Mar Albà 's evolutionary genomics LAB
Mar
Albà
Principal Investigator
Mar obtained her PhD at the University of Barcelona in 1997 and a Master in Bioinformatics and Molecular Modeling at the University of London in 1999. She worked as a postdoc in the laboratories of John Hancock (Medical Research Council, UK), on the evolution of amino acid tandem repeats, and of Paul Kellam (University College London), on virus genomics.
In 2002 she obtained a tenure-track position at Universitat Pompeu Fabra (UPF, Barcelona) and in 2005 she was appointed ICREA Research Professor at Hospital del Mar Research Institute (HMRIB) She leads the Evolutionary Genomics group at GRIB (HMRIB-UPF), which specializes in transcriptomics approaches to understand the evolution of genes and the expression of microproteins in cancer.
recent publications
Boll, L., Vázquez Montes de Oca, S., Camarena, M.E., Castelo, R, Bellmunt J, Perera-Bel, J., Albà, M.M. 2025
Predicting immunotherapy response of advanced bladder cancer through a meta-analysis of six independent cohorts
Nature Communications 16(1):1213
Camarena, M.E., Theunissen, P., Ruiz, M., Ruiz-Orera, J., Calvo-Serra, B., Castelo, R., Castro, C., Sarobe, P., Fortes, P. * , Perera-Bel, J. * , Albà, M.M. 2024
Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer meta-cohort
Science Advances 10 (28):eadn3628
Vara, C., Montañés, J.C., Albà, M.M. 2024
High polymorphism levels of de novo ORFs in a Yoruba human population
Genome Biology and Evolution 16(7):evae126
Montañés, J.C., Huertas, M., Messeguer, X., Albà, M.M. 2023
Evolutionary trajectories of new duplicated and putative de novo genes
Molecular Biology and Evolution 40(5):msad098
Boll, L. #, Perera-Bel, J. #, Rodríguez-Vida, A., Arpí, O., Rovira, A., Juanpere, N., Vázquez, S., Hernández-Llodrà, S., Lloreta, J., Albà, M.M. *, Bellmunt, J. * 2023
The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer.
Scientific Reports 13:15287
Papadopoulos, C., Albà, M.M. 2023
Newly evolved genes in the human lineage are functional.
Trends in Genetics 39(4):235-236
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.
Boix, O., Martinez, M., Vidal, S., ..(including Albà, M.M.).., 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, M.M.).., 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
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
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
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
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
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
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
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., Albà, M.M. 2002
PROMO: detection of known transcription regulatory elements using species-tailored searches
Bioinformatics vol. 18 333-334
* co-corresponding
# co-first
Mar Albà 's evolutionary genomics LAB
@ Barcelona Biomedical Research Park (PRBB)