Ignacio Marín

Summary

Affiliation: University of Valencia
Country: Spain

Publications

  1. ncbi request reprint Comparative genomics of the RBR family, including the Parkinson's disease-related gene parkin and the genes of the ariadne subfamily
    Ignacio Marín
    Departamento de Genetica, Universidad de Valencia, Calle Doctor Moliner 50, Burjassot 46100, Valencia, Spain
    Mol Biol Evol 19:2039-50. 2002
  2. ncbi request reprint Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data
    I Marin
    Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
    Mol Biol Evol 17:1040-9. 2000
  3. ncbi request reprint The Parkinson disease gene LRRK2: evolutionary and structural insights
    Ignacio Marín
    Departamento de Genetica, Universidad de Valencia, Burjassot, Spain
    Mol Biol Evol 23:2423-33. 2006
  4. ncbi request reprint Parkin and relatives: the RBR family of ubiquitin ligases
    Ignacio Marín
    Departamento de Genetica, Universidad de Valencia, 46100 Burjassot, Valencia, Spain
    Physiol Genomics 17:253-63. 2004
  5. ncbi request reprint Evolution of chromatin-remodeling complexes: comparative genomics reveals the ancient origin of "novel" compensasome genes
    Ignacio Marín
    Departamento de Genetica, Universidad de Valencia, Calle Doctor Moliner 50, Burjassot 46100, Spain
    J Mol Evol 56:527-39. 2003
  6. ncbi request reprint Evolutionary relationships among the members of an ancient class of non-LTR retrotransposons found in the nematode Caenorhabditis elegans
    I Marin
    Departamento de Genética and Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Spain
    Mol Biol Evol 15:1390-402. 1998
  7. ncbi request reprint Origin and evolution of the regulatory gene male-specific lethal-3
    I Marin
    Department of Biological Sciences, Stanford University, CA, USA
    Mol Biol Evol 17:1240-50. 2000
  8. ncbi request reprint Detecting changes in the functional constraints of paralogous genes
    I Marin
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Dr Moliner, 50, Burjassot 46100, Valencia, Spain
    J Mol Evol 52:17-28. 2001
  9. ncbi request reprint Iterative cluster analysis of protein interaction data
    Vicente Arnau
    Departamento de Informatica, Universidad de Valencia, Burjassot 46100, Valencia, Spain
    Bioinformatics 21:364-78. 2005
  10. ncbi request reprint Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism
    J Ignasi Lucas
    Departamento de Genetica, Universidad de Valencia, Burjassot, Spain
    J Mol Biol 357:9-17. 2006

Detail Information

Publications34

  1. ncbi request reprint Comparative genomics of the RBR family, including the Parkinson's disease-related gene parkin and the genes of the ariadne subfamily
    Ignacio Marín
    Departamento de Genetica, Universidad de Valencia, Calle Doctor Moliner 50, Burjassot 46100, Valencia, Spain
    Mol Biol Evol 19:2039-50. 2002
    ..On the basis of the evidence provided by cases of gene fusion, we suggest that Ariadne proteins interact with cullin domain-containing proteins to form complexes with ubiquitin-ligase activity...
  2. ncbi request reprint Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data
    I Marin
    Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universidad de Valencia, Spain
    Mol Biol Evol 17:1040-9. 2000
    ..melanogaster. Finally, we suggest that the presence of a chromodomain-containing integrase, a feature of some closely related Ty3/GYPSY: elements of fungi, plants, and animals, may be used to define a new METAVIRIDAE: genus...
  3. ncbi request reprint The Parkinson disease gene LRRK2: evolutionary and structural insights
    Ignacio Marín
    Departamento de Genetica, Universidad de Valencia, Burjassot, Spain
    Mol Biol Evol 23:2423-33. 2006
    ..Modeling based on known kinase structures suggests that mutations in LRRK2 that cause familiar PD may alter the local 3-dimensional folding of the LRRK2 protein without affecting its overall structure...
  4. ncbi request reprint Parkin and relatives: the RBR family of ubiquitin ligases
    Ignacio Marín
    Departamento de Genetica, Universidad de Valencia, 46100 Burjassot, Valencia, Spain
    Physiol Genomics 17:253-63. 2004
    ..Recent data on Parkin protein agrees with that hypothesis. We discuss the involvement of RBR proteins in several neurodegenerative diseases and cancer...
  5. ncbi request reprint Evolution of chromatin-remodeling complexes: comparative genomics reveals the ancient origin of "novel" compensasome genes
    Ignacio Marín
    Departamento de Genetica, Universidad de Valencia, Calle Doctor Moliner 50, Burjassot 46100, Spain
    J Mol Evol 56:527-39. 2003
    ..The evolutionary relationships of the compensasome and the NuA4 complex, another chromatin-remodeling complex that contains related subunits, are discussed...
  6. ncbi request reprint Evolutionary relationships among the members of an ancient class of non-LTR retrotransposons found in the nematode Caenorhabditis elegans
    I Marin
    Departamento de Genética and Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Spain
    Mol Biol Evol 15:1390-402. 1998
    ..Elements of this subgroup are thus ancient components of the genome of animal species. However, we discuss the possibility that these elements may occasionally be horizontally transmitted...
  7. ncbi request reprint Origin and evolution of the regulatory gene male-specific lethal-3
    I Marin
    Department of Biological Sciences, Stanford University, CA, USA
    Mol Biol Evol 17:1240-50. 2000
    ..The possible functional roles of these proteins are discussed...
  8. ncbi request reprint Detecting changes in the functional constraints of paralogous genes
    I Marin
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Dr Moliner, 50, Burjassot 46100, Valencia, Spain
    J Mol Evol 52:17-28. 2001
    ..Our results suggest that, even for universal and essential proteins, selective constraints may be occasionally altered. On the other hand, in some cases no changes were detected after periods of more than 2.2 billion years...
  9. ncbi request reprint Iterative cluster analysis of protein interaction data
    Vicente Arnau
    Departamento de Informatica, Universidad de Valencia, Burjassot 46100, Valencia, Spain
    Bioinformatics 21:364-78. 2005
    ..Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data...
  10. ncbi request reprint Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism
    J Ignasi Lucas
    Departamento de Genetica, Universidad de Valencia, Burjassot, Spain
    J Mol Biol 357:9-17. 2006
    ..Our results show that global bioinformatic approaches, involving comparative genomics and domain network analyses, may unearth novel functional relationships involving well-known and thoroughly studied groups of proteins...
  11. ncbi request reprint Evolutionary and structural analyses of GDAP1, involved in Charcot-Marie-Tooth disease, characterize a novel class of glutathione transferase-related genes
    Antonio Marco
    Departamento de Genetica, Universidad de Valencia, Valencia, Spain
    Mol Biol Evol 21:176-87. 2004
    ..Mutations affecting any of those characteristic domains are known to cause Charcot-Marie-Tooth disease. These features define the GDAP1 class of GST-like proteins...
  12. ncbi request reprint Selection on coding regions determined Hox7 genes evolution
    Mario Ali Fares
    Departamento de Genetica, Univesidad de Valencia, Valencia, Spain
    Mol Biol Evol 20:2104-12. 2003
    ..Our results show that both positive and negative selection on coding regions are influencing Hox7 genes evolution...
  13. ncbi request reprint Proteasome-related HslU and HslV genes typical of eubacteria are widespread in eukaryotes
    Mario X Ruiz-González
    Departamento de Genetica, Universidad de Valencia, Calle Doctor Moliner 50, Burjassot, 46100, Valencia, Spain
    J Mol Evol 63:504-12. 2006
    ....
  14. pmc A sequence motif enriched in regions bound by the Drosophila dosage compensation complex
    Miguel Gallach
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas IBV CSIC, Valencia, Spain
    BMC Genomics 11:169. 2010
    ..How the DCC recognizes the fly X chromosome is still poorly understood. Characteristic sequence signatures at all DCC binding sites have not hitherto been found...
  15. doi request reprint The Roco protein family: a functional perspective
    Ignacio Marín
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
    FASEB J 22:3103-10. 2008
    ..Thus, Roco proteins may act as stand-alone transduction units, performing roles that were thought so far to require multiple proteins, as occur in the Ras transduction pathway...
  16. pmc Global patterns of sequence evolution in Drosophila
    Miguel Gallach
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas IBV CSIC, Valencia, Spain
    BMC Genomics 8:408. 2007
    ..A basic question is whether there are characteristic features that differentiate chromosomes within a species or between different species...
  17. ncbi request reprint A new evolutionary paradigm for the Parkinson disease gene DJ-1
    J Ignasi Lucas
    Departamento de Genetica, Universidad de Valencia, Burjassot, Spain
    Mol Biol Evol 24:551-61. 2007
    ..This finding opens new ways for the analysis of the functions of this group of genes...
  18. pmc Jerarca: efficient analysis of complex networks using hierarchical clustering
    Rodrigo Aldecoa
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas IBV CSIC, Valencia, Spain
    PLoS ONE 5:e11585. 2010
    ..However, the amount of computation time required to perform UVCluster analyses imposed significant limitations to its use...
  19. pmc UVPAR: fast detection of functional shifts in duplicate genes
    Vicente Arnau
    Departamento de Genetica, Universidad de Valencia, Burjassot, Spain
    BMC Bioinformatics 7:174. 2006
    ..The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest...
  20. pmc Diversification and Specialization of Plant RBR Ubiquitin Ligases
    Ignacio Marín
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
    PLoS ONE 5:e11579. 2010
    ..They are characterized by having the RBR (RING - IBR - RING) supradomain. In this study, the patterns of emergence of RBR genes in plants are described...
  21. pmc Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell
    Antonio Marco
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas IBV CSIC, Valencia, Spain
    BMC Syst Biol 3:69. 2009
    ..The characterization of the global functional structure of a cell is a major goal in bioinformatics and systems biology. Gene Ontology (GO) and the protein-protein interaction network offer alternative views of that structure...
  22. pmc Deciphering network community structure by surprise
    Rodrigo Aldecoa
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
    PLoS ONE 6:e24195. 2011
    ..These results indicate that it is possible to define an effective global criterion for community structure and open new routes for the understanding of complex networks...
  23. pmc Ancient origin of animal U-box ubiquitin ligases
    Ignacio Marín
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
    BMC Evol Biol 10:331. 2010
    ..U-box ubiquitin ligases (UULs) are proteins characterized by containing a peculiar protein domain known as U box. In this study, the origin of the animal UUL genes is described...
  24. doi request reprint GIN transposons: genetic elements linking retrotransposons and genes
    Ignacio Marín
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
    Mol Biol Evol 27:1903-11. 2010
    ..In summary, GIN transposons may be the "missing link" that explain how GIN genes evolved from retrotransposons. GIN1 and GIN2 may have contributed to control the expansion of GIN elements and Gypsy/Ty3 retrotransposons in chordates...
  25. pmc Diversification of the cullin family
    Ignacio Marín
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
    BMC Evol Biol 9:267. 2009
    ..In this study, I use comparative genomic data to establish the pattern of emergence and diversification of cullins in eukaryotes...
  26. pmc Fast comparison of DNA sequences by oligonucleotide profiling
    Vicente Arnau
    Departmento de Informática Universidad de Valencia, Spain
    BMC Res Notes 1:5. 2008
    ..The comparison of DNA sequences is a traditional problem in genomics and bioinformatics. Many new opportunities emerge due to the improvement of personal computers, allowing the implementation of novel strategies of analysis...
  27. ncbi request reprint New insights into the evolutionary history of type 1 rhodopsins
    Mario X Ruiz-González
    Departamento de Genetica, Universidad de Valencia, Calle Doctor Moliner 50, Burjassot 46100, Valencia, Spain
    J Mol Evol 58:348-58. 2004
    ..However, the possibility of ancient horizontal transfer events between distant relatives cannot be dismissed...
  28. pmc Evolution of plant HECT ubiquitin ligases
    Ignacio Marín
    Instituto de Biomedicina de Valencia Consejo Superior de Investigaciones Científicas IBV CSIC, Valencia, Spain
    PLoS ONE 8:e68536. 2013
    ..These results are discussed in the context of the evolution of the gene families required for ubiquitination in plants. ..
  29. pmc A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification
    Antonio Marco
    Departamento de Genetica, Universidad de Valencia, Burjassot, Spain
    BMC Bioinformatics 8:442. 2007
    ....
  30. pmc Animal HECT ubiquitin ligases: evolution and functional implications
    Ignacio Marín
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas IBV CSIC, Valencia, Spain
    BMC Evol Biol 10:56. 2010
    ..In this study, I analyze the patterns of diversification of HECT E3s since animals emerged in order to provide the right framework to understand the functional data available for proteins of this family...
  31. pmc Origin and diversification of TRIM ubiquitin ligases
    Ignacio Marín
    Instituto de Biomedicina de Valencia IBV CSIC, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
    PLoS ONE 7:e50030. 2012
    ..The structural and evolutionary links with the TRAF family of ubiquitin ligases can be experimentally explored to determine whether functional connections also exist...
  32. pmc Exploring the limits of community detection strategies in complex networks
    Rodrigo Aldecoa
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Calle Jaime Roig 11, 46010, Valencia, Spain
    Sci Rep 3:2216. 2013
    ....
  33. ncbi request reprint Closed benchmarks for network community structure characterization
    Rodrigo Aldecoa
    Instituto de Biomedicina de Valencia Consejo Superior de Investigaciones Científicas IBV CSIC Calle Jaime Roig 11, E 46010, Valencia, Spain
    Phys Rev E Stat Nonlin Soft Matter Phys 85:026109. 2012
    ..These properties make our benchmarks a general standard for comparing community detection algorithms...
  34. ncbi request reprint Closed benchmarks for network community structure characterization
    Rodrigo Aldecoa
    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Calle Jaime Roig 11, E 46010 Valencia, Spain
    Phys Rev E Stat Nonlin Soft Matter Phys 85:026109. 2012
    ..These properties make our benchmarks a general standard for comparing community detection algorithms...