Browsing by Author "Albà Soler, Mar"

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  • Improving genome-wide scans of positive selection by using protein isoforms of similar length
    Villanueva Cañas, José Luis, 1984-; Laurie, Steven, 1973-; Albà Soler, Mar (Oxford University Press, 2013)
    Large-scale evolutionary studies often require the automated construction of alignments of a large number of homologous gene families. The majority of eukaryotic genes can produce different transcripts due to alternative ...
  • In silico analysis of regulatory motifs in gene promoters
    Bellora Pereyra, Nicolás (Universitat Pompeu Fabra, 2010-02-26)
    Regulation of gene transcription is a complex process involving many different proteins, some of which bind in a sequence-specific manner to DNA motifs in the gene promoter. The need to maintain specific interactions between ...
  • Insights into mammalian adaptive evolution through genomics data
    Villanueva Cañas, José Luis, 1984- (Universitat Pompeu Fabra, 2015-11-20)
    Although the genome sequencing revolution is still in its infancy, we must acknowledge it as the major driver of biology since the beginning of the 21st century. The availability of a large collection of complete mammalian ...
  • Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors.
    Radó i Trilla, Núria, 1985-; Arató, Krisztina, 1981-; Pegueroles Queralt, Maria Cinta; Raya, Alicia; Luna, Susana de la; Albà Soler, Mar (Open University Press, 2015)
    The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental ...
  • LCOR mediates interferon-independent tumor immunogenicity and responsiveness to immune-checkpoint blockade in triple-negative breast cancer
    Pérez-Núñez, Iván; Rozalén, Catalina; Palomeque, José Ángel; Sangrador, Irene; Dalmau, Mariona; Comerma Blesa, Laura, 1983-; Hernández Prat, Anna, 1984-; Casadevall Aguilar, David; Menendez Romero, Silvia; Liu, Daniel Dan; Berenguer De Felipe, Jordi; Peña Arranz, Raúl, 1976; Montañés, José Carlos; Albà Soler, Mar; Bonnin, Sarah; Ponomarenko, Julia; Servitja Tormo, Sonia; Arribas, Joaquín; Albanell Mestres, Joan; Celià-Terrassa, Toni (Nature Research, 2022)
    Ligand-dependent corepressor (LCOR) mediates normal and malignant breast stem cell differentiation. Cancer stem cells (CSCs) generate phenotypic heterogeneity and drive therapy resistance, yet their role in immunotherapy ...
  • Long non-coding RNAs as a source of new peptides
    Ruiz Orera, Jorge, 1988-; Messeguer, Xavier; Subirana, Juan A.; Albà Soler, Mar (eLife, 2014)
    Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs ...
  • Low-complexity regions in proteins as a source of evolutionary innovation
    Radó i Trilla, Núria, 1985- (Universitat Pompeu Fabra, 2013-05-03)
    In this thesis we aimed to study evolutionary implications of low-complexity regions, protein sequences of very simple amino acid composition. Its uncontrolled expansion causes several human diseases, including ...
  • Mechanisms of evolutionary innovation in mammalian genes
    Toll i Riera, Macarena, 1984- (Universitat Pompeu Fabra, 2012-03-28)
    Actualment, degut a la disponibilitat d’un gran nombre de genomes seqüenciats, el camp de la genòmica comparativa està experimentant grans avenços. Ara són possibles una àmplia gama d’estudis que fins fa poc eren inimaginables. ...
  • Mutation patterns of amino acid tandem repeats in the human proteome
    Mularoni, Loris; Guigó Serra, Roderic; Albà Soler, Mar (BioMed Central, 2006)
    Background: Amino acid tandem repeats are found in nearly one-fifth of human proteins. Abnormal expansion of these regions is associated with several human disorders. To gain further insight into the mutational mechanisms ...
  • Mutation, duplication, and selection in mammalian genomes
    Laurie, Steven, 1973- (Universitat Pompeu Fabra, 2013-07-25)
    This thesis comprises comparative genomics analyses primarily focussing on the evolution of mammalian proteins. We concentrate on three species of direct relevance as model organisms, for which high quality genome sequences ...
  • Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
    Montañés, José Carlos; Huertas, Marta; Moro, Simone G.; Blevins, William Robert, 1987-; Carmona, Mercè; Ayté del Olmo, José; Hidalgo Hernando, Elena; Albà Soler, Mar (Cold Spring Harbor Laboratory Press (CSHL Press), 2022)
    The unicellular yeast Schizosaccharomyces pombe (fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain ...
  • Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
    Albà Soler, Mar (Cold Spring Harbor Laboratory Press (CSHL Press), 2022)
  • New genes and functional innovation in mammals
    Villanueva Cañas, José Luis, 1984-; Ruiz Orera, Jorge, 1988-; Agea, M. Isabel; Gallo, María, 1989-; Andreu Martínez, David; Albà Soler, Mar (Oxford University Press, 2017)
    The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected ...
  • No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution
    Domazet-Lošo, Tomislav; Carvunis, Anne-Ruxandra; Albà Soler, Mar; Šestak, Martin Sebastijan; Bakarić, Robert; Neme, Rafik; Tautz, Diethard (Oxford University Press, 2017)
    Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns ...
  • Non-muscle-invasive micropapillary bladder cancer has a distinct lncRNA profile associated with unfavorable prognosis
    de Jong, Joep J.; Valderrama, Begoña P.; Perera Bel, Júlia; Juanpere, Nuria; Cejas, Paloma; Long, Henry; Albà Soler, Mar; Gibb, Ewan A.; Bellmunt Molins, Joaquim, 1959- (Nature Research, 2022)
    Background: molecular subtyping of bladder cancer has revealed luminal tumors generally have a more favourable prognosis. However, some aggressive forms of variant histology, including micropapillary, are often classified ...
  • On homology searches by protein Blast and the characterization of the age of genes
    Albà Soler, Mar; Castresana Ruiz-Carrillo, José Ignacio (BioMed Central, 2007)
    Background: It has been shown in a variety of organisms, including mammals, that genes that appeared recently in evolution, for example orphan genes, evolve faster than older genes. Low functional constraints at the time ...
  • Origins of de novo genes in human and chimpanzee
    Ruiz Orera, Jorge, 1988-; Hernández Rodríguez, Jéssica, 1983-; Chiva, Cristina; Sabidó Aguadé, Eduard, 1981-; Kondova, Ivanela; Bontrop, Ronald E.; Marquès i Bonet, Tomàs, 1975-; Albà Soler, Mar (Public Library of Science, 2015)
    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these ...
  • Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters
    Bellora Pereyra, Nicolás; Farré, Domènec; Albà Soler, Mar (BioMed Central, 2007)
    Background: The arrangement of regulatory motifs in gene promoters, or promoter/narchitecture, is the result of mutation and selection processes that have operated over many/nmillions of years. In mammals, tissue-specific ...
  • pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation
    Boix, Olga; Albà Soler, Mar; Abad, María (Nature Research, 2022)
    The human transcriptome contains thousands of small open reading frames (sORFs) that encode microproteins whose functions remain largely unexplored. Here, we show that TINCR lncRNA encodes pTINCR, an evolutionary conserved ...
  • RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
    Rubia, Ivan de la; Srivastava, Akanksha; Xue, Wenjing; Indi, Joel A.; Carbonell Sala, Silvia; Lagarde, Julien; Albà Soler, Mar; Eyras Jiménez, Eduardo (BioMed Central, 2022)
    Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study ...