Browsing by Author "Parra Farré, Genís"

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  • Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely-expressed human genes
    Castelo Valdueza, Robert; Reymond, Alexandre; Wyss, Carine; Cámara, Francisco; Parra Farré, Genís; Antonarakis, Stylianos E.; Guigó Serra, Roderic; Eyras Jiménez, Eduardo (Oxford University Press, 2005)
    The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using ...
  • Comparative gene prediction in human and mouse
    Parra Farré, Genís; Agarwal, Pankaj; Abril Ferrando, Josep Francesc; Wiehe, Thomas; Fickett, James W.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press-CSHL Press, 2003)
    The completion of the sequencing of the mouse genome promises to help predict human genes with greater accuracy. While current ab initio gene prediction programs are remarkably sensitive (i.e., they predict at least a ...
  • Computational identification of genes: ab initio and comparative approaches
    Parra Farré, Genís (Universitat Pompeu Fabra, 2004-12-03)
    El trabajo que aquí se presenta, estudia el reconocimiento de las señales que delimitan y definen los genes que codifican para proteínas, así como su aplicabilidad en los programas de predicción de genes. La tesis que aquí ...
  • Gene finding in the chicken genome
    Eyras Jiménez, Eduardo; Reymond, Alexandre; Castelo Valdueza, Robert; Bye, Jacqueline M.; Cámara, Francisco; Flicek, Paul; Huckle, Elizabeth J.; Parra Farré, Genís; Shteynberg, David D.; Wyss, Carine; Rogers, Jane; Antonarakis, Stylianos E.; Birney, Ewan; Guigó Serra, Roderic; Brent, Michael R. (BioMed Central, 2005)
    Background: Despite the continuous production of genome sequence for a number of organisms,/nreliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly/ntrue for genomes for which ...
  • GeneID in "Drosophila"
    Parra Farré, Genís; Blanco, Enrique; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press-CSHL Press, 2000)
    GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using ...
  • Immune cell profiling of the cerebrospinal fluid enables the characterization of the brain metastasis microenvironment
    Rubio Pérez, Carlota; Trincado Alonso, Juan Luis, 1987-; Marchese, Domenica, 1986-; Moutinho, Catia; Ruiz, Sara; Parra Farré, Genís; Heyn, Holger; Seoane, Joan (Nature Research, 2021)
    Brain metastases are the most common tumor of the brain with a dismal prognosis. A fraction of patients with brain metastasis benefit from treatment with immune checkpoint inhibitors (ICI) and the degree and phenotype of ...
  • Immunological and genetic kinetics from diagnosis to clinical progression in chronic lymphocytic leukemia
    Jiménez, Isabel; Tazón-Vega, Bárbara; Abrisqueta, Pau; Nieto, Juan C.; Bobillo, Sabela; Palacio-García, Carles; Carabia, Júlia; Valdés-Mas, Rafael; Munuera, Magdalena; Puigdefàbregas, Lluís; Parra Farré, Genís; Esteve-Codina, Anna; Franco-Jarava, Clara; Iacoboni, Gloria; Terol, María-José; García-Marco, J. A.; Crespo Barrio, Marta; Bosch, Francesc (BioMed Central, 2021)
    Background: Mechanisms driving the progression of chronic lymphocytic leukemia (CLL) from its early stages are not fully understood. The acquisition of molecular changes at the time of progression has been observed in a ...
  • Integrated analysis of germline and tumor DNA identifies new candidate genes involved in familial colorectal cancer
    Díaz-Gay, Marcos; Park, Solip; Parra Farré, Genís; Laurie, Steven, 1973-; Beltran, Sergi; Castellví Bel, Sergi (MDPI, 2019)
    Colorectal cancer (CRC) shows aggregation in some families but no alterations in the known hereditary CRC genes. We aimed to identify new candidate genes which are potentially involved in germline predisposition to familial ...
  • SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
    Romagné, Frédéric; Santesmasses Ruiz, Didac, 1978-; White, Louise; Sarangi, Gaurab K.; Mariotti, Marco, 1984-; Hübler, Ron; Weihmann, Antje; Parra Farré, Genís; Gladyshev, Vadim N.; Guigó Serra, Roderic; Castellano Hereza, Sergi (Oxford University Press, 2014)
    SelenoDB (http://www.selenodb.org) aims to provide high-quality annotations of selenoprotein genes, proteins and SECIS elements. Selenoproteins are proteins that contain the amino acid selenocysteine (Sec) and the first ...
  • Systematic collaborative reanalysis of genomic data improves diagnostic yield in neurologic rare diseases
    Bullich, Gemma; Matalonga, Leslie; Pujadas, Montserrat; Papakonstantinou Ntalis, Anastasios; Piscia, Davide; Tonda, Raúl; González, Juan Ramón; Laurie, Steven, 1973-; Luengo, Cristina; Ovelleiro, David; Parra Farré, Genís; Pérez Jurado, Luis Alberto; Beltran, Sergi; Undiagnosed Rare Disease Program of Catalonia (URD-Cat) Consortium (Elsevier, 2022)
    Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive ...
  • Tandem chimeric transcription as a means to increase protein diversity in the human genome
    Parra Farré, Genís; Reymond, Alexandre; Dabbouseh, Noura; Dermitzakis, Emmanuouil T.; Thomson, Timothy M.; Antonarakis, Stylianos E.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press-CSHL Press, 2006)
    The “one-gene, one-protein” rule, coined by Beadle and Tatum, has been fundamental to molecular biology. The rule implies that the genetic complexity of an organism depends essentially on its gene number. The discovery, ...
  • Wnt genes in colonic polyposis predisposition
    Quintana, Isabel; Tonda, Raúl; Parra Farré, Genís; Piscia, Davide; Beltran, Sergi; Valle, Laura (Elsevier, 2023)