Publication List

2017

M.Mar Albà

Zinc-finger domains in metazoans: evolution gone wild (Article)

Genome Biology, 18 pp. 168, 2017.

(Abstract | Links | BibTeX | Tags: Evolution, Zinc Fingers)

José Luis Villanueva-Cañas, Jorge Ruiz-Orera, M.Isabel Agea, Maria Gallo, David Andreu, M.Mar Albà

New genes and functional innovation in mammals (Article)

Genome Biology and Evolution, 9 pp. 1886–1900, 2017.

(Abstract | Links | BibTeX | Tags: de novo gene, innovation, mammal, protein function)

Jorge Ruiz-Orera, José Luis Villanueva-Cañas, William Blevins, M.Mar Albà

De novo gene evolution: How do we transition from non-coding to coding? (Conference)

PeerJ preprints 5 (e3031v2), 2017, (The SMBE 2017 Collection).

(Abstract | Links | BibTeX | Tags: de novo gene, long non-coding RNA, Ribo-Seq, ribosome profiling)

Willam Blevins, M.Mar Albà, Lucas Carey

Comparative transcriptomics and ribo-seq: Looking at de novo gene emergence in Saccharomycotina (Conference)

PeerJ preprints 5 (e3030v1), 2017, (The SMBE 2017 Collection).

(Abstract | BibTeX | Tags: de novo gene, yeast)

Tomislav Domazet-Lošo, Anne-Ruxandra Carvunis, M.Mar Albà, Martin Sebastijan Šestak, Robert Bakarić, Rafik Neme, Diethard Tautz

No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution (Article)

Molecular Biology and Evolution, doi: 10.1093/molbev/msw284 2017.

(Abstract | Links | BibTeX | Tags: BLAST, de novo gene, Homology, Sequence Analysis)

2016

F Abascal*, A Corvelo*, F Cruz*, J L Villanueva-Cañas, A Vlasova, M Marcet-Houben, B Martínez-Cruz, JY Cheng, P Prieto, V Quesada, J Quilez, G Li, F García, M Rubio-Camarillo, L Frias, P Ribeca, S Capella-Gutiérrez, JM Rodríguez, F Câmara, E Lowy, L Cozzuto, I Erb, ML Tress, JL Rodriguez-Ales, J Ruiz-Orera, (11 more), A Valencia, I Gut, JL García, R Guigó, WJ Murphy, A Ruiz-Herrera, T Marques-Bonet, G Roma, C Notredame, T Mailund, MM Albà, T Gabaldón, T Alioto, JA Godoy

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx (Article)

Genome Biology, 17 pp. 251, 2016.

(Abstract | Links | BibTeX | Tags: adaptive evolution, lynx)

José Luis Villanueva-Cañas Jorge Ruiz-Orera Isabel Agea Maria Gallo David Andreu M.Mar Albà

New genes and functional innovation in mammals (Article)

bioRxiv, 2016.

(Abstract | Links | BibTeX | Tags: adaptation, de novo genes, Evolution, gene family, mammal)

Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer, M Mar Albà

Functional and non-functional classes of peptides produced by long non-coding RNAs (Article)

bioRxiv, 2016, ISBN: http://dx.doi.org/10.1101/064915 .

(Abstract | Links | BibTeX | Tags: long non-coding RNA, micropeptide, mouse, ribosome profiling, smORF, translation)

Sheena L. Faherty, José Luis Villanueva-Cañas, Peter H. Klopfer, M. Mar Albà, Anne D. Yoder

Gene expression profiling in the hibernating primate, Cheirogaleus medius (Article)

Genome Biology and Evolution, advance access (doi: 10.1093/gbe/evw163) 2016.

(Links | BibTeX | Tags: differential gene expression, hibernation, primate, RNA-Seq, transcriptomics)

Vartia S, Villanueva-Cañas JL, Finarelli J, Farrell ED, Collins PC, Hughes GM, Carlsson JE, Gauthier DT, McGinnity P, Cross TF, FitzGerald RD, Mirimin L, Crispie F, Cotter PD, Carlsson J.

A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding (Article)

R Soc Open Sci, 3 (1), pp. 150565, 2016, ISBN: 10.1098/rsos.150565.

(Abstract | Links | BibTeX | Tags: barcoding, Evolution, microsatellite, sequencing)

2015

Ruiz-Orera, Jorge, Hernandez-Rodriguez, Jessica, Chiva, Cristina, Sabidó, Eduard, Kondova, Ivanela, Bontrop, Ronald, Marqués-Bonet, Tomàs, Albà, M.Mar

Origins of de novo genes in human and chimpanzee (Article)

Plos Genetics, 11 (12), pp. e1005721, 2015.

(Links | BibTeX | Tags: chimpanzee, de novo gene, Evolution, Humans, lncRNA, Promoter, proteomics, ribosome profiling, RNA-Seq, transcription factor binding site, transcriptomics)

van Dijk, David, Dhar, Riddhiman, Missarova, Alsu M, Espinar, Lorena, Blevins, William R, Lehner, Ben, Carey, Lucas B

Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage (Article)

Nature Communications, 6 pp. 7972, 2015, ISBN: 10.1038/ncomms8972.

(Links | BibTeX | Tags: RNA polymerase error rate, transcriptomics, yeast)

Baldo, Laura, Riera, Joan Lluís, Tooming-Klunderud, Ave, Albà, M Mar, Salzburger, Walter

Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes. (Article)

PloS one, 10 (5), pp. e0127462, 2015, ISSN: 1932-6203.

(Abstract | Links | BibTeX | Tags: cichlid fishes, diet, transcriptomics)

Radó-Trilla, Núria, Arató, Krisztina, Pegueroles, Cinta, Raya, Alicia, de la Luna, Susana, Albà, M Mar

Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors. (Article)

Molecular biology and evolution, 2015, ISSN: 1537-1719.

(Abstract | Links | BibTeX | Tags: amino acid tandem repeat, Evolution, Gene Duplication, polyalanine, transcription factor, vertebrates)

Subirana, Juan A., Albà, M. Mar, Messeguer, Xavier

High evolutionary turnover of satellite families in Caenorhabditis (Article)

BMC Evolutionary Biology, 15 (1), pp. 218, 2015, ISSN: 1471-2148.

(Abstract | Links | BibTeX | Tags: Evolution, Repeats, satellite)

2014

Villanueva-Cañas, José Luis, Faherty, Sheena L, Yoder, Anne D, Albà, M Mar

Comparative Genomics of Mammalian Hibernators Using Gene Networks. (Article)

Integrative and comparative biology, 2014, ISSN: 1557-7023.

(Abstract | Links | BibTeX | Tags: )

Ruiz-Orera, Jorge, Messeguer, Xavier, Subirana, Juan Antonio, Alba, M Mar

Long non-coding RNAs as a source of new peptides (Article)

eLife, 3 2014, ISSN: 2050-084X.

(Abstract | Links | BibTeX | Tags: )

Santpere, Gabriel, Darre, Fleur, Blanco, Soledad, Alcami, Antonio, Villoslada, Pablo, Mar Albà, M, Navarro, Arcadi

Genome-wide analysis of wild-type Epstein-Barr virus genomes derived from healthy individuals of the 1,000 Genomes Project. (Article)

Genome biology and evolution, 6 (4), pp. 846–60, 2014, ISSN: 1759-6653.

(Abstract | Links | BibTeX | Tags: )

Gayà-Vidal, Magdalena, Albà, M Mar

Uncovering adaptive evolution in the human lineage (Article)

BMC Genomics, 15 (1), pp. 599, 2014, ISSN: 1471-2164.

(Abstract | Links | BibTeX | Tags: )

2013

Bornberg-Bauer, Erich, Albà, M Mar

Dynamics and adaptive benefits of modular protein evolution (Article)

Current Opinion in Structural Biology, 2013, ISSN: 0959440X.

(Abstract | Links | BibTeX | Tags: )

Villanueva-Cañas, José Luis, Laurie, Steve, Albà, M Mar

Improving genome-wide scans of positive selection by using protein isoforms of similar length. (Article)

Genome biology and evolution, 5 (2), pp. 457–67, 2013, ISSN: 1759-6653.

(Abstract | Links | BibTeX | Tags: )

Mulero, María Carmen, Ferres-Marco, Dolors, Islam, Abul, Margalef, Pol, Pecoraro, Matteo, Toll, Agustí, Drechsel, Nils, Charneco, Cristina, Davis, Shelly, Bellora, Nicolás, Gallardo, Fernando, López-Arribillaga, Erika, Asensio-Juan, Elena, Rodilla, Verónica, González, Jessica, Iglesias, Mar, Shih, Vincent, Albà, M Mar, Di Croce, Luciano, Hoffmann, Alexander, Miyamoto, Shigeki, Villà-Freixa, Jordi, López-Bigas, Nuria, Keyes, Wil

Chromatin-Bound I$kappa$B$alpha$ Regulates a Subset of Polycomb Target Genes in Differentiation and Cancer. (Article)

Cancer cell, 24 (2), pp. 151–66, 2013, ISSN: 1878-3686.

(Abstract | Links | BibTeX | Tags: )

Pegueroles, Cinta, Laurie, Steve, Albà, M Mar

Accelerated evolution after gene duplication: a time-dependent process affecting just one copy. (Article)

Molecular biology and evolution, 2013, ISSN: 1537-1719.

(Abstract | Links | BibTeX | Tags: )

Toll-Riera, Macarena, Albà, M Mar

Emergence of novel domains in proteins. (Article)

BMC evolutionary biology, 13 (1), pp. 47, 2013, ISSN: 1471-2148.

(Abstract | Links | BibTeX | Tags: )

Trilling, Mirko, Bellora, Nicolás, Rutkowski, Andrzej J, de Graaf, Miranda, Dickinson, Paul, Robertson, Kevin, Prazeres da Costa, Olivia, Ghazal, Peter, Friedel, Caroline C, Albà, M Mar, Dölken, Lars

Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis. (Article)

Nucleic acids research, 2013, ISSN: 1362-4962.

(Abstract | Links | BibTeX | Tags: )

2012

Laurie, Steve, Toll-Riera, Macarena, Radó-Trilla, Núria, Albà, M Mar

Sequence shortening in the rodent ancestor. (Article)

Genome research, 22 (3), pp. 478–85, 2012, ISSN: 1549-5469.

(Abstract | Links | BibTeX | Tags: )

Radó-Trilla, Núria, Albà, M Mar

Dissecting the role of low-complexity regions in the evolution of vertebrate proteins. (Article)

BMC evolutionary biology, 12 (1), pp. 155, 2012, ISSN: 1471-2148.

(Abstract | Links | BibTeX | Tags: )

Shikhagaie, Medya, Mercé-Maldonado, Eva, Isern, Elena, Muntasell, Aura, Albà, M Mar, López-Botet, Miguel, Hengel, Hartmut, Angulo, Ana

The HCMV-specific UL1 gene encodes a late phase glycoprotein incorporated in the virion envelope. (Article)

Journal of virology, 2012, ISSN: 1098-5514.

(Abstract | Links | BibTeX | Tags: )

Toll-Riera, Macarena, Bostick, David, Albà, M Mar, Plotkin, Joshua B

Structure and age jointly influence rates of protein evolution. (Article)

PLoS computational biology, 8 (5), pp. e1002542, 2012, ISSN: 1553-7358.

(Abstract | Links | BibTeX | Tags: Animals, Binding Sites, Computational Biology, Eukaryota, Evolution, Humans, Mice, Molecular, Protein Conformation, Protein Stability, Proteins, Proteins: chemistry, Proteins: genetics, Proteins: metabolism, Solvents)

Toll-Riera, Macarena, Radó-Trilla, Núria, Martys, Florian, Albà, M Mar

Role of Low-Complexity Sequences in the Formation of Novel Protein Coding Sequences. (Article)

Molecular biology and evolution, 29 (3), pp. 883–6, 2012, ISSN: 1537-1719.

(Abstract | Links | BibTeX | Tags: )

2011

Toll-Riera, M, Laurie, S, Radó-Trilla, N, Albà, MM

Partial gene duplication and the formation of novel genes (Incollection)

Friedberg, Felix (Ed.): Gene Duplication, Intech, Rijeka, 2011.

(Links | BibTeX | Tags: )

Toll-Riera, Macarena, Laurie, Steve, Albà, M Mar

Lineage-specific variation in intensity of natural selection in mammals. (Article)

Molecular biology and evolution, 28 (1), pp. 383–98, 2011, ISSN: 1537-1719.

(Abstract | Links | BibTeX | Tags: Amino Acid Sequence, Amino Acid Substitution, Animals, Evolution, F-Box Proteins, F-Box Proteins: genetics, G-Protein-Coupled, G-Protein-Coupled: genetics, Genetic, Genetic Variation, Humans, Mammals, Mammals: genetics, Molecular, Molecular Sequence Data, N-Methyl-D-Aspartate, N-Methyl-D-Aspartate: genetics, Odorant, Odorant: genetics, Receptors, Selection, Sequence Alignment)

Engel, Pablo, Pérez-Carmona, Natàlia, Albà, M Mar, Robertson, Kevin, Ghazal, Peter, Angulo, Ana

Human cytomegalovirus UL7, a homologue of the SLAM-family receptor CD229, impairs cytokine production. (Article)

Immunology and cell biology, 89 (7), pp. 753–66, 2011, ISSN: 1440-1711.

(Abstract | Links | BibTeX | Tags: )

2010

Morcillo, C, Albà, MM, Navarro, A

Genoma y enfermedades complejas (Incollection)

Villoslada, Pablo (Ed.): Tratado de Esclerosis Múltiple, Marge Books, Barcelona, 2010.

(BibTeX | Tags: )

Mularoni, Loris, Ledda, Alice, Toll-Riera, Macarena, Albà, M Mar

Natural selection drives the accumulation of amino acid tandem repeats in human proteins. (Article)

Genome research, 20 (6), pp. 745–54, 2010, ISSN: 1549-5469.

(Abstract | Links | BibTeX | Tags: Amino Acid, Amino Acid Sequence, Amino Acids, Amino Acids: chemistry, Amino Acids: genetics, Animals, Genetic, Humans, Molecular Sequence Data, Proteins, Proteins: chemistry, Proteins: genetics, Repetitive Sequences, Selection, Sequence Homology)

Farré, Domènec, Albà, M Mar

Heterogeneous patterns of gene-expression diversification in mammalian gene duplicates. (Article)

Molecular biology and evolution, 27 (2), pp. 325–35, 2010, ISSN: 1537-1719.

(Abstract | Links | BibTeX | Tags: Animals, Evolution, Gene Duplication, Genetic, Humans, Mammals, Mammals: genetics, Models, Molecular)

2009

Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM.

Origin of primate orphan genes: a comparative genomics approach (Article)

Molecular Biology and Evolution, 26 (3), pp. 603-612, 2009.

(BibTeX | Tags: de novo gen, primate)

Albà MM

Temporal aspects of gene evolution (Incollection)

Dopazo,; Navarro, (Ed.): Evolución y Adaptación: 150 años después del origen de las especies, Sociedad Española de Biologia Evolutiva, Barcelona, 2009.

(BibTeX | Tags: )

Rodilla, Verónica, Villanueva, Alberto, Obrador-Hevia, Antonia, Robert-Moreno, Alex, Fernández-Majada, Vanessa, Grilli, Andrea, López-Bigas, Nuria, Bellora, Nicolás, Albà, M Mar, Torres, Ferran, Duñach, Mireia, Sanjuan, Xavier, Gonzalez, Sara, Gridley, Thomas, Capella, Gabriel, Bigas, Anna, Espinosa, Lluís

Jagged1 is the pathological link between Wnt and Notch pathways in colorectal cancer. (Article)

Proceedings of the National Academy of Sciences of the United States of America, 106 (15), pp. 6315–20, 2009, ISSN: 1091-6490.

(Abstract | Links | BibTeX | Tags: Alleles, Animals, beta Catenin, beta Catenin: metabolism, Calcium-Binding Proteins, Calcium-Binding Proteins: genetics, Calcium-Binding Proteins: metabolism, Cell Line, Cell Nucleus, Cell Nucleus: metabolism, Colorectal Neoplasms, Colorectal Neoplasms: blood supply, Colorectal Neoplasms: genetics, Colorectal Neoplasms: metabolism, Colorectal Neoplasms: pathology, Gene Expression Profiling, Gene Expression Regulation, Genetic, Genetic: genetics, Humans, Intercellular Signaling Peptides and Proteins, Intercellular Signaling Peptides and Proteins: gen, Intercellular Signaling Peptides and Proteins: met, Membrane Proteins, Membrane Proteins: genetics, Membrane Proteins: metabolism, Mice, Neoplastic, Notch, Notch: metabolism, Receptors, Signal Transduction, TCF Transcription Factors, TCF Transcription Factors: metabolism, Transcription, Transgenic, Wnt Proteins, Wnt Proteins: metabolism)

Salichs, Eulàlia, Ledda, Alice, Mularoni, Loris, Albà, M Mar, de la Luna, Susana

Genome-wide analysis of histidine repeats reveals their role in the localization of human proteins to the nuclear speckles compartment. (Article)

PLoS genetics, 5 (3), pp. e1000397, 2009, ISSN: 1553-7404.

(Abstract | Links | BibTeX | Tags: Amino Acids, Cell Line, Cell Nucleus, Cell Nucleus: chemistry, Cell Nucleus: genetics, Cell Nucleus: metabolism, Genome, Histidine, Histidine: chemistry, Histidine: genetics, Histidine: metabolism, human, Humans, Molecular Sequence Data, Nuclear Localization Signals, Nuclear Proteins, Nuclear Proteins: chemistry, Nuclear Proteins: genetics, Nuclear Proteins: metabolism, Protein Transport, Proteins, Proteins: chemistry, Proteins: genetics, Proteins: metabolism, Sequence Alignment, Tandem Repeat Sequences)

Toll-Riera, Macarena, Castelo, Robert, Bellora, Nicolás, Albà, M Mar

Evolution of primate orphan proteins. (Article)

Biochemical Society transactions, 37 (Pt 4), pp. 778–82, 2009, ISSN: 1470-8752.

(Abstract | Links | BibTeX | Tags: Animals, Evolution, Gene Duplication, Genome, Genome: genetics, Molecular, Primates, Primates: genetics, Proteins, Proteins: genetics)

2008

Mularoni, L, Toll-Riera, M, Albà, MM

Trinucleotide repeats in the human and ape genomes (Incollection)

Kehrer-Sawatzki,; Cooper, (Ed.): Handbook of human molecular evolution 2, John Wiley and Sons, Chichester, 2008.

(BibTeX | Tags: )

Mularoni, L, Toll-Riera, M, Albà, MM

Trinucleotide repeats in human and ape genomes (Incollection)

Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, UK, 2008, ISBN: 0470016175.

(Links | BibTeX | Tags: )

Racz, Ildiko, Nadal, Xavier, Alferink, Judith, Baños, Josep E, Rehnelt, Jennifer, Martín, Miquel, Pintado, Belén, Gutierrez-Adan, Alfonso, Sanguino, Elena, Bellora, Nicolas, Manzanares, Jorge, Zimmer, Andreas, Maldonado, Rafael

Interferon-gamma is a critical modulator of CB(2) cannabinoid receptor signaling during neuropathic pain. (Article)

The Journal of neuroscience : the official journal of the Society for Neuroscience, 28 (46), pp. 12136–45, 2008, ISSN: 1529-2401.

(Abstract | Links | BibTeX | Tags: Animals, Astrocytes, Astrocytes: immunology, Cannabinoid, CB2, CB2: genetics, CB2: immunology, CB2: metabolism, CCR2, CCR2: immunology, CCR2: metabolism, Cells, Cultured, Gene Knockout Techniques, Gene Knockout Techniques: methods, Hyperalgesia, Hyperalgesia: immunology, Hyperalgesia: physiopathology, Interferon-gamma, Interferon-gamma: genetics, Interferon-gamma: immunology, Interferon-gamma: metabolism, Knockout, Male, Mice, Microglia, Microglia: drug effects, Microglia: immunology, Microglia: metabolism, Neuralgia, Neuralgia: genetics, Neuralgia: immunology, Neuralgia: metabolism, Neurons, Neurons: immunology, Nitric Oxide Synthase Type II, Nitric Oxide Synthase Type II: immunology, Nitric Oxide Synthase Type II: metabolism, Peripheral Nerves, Peripheral Nerves: immunology, Peripheral Nerves: injuries, Peripheral Nerves: physiopathology, Peripheral Nervous System Diseases, Peripheral Nervous System Diseases: genetics, Peripheral Nervous System Diseases: immunology, Peripheral Nervous System Diseases: metabolism, Receptor, Receptors, Signal Transduction, Signal Transduction: genetics, Signal Transduction: immunology, Spinal Cord, Spinal Cord: immunology, Spinal Cord: metabolism, Spinal Cord: physiopathology, Up-Regulation, Up-Regulation: immunology)

Toll-Riera, Macarena, Castresana, Jose, Albà, M. Mar

Evolutionary Biology from Concept to Application (Book)

Springer Berlin Heidelberg, Berlin, Heidelberg, 2008, ISBN: 978-3-540-78992-5.

(Abstract | Links | BibTeX | Tags: Biomedical and Life Sciences)

2007

Bellora, Nicolás, Farré, Domènec, Albà, M Mar

Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters. (Article)

BMC genomics, 8 pp. 459, 2007, ISSN: 1471-2164.

(Abstract | Links | BibTeX | Tags: Animals, Databases, Gene Expression Regulation, Gene Expression Regulation: genetics, Genetic, Genetic: genetics, Mice, Nucleic Acid, Organ Specificity, Organ Specificity: genetics, Promoter Regions, Software, Transcription Factors, Transcription Factors: metabolism)

Bellora, Nicolás, Farré, Domènec, Mar Albà, M

PEAKS: identification of regulatory motifs by their position in DNA sequences. (Article)

Bioinformatics (Oxford, England), 23 (2), pp. 243–4, 2007, ISSN: 1367-4811.

(Abstract | Links | BibTeX | Tags: Algorithms, Automated, Automated: methods, Base Sequence, Chromosome Mapping, Chromosome Mapping: methods, DNA, DNA: genetics, DNA: methods, Molecular Sequence Data, Nucleic Acid, Nucleic Acid: genetics, Pattern Recognition, Regulatory Sequences, Sequence Alignment, Sequence Alignment: methods, Sequence Analysis, Software, Transcriptional Activation, Transcriptional Activation: genetics)

Albà, M M, Tompa, P, Veitia, R A

Amino acid repeats and the structure and evolution of proteins. (Article)

Genome dynamics, 3 pp. 119–30, 2007, ISSN: 1660-9263.

(Abstract | Links | BibTeX | Tags: Amino Acid, Animals, Base Composition, Evolution, Humans, Molecular, Open Reading Frames, Open Reading Frames: genetics, Peptides, Peptides: chemistry, Proteins, Proteins: chemistry, Proteins: genetics, Repetitive Sequences)

Mularoni, Loris, Veitia, Reiner A, Albà, M Mar

Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. (Article)

Genomics, 89 (3), pp. 316–25, 2007, ISSN: 0888-7543.

(Abstract | Links | BibTeX | Tags: Amino Acid, Amino Acid Sequence, Animals, Complementary, Conserved Sequence, DNA, Evolution, Genetic, Humans, Mice, Molecular, Point Mutation, Proteins, Proteins: chemistry, Proteins: genetics, Repetitive Sequences, Selection, Trinucleotide Repeats)

Farré, Domènec, Bellora, Nicolás, Mularoni, Loris, Messeguer, Xavier, Albà, M Mar

Housekeeping genes tend to show reduced upstream sequence conservation. (Article)

Genome biology, 8 (7), pp. R140, 2007, ISSN: 1465-6914.

(Abstract | Links | BibTeX | Tags: Animals, Base Sequence, Conserved Sequence, CpG Islands, Evolution, Gene Expression, Genetic, Genetic Variation, Humans, Mice, Molecular, Molecular Sequence Data, Promoter Regions)

Albà, M Mar, Castresana, Jose

On homology searches by protein Blast and the characterization of the age of genes. (Article)

BMC evolutionary biology, 7 pp. 53, 2007, ISSN: 1471-2148.

(Abstract | Links | BibTeX | Tags: Amino Acid, Animals, Computational Biology, Databases, Evolution, Genes, Humans, Molecular, Phylogeny, Protein, Sequence Analysis, Sequence Homology)

2006

Blanco, Enrique, Farré, Domènec, Albà, M Mar, Messeguer, Xavier, Guigó, Roderic

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. (Article)

Nucleic acids research, 34 (Database issue), pp. D63–7, 2006, ISSN: 1362-4962.

(Abstract | Links | BibTeX | Tags: Animals, Binding Sites, Chickens, Chickens: genetics, Databases, Genetic, Genomics, Humans, Internet, Mice, Nucleic Acid, Promoter Regions, Rats, Transcription Factors, Transcription Factors: metabolism, User-Computer Interface)

Mularoni, Loris, Guigó, Roderic, Albà, M Mar

Mutation patterns of amino acid tandem repeats in the human proteome. (Article)

Genome biology, 7 (4), pp. R33, 2006, ISSN: 1465-6914.

(Abstract | Links | BibTeX | Tags: Amino Acid, Amino Acid Substitution, Amino Acid: genetics, Codon, Expressed Sequence Tags, Genetic, Humans, Mutation, Polymorphism, Protein, Proteome, Proteome: genetics, Repetitive Sequences, Sequence Analysis)

Furney, Simon J, Albà, M Mar, López-Bigas, Núria

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. (Article)

BMC genomics, 7 pp. 165, 2006, ISSN: 1471-2164.

(Abstract | Links | BibTeX | Tags: Amino Acid, Animals, Caenorhabditis elegans, Caenorhabditis elegans: genetics, Computational Biology, Conserved Sequence, Dominant, Essential, Evolution, Genes, Genetic, Genetic Diseases, Genetic Structures, Humans, Inborn, Inborn: classification, Inborn: genetics, Mice, Molecular, Mutation, Pan troglodytes, Pan troglodytes: genetics, Recessive, Selection, Sequence Homology)

2005

Albà, M Mar, Castresana, Jose

Inverse relationship between evolutionary rate and age of mammalian genes. (Article)

Molecular biology and evolution, 22 (3), pp. 598–606, 2005, ISSN: 0737-4038.

(Abstract | Links | BibTeX | Tags: Animals, DNA, Evolution, Genome, human, Humans, Mice, Molecular, Sequence Analysis)

2004

Albà, M Mar, Guigó, Roderic

Comparative analysis of amino acid repeats in rodents and humans. (Article)

Genome research, 14 (4), pp. 549–54, 2004, ISSN: 1088-9051.

(Abstract | Links | BibTeX | Tags: Amino Acid, Amino Acid: genetics, Amino Acid: physiology, Animals, Chromosome Mapping, Chromosome Mapping: methods, Chromosome Mapping: statistics & numerical data, Computational Biology, Computational Biology: methods, Computational Biology: statistics & numerical data, GC Rich Sequence, GC Rich Sequence: genetics, Humans, Mice, Proteins, Proteins: chemistry, Proteins: genetics, Proteins: physiology, Rats, Repetitive Sequences, Trinucleotide Repeats, Trinucleotide Repeats: genetics)

Huang, Hui, Winter, Eitan E, Wang, Huajun, Weinstock, Keith G, Xing, Heming, Goodstadt, Leo, Stenson, Peter D, Cooper, David N, Smith, Douglas, Albà, M Mar, Ponting, Chris P, Fechtel, Kim

Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. (Article)

Genome biology, 5 (7), pp. R47, 2004, ISSN: 1465-6914.

(Abstract | Links | BibTeX | Tags: Amino Acid, Amino Acid: genetics, Animal, Animals, Chromosome Mapping, Chromosome Mapping: methods, Conserved Sequence, Conserved Sequence: genetics, Disease Models, Evolution, Fishes, Fishes: genetics, Fungal, Fungal: genetics, Genes, Genes: genetics, Genes: physiology, Genetic, Genetic Diseases, Genome, Helminth, Helminth: genetics, human, Humans, Inborn, Inborn: genetics, Inborn: physiopathology, Insect, Insect: genetics, Mice, Molecular, Mutagenesis, Mutagenesis: genetics, Nucleic Acid, Nucleotides, Nucleotides: genetics, Point Mutation, Point Mutation: genetics, Rats, Repetitive Sequences, Selection, Sequence Homology, Trinucleotide Repeat Expansion, Trinucleotide Repeat Expansion: genetics)

Castresana, Jose, Guigó, Roderic, Albà, M Mar

Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome. (Article)

Journal of molecular evolution, 59 (1), pp. 72–9, 2004, ISSN: 0022-2844.

(Abstract | Links | BibTeX | Tags: Base Composition, Base Composition: genetics, Chromatin, Chromatin: metabolism, Chromosomes, Computational Biology, Databases, DNA-Binding Proteins, DNA-Binding Proteins: genetics, DNA-Binding Proteins: metabolism, Evolution, Genetic, Genome, human, Humans, Introns, Introns: genetics, Models, Molecular, Multigene Family, Multigene Family: genetics, Pair 19, Pair 19: genetics, Phylogeny, Zinc Fingers, Zinc Fingers: genetics)

Gibbs, Richard A, Et al.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. (Article)

Nature, 428 (6982), pp. 493–521, 2004, ISSN: 1476-4687.

(Abstract | Links | BibTeX | Tags: Animals, Base Composition, Centromere, Centromere: genetics, Chromosomes, CpG Islands, CpG Islands: genetics, DNA, DNA Transposable Elements, DNA Transposable Elements: genetics, Evolution, Gene Duplication, Genome, Genomics, Humans, Inbred BN, Inbred BN: genetics, Introns, Introns: genetics, Male, Mammalian, Mammalian: genetics, Mice, Mitochondrial, Mitochondrial: genetics, Models, Molecular, Mutagenesis, Nucleic Acid, Nucleic Acid: genetics, Polymorphism, Rats, Regulatory Sequences, Retroelements, Retroelements: genetics, RNA, RNA Splice Sites, RNA Splice Sites: genetics, Sequence Analysis, Single Nucleotide, Single Nucleotide: genetics, Telomere, Telomere: genetics, Untranslated, Untranslated: genetics)

2002

Albà, M Mar, Laskowski, Roman A, Hancock, John M

Detecting cryptically simple protein sequences using the SIMPLE algorithm. (Article)

Bioinformatics (Oxford, England), 18 (5), pp. 672–8, 2002, ISSN: 1367-4803.

(Abstract | Links | BibTeX | Tags: Algorithms, Amino Acid, Amino Acid Sequence, Amino Acid: genetics, Databases, Genetic, Genetic Variation, Internet, Minisatellite Repeats, Minisatellite Repeats: genetics, Models, Molecular Sequence Data, Protein, Protein: methods, Proteins, Proteins: chemistry, Repetitive Sequences, Saccharomyces cerevisiae, Saccharomyces cerevisiae: genetics, Sensitivity and Specificity, Sequence Analysis, Sequence Homology, Software, Statistical)

Messeguer, Xavier, Escudero, Ruth, Farré, Domènec, Núñez, Oscar, Martínez, Javier, Albà, M Mar

PROMO: detection of known transcription regulatory elements using species-tailored searches. (Article)

Bioinformatics (Oxford, England), 18 (2), pp. 333–4, 2002, ISSN: 1367-4803.

(Abstract | Links | BibTeX | Tags: Animals, Binding Sites, Binding Sites: genetics, Computational Biology, DNA, DNA: genetics, DNA: metabolism, Humans, Software, Species Specificity, Transcription Factors, Transcription Factors: metabolism)