Publications

Boix, O., Martinez, M., Vidal, S.,..(including Albà MM).., Abad, M. (2022). pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation. Nature Communications, 13(1):6840.

Mudge, J.M., Ruiz-Orera, J., Prensner, J.R., .. (including Albà MM).., van Heesch, S. (2022). Standardized annotation of translated open reading frames. Nature Biotechnology, 40(7):994-999.

de la Rubia, I., Srivastava1, A., Xue, W., Indi, J.A., Carbonell‑Sala, S., Lagarde, J., Albà, M.M.*, Eyras, E.*(2022). RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing. Genome Biology, 23:153. *co-corresponding

Montañés, J.C., Huertas, M., Moro, S.G., Blevins, W.R., Carmona, M., Ayté, J., Hidalgo, E., Albà, M.M. (2022). Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms. Genome Research, 32:1215-1227.

de Jong, J.J., Valderrama, B.P., Perera-Bel, J., Juanpere, N., Cejas, P., Long, H., Albà, M.M., Gibb, E.A., Bellmunt, J. (2022). Non-muscle-invasive micropapillary bladder cancer has a distinct lncRNA profile associated with unfavorable prognosis. British Journal of Cancer, 127(2):313-320.

Pérez-Núñez, I., Rozalén, C., Palomeque, J.A., Sangrador, I, Dalmau, M., Comerma, L, Hernández-Prat, A., Casadevall, D., Menéndez, S., Liu, D.D., Shen, M., Berenguer, J., Rius Ruiz, I., Peña, R., Montañés, J.C., Albà, M.M., Bonnin, S., Ponomarenko, J., Gomis, R.R., Cejalvo, J.M., Servitja, S., Marzese, D.M., Morey, Ll., Woorwerk, L., Arribas, J., Bermejo, B., Kok, M., Pusztai, L., Kang, Y., Albanell, J., Celià-Terrassa, T. (2022). LCOR mediates interferon-independent tumor immunity and responsiveness to immune-checkpoint blockade in triple-negative breast cancer. Nature Cancer, vol. 3:355-370.

Senís, E., Esgleas, M., Najas, S., Jiménez, V., Bertani, C., Giménez-Alejandre, M., Ruiz-Orera, J., Hergueta, M., Jiménez, M., Giralt, A., Nuciforo, P., Albà, M.M., Del Toro, D., Peinado, H., Hove-Madsen, J., Götz, M. Abad, M. (2021). TUNAR lncRNA encodes a microprotein that regulates neural differentiation and neurite formation by modulating calcium dynamics. Frontiers in Cell and Developmental Biology, vol. 9:747667.

Hernández-Fernández, J., Pinzón Velasco, A.M., López Barrera, E.A., Rodríguez Becerra, M.D.P., Villanueva-Cañas, J.L., Albà, M.M., Mariño Ramírez, L. (2021). De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins. PeerJ, vol. 9: e12395.

Moro, S.G., Hermans, C., Ruiz-Orera, J., Albà, M.M. (2021) Impact of uORFs in mediating regulation of translation in stress conditions. BMC Mol Cell Biol, vol. 22: 29.

Blevins, W.R., Ruiz-Orera, J., Messeguer, X., Blasco-Moreno, B., Villanueva-Cañas, J-L., Espinar, L., Díez, J., Carey, L.B., Albà, M.M. (2021) Uncovering de novo gene birth in yeast using deep transcriptomics. Nature Communications, vol. 12:604.

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 M.M. (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., Albà, 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 Biology, 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.