Mar Albà 's evolutionary genomics LAB: 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