publications M.Mar Albà

Radó-Trilla, N., Arató, K., Pegueroles, C., Raya, A., de la Luna S., Albà M.M.(2015) Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors. Molecular Biology and Evolution , 32(9):2263-72.

Baldo, L., Riera, J.L., Tooming-Klunderud, A., Albà, M.M., Salzburger, W. (2015) Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes. Plos ONE , May 15;10(5):e0127462.

Gayà-Vidal, M. Albà, M.M. (2014) Uncovering adaptive evolution in the human lineage. BMC Genomics, vol. 15, iss. 1, p. 599.

Ruiz-Orera, J., Messeguer, X., Subirana, J.A., Alba, M.M. (2014) Long non-coding RNAs as a source of new peptides. eLife, vol. 3, e03523.

Santpere, G., Darre, F., Blanco, S., Alcami, A., Villoslada, P., Albà, M.M., Navarro, A. (2014) Genome-wide analysis of wild-type Epstein-Barr virus genomes derived from healthy individuals of the 1,000 Genomes Project. Genome Biology and Evolution, vol. 6, iss. 4, p. 846-60, 2014.

Villanueva-Cañas, JL., Faherty, S.L., Yoder, A.D., Albà, M.M. (2014) Comparative Genomics of Mammalian Hibernators Using Gene Networks. Integrative and comparative biology, 54(3):452-62.

Mulero, M.C., D. Ferres-Marco, A. Islam, P. Margalef, M. Pecoraro, A. Toll, N. Drechsel, C. Charneco, S. Davis, N. Bellora, F. Gallardo, E. López-Arribillaga, E. Asensio-Juan, V. Rodilla, J. González, M. Iglesias, V. Shih, M. M. Albà, L. Di Croce, A. Hoffmann, S. Miyamoto, J. Villà-Freixa, N. López-Bigas, W. M. Keyes, M. Dominguez, A. Bigas, and L. Espinosa (2013) Chromatin-Bound IKBalpha Regulates a Subset of Polycomb Target Genes in Differentiation and Cancer. Cancer cell, vol. 24, iss. 2, p. 151-66, 2013.

Trilling, M.+, Bellora, N.+, Rutkowski, A.J., de Graaf, M., Dickinson, P., Robertson, K., Prazeres da Costa, O., Ghazal, P., Friedel, C.C., Albà, M.M., Dölken, L. (2013) Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis. Nucleic Acids Res. 41(17):8107-25.
+ Contributed equally

Pegueroles, C.+, Laurie, S.+, Albà, M.M. (2013) Accelerated Evolution after Gene Duplication: A Time-Dependent Process Affecting Just One Copy. Molecular Biology and Evolution May 18. 30(8):1830-42.
+ Contributed equally

Bornberg-Bauer, E., Albà, M.M. (2013) Dynamics and adaptive benefits of modular protein evolution. Current Opinion in Structural Biology, 23:459-66.

Toll-Riera, M., Albà, M.M. (2013) Emergence of novel domains in proteins. BMC Evolutionary Biology, 13:47.

Villanueva-Cañas J., Laurie, S., Albà, M.M. (2013). Improving genome-wide scans of positive selection by using protein isoforms of similar length. Genome Biology and Evolution, 5:457-67.

Radó-Trilla, N., Albà, M.M. (2012). Dissecting the role of low-complexity sequences in the evolution of vertebrate proteins. BMC Evolutionary Biology, 12:155.

Toll-Riera, M., Bostick, D., Albà*, M.M. and Plotkin*, J.B. (2012) Structure and age jointly influence rates of protein evolution. Plos Computational Biology, 8(5):e1002542. *Co-corresponding.

Laurie, S., Toll-Riera, M., Radó-Trilla, N., Albà, M.M. (2012) Sequence shortening in the rodent ancestor. Genome Research, 22: 478-485.

Shikhagaie, M., Mercé-Maldonada, E., Isern, E., Muntasell, A., Albà, M.M., López-Botet, M., Hengel, H., Angulo. A. (2012). The HCMV-specific UL1 gene encodes a late phase glycoprotein incorporated in the virion envelope. Journal of Virology, 86:4091-4101.

Toll-Riera, M., Radó-Trilla, N., Martys, F., Albà, M.M. (2012) Role of low-complexity sequences in the formation of novel protein coding sequences”. Molecular Biology and Evolution, 29:883-886.

Engel, P., Perez-Carmona, N., Albà, M.M., Robertson, K., Ghazal, P., Angulo, A. (2011) Human cytomegalovirus-encoded UL7 molecule, a cellular homologue of the SLAM family receptor CD229, attenuates cytokine production. Immunology and Cell Biology, 89:753-66.

Toll-Riera, M., Laurie, S., Radó-Trilla, N., Albà, M.M. (2011). Partial gene duplication and the formation of novel genes. Gene Duplication / Book 1, Intech. ISBN 978-953-307-387-3.

Toll-Riera, M.,Laurie, S., Albà, M.M. (2011) Lineage-specific Variation in Intensity of Natural Selection in Mammals. Molecular Biology and Evolution, 28: 383-398.

Mularoni, L., Ledda, A., Toll-Riera, M., Albà, M.M. (2010) Natural selection drives the accumulation of amino acid tandem repeats in human proteins. Genome Research, 20: 745-754.

Farré, D., Albà, M.M. (2010) Heterogeneous patterns of gene expression diversification in mammalian gene duplicates. Molecular Biology and Evolution, 27:325-335.

Morcillo-Suarez, C., Albà, M.M., Navarro, A. (2010) Genoma y enfermedades complejas. Tratado de Esclerosis Múltiple. Ed. Marge Medica Books.

Albà, M.M. (2009) Temporal aspects of gene evolution. Evolución y Adaptación: 150 años después del origen de las especies. Año Darwin, Sociedad Española de Biología Evolutiva.

Toll-Riera, M., Castelo, R., Bellora, N., Albà, M.M. (2009) Evolution of primate orphan genes. Biochemical Society Transactions, 37:778-782.

Rodilla, V., Villanueva, A., Obrador, A., Robert-Moreno, A., Fernandez-Majada, V., Bellora, N., Albà, M.M., Duñach, M., Capella, G., Bigas, A., Espinosa, Ll. (2009) Notch is downstream of Wnt signaling in colorectal cancer cells and cooperates with beta-catenin to activate a specific gene program. Proceedings of the National Academy of Sciences, 106:6315-6320.

Salichs, E., Ledda, A., Mularoni, L., Albà, M.M., De la Luna, S. (2009) Genome-wide analysis of histidine repeats reveals their role in the localization of human proteins to the nuclear speckles compartment. Plos Genetics, 5: e1000397.

Toll-Riera, M., Bosch, N., Bellora, N., Castelo, R., Armengol, Ll., Estivill, X., Albà, M.M. (2009) Origin of primate orphan genes: a compartive genomics approach. Molecular Biology and Evolution 26: 603-612.

Toll-Riera, M., Castresana, J., Albà, M.M. (2008). Accelerated Evolution of Genes of Recent Origin. Evolutionary Biology: from concept to application. Ed. P. Pontarotti. Springer.

Mularoni, L., Toll-Riera, M., Albà, M.M. (2008). Comparative Genetics of Trinucleotide Repeats in the Human and Ape Genomes. Handbook of Human Evolution 2 (Ed. David N. Cooper & Hildegard Kehrer-Sawatzki). Ed. John Wiley & Sons Ltd., Chichester.

Bellora, N., Farré, D., Albà, M.M. (2008). Identification of regulatory motifs by positional bias in mammalian promoters. Proceedings VIII Spanish Bioinformatics Symposium (JdB’08).

Bellora, N. Farré, D., Albà, M.M. (2007) Positional bias of general and tissue-specific regulatory motifs in mouse promoters. BMC Genomics 8: 459.

Farré, D., Bellora, N., Mularoni, L., Messeguer, X., Albà, M.M. (2007) Housekeeping genes tend to show reduced upstream sequence conservation. Genome Biology, Vol. 8: R140.

Albà, M.M., Castresana, J. (2007) On homology searches by protein Blast and the characterization of the age of genes. BMC Evolutionary Biology, Vol 7: 53.

Mularoni, L., Veitia, R.A., Albà, M.M. (2007) Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. Genomics, Vol 89: 316-325.

Bellora, N., Farré, D., Albà, M.M. (2007) PEAKS: Identification of regulatory motifs by their position in DNA sequences. Bioinformatics, Vol 23: 243-244.

Albà, M.M., Tompa, P., Veitia, R.A. (2007). Amino-acid repeats and the structure and evolution of proteins. In Gene and Protein Evolution, Genome Dynamics. Ed. J-N Volff, Karger, Vol. 3: 119-130.

Furney, S.J., Albà, M.M., López-Bigas, N. (2006). Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics, Vol. 7: 165.

Mularoni, L., Guigó, R., Albà, M.M. (2006). Mutation patterns of amino acid tandem repeats in the human proteome. Genome Biology, Vol. 7: R33.

Blanco, E., Farré, D., Albà, M.M., Messeguer, X., Guigó, R. (2006). ABS: a database of annotated regulatory binding sites from orthologous promoters. Nucleic Acids Research, Vol. 34: D63-67.

Albà, M.M., Castresana, J. (2005). Inverse Relationship between Evolutionary Rate and Age of Mammalian Genes. Molecular Biology and Evolution, Vol. 22: 598 – 606.

Castresana, J., Guigó, R., Albà, M.M. (2004) Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome. Journal of Molecular Evolution, Vol. 59: 72-79.

Gibbs et al. (including Albà, M.M.) (2004). Genome Sequence of the Brown Norway Rat yields Insights into Mammalian Evolution. Nature, Vol. 428: 493 – 521.

Huang, H., Winter, E.E., Wang, H., Weinstock, K.G., Xing, H., Goodstadt, L., Stenson, P.D., Cooper, D.N., Smith, D., Albà, M.M., Ponting, C.P., Fechtel, K. (2004). Conservation of human disease genes in the rat genome. Genome Biology, Vol. 5: R47.

Gendra, E., Moreno, A., Albà, M.M., Pagès, M. (2004). Interaction of the plant glycine-rich RNA binding protein MA16 with a novel nucleolar DEAD box RNA helicase protein from Zea mays. The Plant Journal, Vol. 38: 875 – 886.

Albà, M.M., Guigó, R. (2004). Comparative analysis of amino acid repeats in rodents and humans. Genome Research, Vol. 14: 549-554.

Farré, D., Roset, R., Huerta, M., Adsuara, J.E., Roselló, L., Albà, M.M., Messeguer, X. (2003). Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic Acids Research, Vol. 31: 3651-3653.

Farré, D., Messeguer, X., Albà, M.M. (2002). PROMO: detection of known transcription regulatory elements common to multiple sequences. Proceedings 3rd Annual Spanish Bioinformatics Conference (JBI’02).

Holzerdlandt, R., Orengo, C.A., Kellam, P., Albà, M.M. (2002). Identification of novel herpesvirus homologues in the human genome. Genome Research, Vol. 12:1739-1748.

Kellam, P., Albà, M.M. (2002). Virus Bioinformatics: Databases and recent applications. pplied Bioinformatics, Vol. 1: 37-42.

Albà, M.M., Laskowski, R.A., Hancock, J.M. (2002). Detecting Cryptically Simple Protein Sequences using the SIMPLE Algorithm. Bioinformatics, Vol. 18: 672-688.

Messeguer, X., Escudero, R., Farré, D., Núñez, O., Martínez, J. and Albà, M.M. (2002). PROMO: detection of known transcription regulatory elements using species-tailored searches. Bioinformatics, Vol. 18 333-334.

Albà, M.M., Das, R., Orengo, C., Kellam, P. (2001) Genome wide function conservation and phylogeny in the Herpesviridae. Genome Research, Vol. 11: 43-54.

Albà, M.M., Lee, D., Pearl, F.M.G., Shepherd, A.J., Martin, N., Orengo, C.A., Kellam, P. (2001) VIDA: A virus database system for the organization of virus genome open reading frames. Nucleic Acids Research, Vol. 29: 133-136.

Jenner, R., Albà, M.M., Boshoff, C., Kellam, P. (2001) Kaposi’s sarcoma-associated herpesvirus latent and lytic gene expression as revealed by DNA arrays. Journal of Virology, Vol. 75: 891-902.

Lumbreras, V., Albà, M.M., Kleinow, T., Koncz, C., Pagès, M. (2001) Domain fusion between SNF1-related kinase subunits during plant evolution. EMBO Reports, Vol. 2: 55-60.

Albà, M.M., Santibáñez-Koref, M.F., Hancock, J.M. (2001) The comparative genomics of polyglutamine repeats: extreme difference in the codon organization of repeat-encoding regions between mammals and Drosophila. Journal of Molecular Evolution, Vol. 52: 249-259.

Albà, M.M. (2001) Replicative DNA polymerases. Genome Biology, Vol. 2(1): reviews 30021-30024.

Albà, M.M., Santibáñez-Koref, M.F., Hancock, J.M. (1999). Conservation of polyglutamine tract size between mouse and human depends on codon interruption. Molecular Biology and Evolution 16: 1641-1644.

Albà, M.M., Santibáñez-Koref, M.F., Hancock, J.M. (1999). Amino acid reiterations in yeast are over-represented in particular classes of proteins and show evidence of a slippage-like mutational process. Journal of Molecular Evolution 49: 789-797.

Albà, M.M., Pagès, M. (1998). Plant proteins containing the RNA recognition motif. Trends in Plant Science 3:15-21.

Albà, M.M., Vinti, G., Messeguer, R., Pagès, M. (1998). Identification of RNAs associated in vivo with the maize MA16 RNA-binding protein by a PCR-based method. Plant Physiology and Biochemistry 36: 913-918.

Niogret, M.F., Culiáñez-Macià, F.A., Goday, A., Albà, M.M., Pagès, M. (1996). Expression and cellular localization of rab28 mRNA and rab28 protein during maize embryogenesis. The Plant Journal, Vol.9, 549-557.

Jensen, A.B., Busk, P.K., Figueras, M., Albà ,M.M., Peracchia, G., Messeguer, R., Goday, A., Pagès, M. (1996). Drougth signal transduction in plants. Plant Growth Regulation 20, 105-110.

Pagès, M., Albà, M.M., Culiáñez-Macià, F.A., Goday A. (1995). The maize RNA-binding protein, MA16, is a nucleolar protein located in the dense fibrillar component. J. Cellular Biochemistry, Suppl. 19A, 146.

Pagès, M., Albà, M.M., Arenas, C., Busk, P.K., Culiáñez-Macià, F.A., Figueras, M., Jensen, A.B., Jessop, A.C., Peracchia, G., Goday, A. (1994). Abscissic acid and water-stress responsive genes in maize. Genet. Pol. 35 B, pp 15-24.

Albà, M.M., Culiáñez-Macià-F.A., Goday, A., Freire,M.A., Nadal, B., Pagès, M. (1994). The maize RNA-binding protein, MA16, is a nucleolar protein located in the dense fibrillar component. The Plant Journal, Vol.6, 825-834.

Goday, A., Jensen, A.B., Culiáñez-Macià, F.A., Albà, M.M., Figueras, M., Serratosa, J., Torrent, M., Pagès, M. (1994). The maize abscisic acid-responsive protein Rab17 is located in the nucleus and interacts with nuclear localization signals. The Plant Cell, Vol.6, 351-360.

Freire, M.A., Albà, M.M., Jensen, A.B., Niogret, M.F., Goday, A., Pagès, M. (1994). Gene regulation by abscisic acid and water stress in maize. In “Biotechnology for Aridland Plants”. Ed. G.Coruzzi and P. Puigdomenech. NATO ASI Series, Vol.H 81, 257-266.

Pagès, M., Vilardell, J., Jensen, A.B., Albà, M.M., Torrent, M., Goday, A. (1993). Molecular biological responses to drought in maize. In “Interacting Stresses on Plants in a Changing Climate”. Ed. M.B. Jackson and C.R. Black. NATO-ASI Series, Vol.I 16, 583-591.