis, 1987-; Entizne, Juan Carlos; Hysenaj, Gerald; Singh, Babita, 1986-; Skalic, Miha, 1990-; Elliott, David, 1947-; Eyras Jiménez, Eduardo (BioMed Central, 2018)
    Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses ...
  • The European Genome-phenome Archive in 2021
    Freeberg, Mallory Ann; Fromont, Lauren A.; D'Altri, Teresa, 1984-; Jene, Aina; Moldes, Mauricio; Ariosa, Roberto; Fernández-Orth, Dietmar; Haziza, Frédéric; Martinez Llobet, Oscar; Milla, Gemma; Rueda, Manuel; Singh, Babita, 1986-; Torre, Sabela de la; Uyan, Umuthan; Vasallo, Claudia; Guigó Serra, Roderic; Navarro i Cuartiellas, Arcadi, 1969-; Rambla de Argila, Jordi (Oxford University Press, 2022)
    The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical ...
  • The role of alternative splicing in cancer
    Singh, Babita, 1986-; Eyras Jiménez, Eduardo (Taylor & Francis (Routledge), 2017)
    The functional capacity of cells is defined by the transcriptome. Many recent studies have identified variations in the transcriptome of tumors due to alternative splicing changes, as well as mutations in splicing factors ...

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