Publications

Hong, S.Y., Sun, B., Straub, D., Blaakmeer, A., Mineri, L., Koch, J., Brinch-Pedersen, H., Holme, I.B., Burow, M., Lyngs Jørgensen, H.J., Albà, M.M., Wenkel, S. (2020) Heterologous microProtein expression identifies LITTLE NINJA, a dominant regulator of jasmonic acid signaling. Proceedings of the National Academy of Sciences USA, vol. 117: 26197 – 26205.

Ruiz-Orera, J., Villanueva-Cañas, J.L., Albà, M.M. (2020) Evolution of new proteins from translated sORFs in long non-coding RNAs. Experimental Cell Research, vol. 391: 111940 – 111940.

Reixachs-Solé, M., Ruiz-Orera, J., Albà, M.M., Eyras, E. (2020) Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome. Nature Communications, vol. 11: 1768.

Blevins, W.R., Tavella, T., Moro, S.G., Blasco-Moreno, B., Closa-Mosquera, A., Diez, J., Carey, L.B., Albà, M.M. (2019) Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker’s yeast. Scientific Reports, vol. 9: 11005.

Ruiz-Orera, J., Albà MM (2019) Conserved regions in long non-coding RNAs contain abundant translation and protein-RNA interaction signatures. Nucleic Acids Research Genomics and Bioinformatics, vol. 1: e2.

Blevins, W.R., Carey, L.B., Albà, M.M. (2019) ‘Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions’. BMC Research Notes, vol. 12: 250.

Ruiz-Orera, J., Albà, M.M. (2019) Translation of small ORFs: roles in regulation and evolutionary innovation. Trends in Genetics, vol. 35: 186-198.

Ruiz-Orera, J., Grau-Verdaguer, P., Villanueva-Cañas, J-L., Messeguer, X., Albà, M.M. (2018) Translation of neutrally evolving peptides provides a basis for de novo gene evolution. Nature Ecology and Evolution, vol. 2: 890 – 896.

Faherty, S.L.*, Villanueva-Cañas, J-L., Blanco, M.B., Albà, M.M.*, Yoder, A.D. (2018) Transcriptomics in the wild: Hibernation physiology in free-ranging dwarf lemurs. Molecular Ecology, vol 27: 709-722.*co-corresponding.

Domazet-Lošo, T., Carvunis, A.R., Albà, M.M., Šestak, M.S., Bakarić, R., Neme, R., Tautz, D. (2017) No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution. Molecular Biology and Evolution, vol. 34: 843–856.

Villanueva-Cañas, J-L., Ruiz-Orera, J., Agea, M.I., Gallo, M., Andreu, D., Albà, M.M. (2017) New genes and functional innovation in mammals. Genome Biology and Evolution, vol 9: 1888-1900.

Faherty, S.L., Villanueva-Cañas, J-L., Klopfer, P.H., Albà, M.M., Yoder, A.D. (2016) Gene expression profiling in the hibernating primate, Cheirogaleus medius. Genome Biology and Evolution, vol 8: 2413-2426.

Abascal, F., Corvelo, A., Cruz, F., Villanueva-Cañas, J-L., Vlasova, A., (40 more), Mailund, T., Albà, M.M., Gabaldón, T., Alioto, T., Godoy, J.A. (2016) Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian Lynx. Genome Biology, vol 17: 251.

Subirana, J.A., Albà, M.M., Messeguer, X. (2015) High evolutionary turnover of satellite families in Caenorhabditis. BMC Evolutionary Biology, vol 15: 218.

Ruiz-Orera, J., Hernández-Rodríguez, J., Chiva, C., Sabidó, E., Kondova, I., Bontrop, R., Marqués-Bonet, T., Albà, M.M. (2015). Origins of de novo genes in human and chimpanzee. Plos Genetics, vol 11: e1005721.

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, vol 10: e0127462.

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, vol 32: 2263-2272.*co-corresponding.

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: 846-860.

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

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

Villanueva-Cañas, J-L., Faherty, S.L., Yoder, A.D., Alba, M.M. (2014) Comparative Genomics of Mammalian Hibernators Using Gene Networks. Integrative and Comparative Biology, vol 54: 452-462.

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 vol. 30: 1830-1842.

Bornberg-Bauer, E., Albà, M.M. (2013) Dynamics and adaptive benefits of modular protein evolution. Current Opinion in Structural Biology vol. 23: 459-466.

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

Villanueva-Cañas, J-L., Laurie, S., Albà, M.M. (2013) Improving genome-wide scans of positive selection by using protein isoforms of similar length. Genome Biology and Evolution vol. 5: 457-467.

Trilling, M., Bellora, N., Rutkowski, A., de Graaf, M., Dickinson, P., Robertson, K., Prazeres da Costa, M., Ghazal, P., Friedel, C.C., Albà, M.M., Doelken, 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 Research vol. 41: 8107-8125.

Mulero, et al. (including Bellora, N., Albà, M.M.) (2013) Chromatin-bound IkBa is a modulator of PRC2-dependent repression in development and cancer. Cancer Cell vol. 24: 151-166.

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

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

Shikhagaie, M., Mercé-Maldonado, 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, vol. 86: 4091-101.

Toll-Riera, M., Bostick, D., Albà*, M.M., Plotkin*, J.B. (2012) Structure and age jointly influence rates of protein evolution. PLoS Computational Ciology, vol. 8: e1002542. *co-corresponding

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, vol. 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, vol. 89: 753-66.

Toll-Riera, M.,Laurie, S., Albà, M.M. (2011) Lineage-specific Variation in Intensity of Natural Selection in Mammals. Molecular Biology and Evolution, vol. 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, vol. 20: 745-754.

Farré, D., Albà, M.M. (2010) Heterogeneous patterns of gene expression diversification in mammalian gene duplicates. Molecular Biology and Evolution, vol. 27:325-335. [Evaluated by the Faculty of 1000].

Toll-Riera, M., Castelo, R., Bellora, N., Albà, M.M. (2009) Evolution of primate orphan genes. Biochemical Society Transactions, vol 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, vol 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, vol 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 comparative genomics approach. Molecular Biology and Evolution, vol 26: 603-612.

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

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.

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.

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.