Bioinformatics Unit

Instituto de Biomedicina de Valencia (CSIC) / Universidad de Valencia











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Updated October 11th, 2010

Aldecoa R, Marín I (2010) Jerarca: efficient analysis of complex networks using hierarchical clustering. PloS ONE 5: 11585. [PDF]

Marín I (2010) Diversification and specialization of plant RBR ubiquitin ligases. PLoS ONE 5: e11579. [PDF]

Marín I (2010) GIN transposons: Genetic elements linking retrotransposons and genes. Molecular Biology and Evolution 27: 1903-1911. [PDF]

Gallach M, Arnau V, Aldecoa R, Marín I (2010) A sequence motif enriched in regions bound by the Drosophila dosage compensation complex. BMC Genomics 11: 169 [PDF]

Marín I (2010) Animal HECT ubiquitin ligases: evolution and functional implications. BMC Evolutionary Biology 10: 56 [PDF]

Marín I (2009) Diversification of the culllin family. BMC Evolutionary Biology 9: 267 [PDF]

Marco A, Marín I (2009) Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell. BMC Systems Biology 3: 69. [PDF]

Marco A, Marín I (2009) CGIN1: a retroviral contribution to mammalian genomes. Molecular Biology and Evolution 26: 2167-2170. [PDF]

Marín I (2009) RBR ubiquitin ligases: Diversification and streamlining in animal lineages. Journal of Molecular Evolution 69:54-64 [PDF]

Marín I, Hoyas S (2009) Basic networks: definition and applications. Journal of Theoretical Biology 258: 53-59 [PDF]

Marín I (2008) Ancient Origin of the Parkinson Disease Gene LRRK2. Journal of Molecular Evolution 67: 41-50 [PDF]

Marín I, van Egmond WN, van Haastert PJ (2008) The Roco protein family: a functional perspective. FASEB Journal 22: 3103-3110  [PDF]

Marco A, Marín I (2008) How Athila retrotransposons survive in the Arabidopsis genome. BMC Genomics 9: 219 [PDF]

Marín I (2008) Dosage Compensation Mechanisms: Evolution. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester. [DOI:10.1002/9780470015902.a0006128.pub2] [ELS web page]

Arnau V, Gallach M, Marín I (2008) Fast comparison of DNA sequences by oligonucleotide profiling. BMC Research Notes 1: 5 [PDF] [Supplementary information] [UVWORD web page]

Gallach M, Arnau V, Marín I (2007) Global patterns of sequence evolution in Drosophila. BMC Genomics. 8: 408 [PDF]

Marco A, Marín I (2007)  A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification. BMC Bioinformatics 8: 442 [PDF]

Lucas JI, Marín I (2007) A new evolutionary paradigm for the Parkinson disease gene DJ-1. Molecular Biology and Evolution 24: 551-61 [PDF]

Yang XY, Ripoll A, Arnau V, Marín I, Luque E (2006) Genomic-scale analysis of DNA words of arbitrary length by parallel computation. NIC Series 33: 623-630. [PDF]

Marín I (2006) The Parkinson disease gene LRRK2: evolutionary and structural insights. Molecular Biology and Evolution 23: 2423-2433 [PDF]  [Supplementary material]

Ruiz-González MX, Marín I (2006) Proteasome-related HslU and HslV genes typical of eubacteria are widespread in eukaryotes. Journal of Molecular Evolution 63: 504-512 [PDF]

Arnau V, Gallach M, Lucas JI, Marín I (2006) UVPAR: fast detection of functional shifts in duplicate genes. BMC Bioinformatics. 7:174 [PDF]

Lucas JL, Arnau V, Marín I (2006) Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism. Journal of Molecular Biology 357: 9-17 [PDF] [Supplementary information]

Marín I, Vallejo J (2005) Parkinson disease: from cellular and animal models to genomics. Current Genomics 6: 241-50 [PDF]

Marco A, Marín I (2005) Retrovirus-like elements in plants. Recent Research Developments in Plant Science 3: 15-24 [PDF]

Arnau V,  Mars S, Marín I (2005) Iterative cluster analysis of protein interaction data. Bioinformatics. 21: 364-78 [UVCLUSTER web page]  [PDF]

Marín I, Lucas JI, Gradilla AC, Ferrús A (2004) Parkin and relatives: the RBR family of ubiquitin ligases. Physiological Genomics. 17: 253–63 [PDF]

Ruiz-Gonzalez MX, Marín I (2004) New insights into the evolutionary history of Type 1 rhodopsins. Journal of Molecular Evolution  58: 348–358  [PDF] 

Marco A, Cuesta A, Pedrola L, Palau F, Marín I (2004) Evolutionary and Structural analyses of GDAP1, involved in Charcot-Marie-Tooth disease, characterize a novel class of Glutathione transferase-related genes. Molecular Biology and Evolution 21: 176-187  [PDF]

Arnau V, Marín I (2004) Fast analysis of highly repetitive sequences in human chromosomes using a novel search algorithm. WSEAS Transactions on Biology and Biomedicine 1: 107-111. [PDF]

Arnau V, Marín I (2003) A fast algorithm for the exhaustive analysis of 12-nucleotide-long DNA sequences. Applications to human genomics.  Proceedings of the International Parallel and Distributed Processing Symposium (IPDPS’03). [PDF]

Arnau V, Marín I (2003) A hierarchical clustering strategy and its application to proteomic interaction data. Lecture Notes in Computer Science 2652: 62-69. [PDF]

Marín I (2003) Dosage Compensation Mechanisms: Evolution. Nature Encyclopedia of the Human Genome. Nature Publishing Group. [NPG] [PDF] Also published by John Wiley & Sons as "Encyclopedia of the Human Genome". 

Fares MA, Bezemer D, Moya A, Marín I (2003) Selection on coding regions determined Hox7 genes evolution. Molecular Biology and Evolution 20: 2104-2112.  [PDF]

Marín I (2003) Evolution of chromatin-remodeling complexes: comparative genomics reveals the ancient origin of  "novel" compensasome genes. Journal of Molecular Evolution 56: 527-539. [PDF]

Marín I, Ferrús A (2002) Comparative genomics of the RBR family, including the Parkinson's disease-related gene parkin and the genes of the Ariadne Subfamily. Molecular Biology and Evolution 19: 2039-2050. [PDF]

Cuesta A, Pedrola L, Sevilla T, Garcia-Planells J, Chumillas MJ, Mayordomo F, LeGuern E, Marín I, Vilchez JJ, Palau F (2002) The gene encoding ganglioside-induced differentiation-associated protein 1 is mutated in axonal Charcot-Marie-Tooth type 4A disease. Nature Genetics 30: 22-25. [PDF]

Llorens C, Marín I (2001) A mammalian gene evolved from the integrase domain of an LTR retrotransposon. Molecular Biology and Evolution 18: 1597-1600 [PDF] 

Sanjuan R, Marín I (2001) Tracing the origin of the compensasome: evolutionary history of DEAH helicase and MYST acetyltransferase gene families. Molecular Biology and Evolution18: 330-343. [PDF]

Marín I, Fares MA, Gonzalez-Candelas F, Barrio E, Moya A (2001) Detecting changes in the functional constraints of paralogous genes. Journal of Molecular Evolution 52: 17-28. [PDF]

Marín I, Siegal ML, Baker BS (2000) The evolution of dosage-compensation mechanisms. Bioessays. 22: 1106-1114 [PDF]

Marín I, Baker BS (2000) Origin and evolution of the regulatory gene male-specific lethal-3. Molecular Biology and Evolution 17: 1240-1250 [PDF]

Marín I, Llorens C (2000) Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Molecular Biology and Evolution 17: 1040-1049. [PDF]

Marín I, Baker BS (1998) The evolutionary dynamics of sex determination. Science 281: 1990-1994. [PDF]

Marin I, Plata-Rengifo P, Labrador M, Fontdevila A (1998) Evolutionary relationships among the members of an ancient class of non-LTR retrotransposons found in the nematode Caenorhabditis elegans. Molecular Biology and Evolution 15: 1390-1402. [PDF]

Marín I, Fontdevila A (1998) Stable Drosophila buzzatii-Drosophila koepferae hybrids. Journal of Heredity 89: 336-339.[PDF]

Marín I (1997) Sexual isolation in Drosophila. III. Estimating isolation using male-choice experiments. Journal of Theoretical Biology 188: 515-524. [PDF]

Marín I, Franke A, Bashaw GJ, Baker BS (1996) The dosage compensation system of Drosophila is co-opted by newly evolved X chromosomes. Nature 383: 160-163. [PDF]

Marín I (1996) Genetic architecture of autosome-mediated hybrid male sterility in Drosophila. Genetics 142: 1169-1180. [PDF]

Marín I, Fontdevila A (1996) Evolutionary conservation and molecular characteristics of repetitive sequences of Drosophila koepferae. Heredity. 76: 355-366. [PDF]

Marín I, Fontdevila A (1995) Characterization of Gandalf, a new inverted-repeat transposable element of Drosophila koepferae. Molecular and General Genetics 248: 423-433.  [PDF]

Baker BS, Gorman M, Marín I (1994) Dosage compensation in Drosophila. Annual Review of Genetics 28: 491-521. [PDF]

Marín I (1994) Sexual isolation in Drosophila. II. Intraspecific variation in mate recognition systems. Journal of Evolutionary Biology 7: 303-314. [PDF]

Marín I, Ruiz A, Pla C, Fontdevila A (1993) Reproductive relationships among ten species of the Drosophila repleta group from South America and the West Indies. Evolution. 47: 1616-1624. [PDF]

Marín I, Labrador M, Fontdevila A (1992) The evolutionary history of Drosophila buzzatii. XXIII. High content of nonsatellite repetitive DNA in D. buzzatii and in its sibling D. koepferae. Genome 35: 967-74. [PDF]

Marín I (1991) Sexual isolation in Drosophila. I. Theoretical models for multiple-choice experiments. Journal of Theoretical Biology 152: 271-84. [PDF]