Publication List

@article{Mularoni2006,
title = {Mutation patterns of amino acid tandem repeats in the human proteome.},
author = {Mularoni, Loris and Guigó, Roderic and Albà, M Mar},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1557989&tool=pmcentrez&rendertype=abstract},
issn = {1465-6914},
year = {2006},
date = {2006-01-01},
journal = {Genome biology},
volume = {7},
number = {4},
pages = {R33},
abstract = {Amino acid tandem repeats are found in nearly one-fifth of human proteins. Abnormal expansion of these regions is associated with several human disorders. To gain further insight into the mutational mechanisms that operate in this type of sequence, we have analyzed a large number of mutation variants derived from human expressed sequence tags (ESTs).},
keywords = {Amino Acid, Amino Acid Substitution, Amino Acid: genetics, Codon, Expressed Sequence Tags, Genetic, Humans, Mutation, Polymorphism, Protein, Proteome, Proteome: genetics, Repetitive Sequences, Sequence Analysis}
}

@article{Huang2004,
title = {Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes.},
author = {Huang, Hui and Winter, Eitan E and Wang, Huajun and Weinstock, Keith G and Xing, Heming and Goodstadt, Leo and Stenson, Peter D and Cooper, David N and Smith, Douglas and Albà, M Mar and Ponting, Chris P and Fechtel, Kim},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=463309&tool=pmcentrez&rendertype=abstract},
issn = {1465-6914},
year = {2004},
date = {2004-01-01},
journal = {Genome biology},
volume = {5},
number = {7},
pages = {R47},
abstract = {Model organisms have contributed substantially to our understanding of the etiology of human disease as well as having assisted with the development of new treatment modalities. The availability of the human, mouse and, most recently, the rat genome sequences now permit the comprehensive investigation of the rodent orthologs of genes associated with human disease. Here, we investigate whether human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change.},
keywords = {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}
}

@article{Alba2004,
title = {Comparative analysis of amino acid repeats in rodents and humans.},
author = {Albà, M Mar and Guigó, Roderic},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=383298&tool=pmcentrez&rendertype=abstract},
issn = {1088-9051},
year = {2004},
date = {2004-01-01},
journal = {Genome research},
volume = {14},
number = {4},
pages = {549--54},
abstract = {Amino acid tandem repeats, also called homopolymeric tracts, are extremely abundant in eukaryotic proteins. To gain insight into the genome-wide evolution of these regions in mammals, we analyzed the repeat content in a large data set of rat-mouse-human orthologs. Our results show that human proteins contain more amino acid repeats than rodent proteins and that trinucleotide repeats are also more abundant in human coding sequences. Using the human species as an outgroup, we were able to address differences in repeat loss and repeat gain in the rat and mouse lineages. In this data set, mouse proteins contain substantially more repeats than rat proteins, which can be at least partly attributed to a higher repeat loss in the rat lineage. The data are consistent with a role for trinucleotide slippage in the generation of novel amino acid repeats. We confirm the previously observed functional bias of proteins with repeats, with overrepresentation of transcription factors and DNA-binding proteins. We show that genes encoding amino acid repeats tend to have an unusually high GC content, and that differences in coding GC content among orthologs are directly related to the presence/absence of repeats. We propose that the different GC content isochore structure in rodents and humans may result in an increased amino acid repeat prevalence in the human lineage.},
keywords = {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}
}

@article{Alba2002,
title = {Detecting cryptically simple protein sequences using the SIMPLE algorithm.},
author = {Albà, M Mar and Laskowski, Roman A and Hancock, John M},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12050063},
issn = {1367-4803},
year = {2002},
date = {2002-01-01},
journal = {Bioinformatics (Oxford, England)},
volume = {18},
number = {5},
pages = {672--8},
abstract = {Low-complexity or cryptically simple sequences are widespread in protein sequences but their evolution and function are poorly understood. To date methods for the detection of low complexity in proteins have been directed towards the filtering of such regions prior to sequence homology searches but not to the analysis of the regions per se. However, many of these regions are encoded by non-repetitive DNA sequences and may therefore result from selection acting on protein structure and/or function.},
keywords = {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}
}