Miklos Csuros

Summary

Country: Canada

Publications

  1. ncbi A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
    Diana Chernikova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 6:26. 2011
  2. ncbi Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:7. 2008
  3. ncbi Pooled Genomic Indexing (PGI): analysis and design of experiments
    Miklos Csuros
    Département d informatique et de recherche opérationnelle, Universite de Montreal, CP 6128 Succ Centre Ville, Montreal, QC H3C 3J7, Canada
    J Comput Biol 11:1001-21. 2004
  4. ncbi Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
    Miklos Csuros
    Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec, Canada
    Bioinformatics 26:1910-2. 2010
  5. ncbi Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model
    Miklos Csuros
    Department of Computer Science and Operations Research, University of Montreal, Montreal, Canada
    Mol Biol Evol 26:2087-95. 2009
  6. ncbi Malin: maximum likelihood analysis of intron evolution in eukaryotes
    Miklos Csuros
    Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec, Canada
    Bioinformatics 24:1538-9. 2008
  7. ncbi Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 25:903-11. 2008
  8. ncbi Reconsidering the significance of genomic word frequencies
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, 8, Succ Centre Ville, Montreal, Quebec, Canada
    Trends Genet 23:543-6. 2007
  9. ncbi In search of lost introns
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Quebec, Canada
    Bioinformatics 23:i87-96. 2007
  10. ncbi Maximum-scoring segment sets
    Miklos Csuros
    Départment d informatique et de recherche opérationnelle, Universite de Montreal, C P 6128, Succ Centre Ville, Montreal, Que H3C 3J7, Canada
    IEEE/ACM Trans Comput Biol Bioinform 1:139-50. 2004

Detail Information

Publications13

  1. ncbi A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
    Diana Chernikova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 6:26. 2011
    ..Estimates of the age of Last Eukaryotic Common Ancestor (LECA) vary approximately twofold, from ~1,100 million years ago (Mya) to ~2,300 Mya...
  2. ncbi Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:7. 2008
    ..However, a non-negligible level of homoplasy was detected...
  3. ncbi Pooled Genomic Indexing (PGI): analysis and design of experiments
    Miklos Csuros
    Département d informatique et de recherche opérationnelle, Universite de Montreal, CP 6128 Succ Centre Ville, Montreal, QC H3C 3J7, Canada
    J Comput Biol 11:1001-21. 2004
    ..The probabilistic model and the pooling schemes are validated in simulated experiments where 625 rat bacterial artificial chromosome (BAC) clones and 207 mouse BAC clones are mapped onto homologous human sequence...
  4. ncbi Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
    Miklos Csuros
    Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec, Canada
    Bioinformatics 26:1910-2. 2010
    ..iro.umontreal.ca/ approximately csuros/gene_content/count.html. It can also be launched using Java Webstart from the same site. The software is distributed under a BSD-style license. Source code is available upon request from the author...
  5. ncbi Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model
    Miklos Csuros
    Department of Computer Science and Operations Research, University of Montreal, Montreal, Canada
    Mol Biol Evol 26:2087-95. 2009
    ..It also suggests that early archaeal genomes were as complex as typical modern ones, and even show signs, in the case of the methanogenic ancestor, of an extremely large gene repertoire...
  6. ncbi Malin: maximum likelihood analysis of intron evolution in eukaryotes
    Miklos Csuros
    Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec, Canada
    Bioinformatics 24:1538-9. 2008
    ..Availability: Malin is available as a stand-alone Java application, as well as an application bundle for MacOS X, at the website http://www.iro.umontreal.ca/~csuros/introns/malin/. The software is distributed under a BSD-style license...
  7. ncbi Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 25:903-11. 2008
    ..It is suggested that, at early stages of evolution, chromalveolates went through major population bottlenecks that were accompanied by intron invasion...
  8. ncbi Reconsidering the significance of genomic word frequencies
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, 8, Succ Centre Ville, Montreal, Quebec, Canada
    Trends Genet 23:543-6. 2007
    ..Our characterization of the entire frequency distribution of genomic words opens a way to a more accurate reasoning about their over- and underrepresentation in genomic sequences...
  9. ncbi In search of lost introns
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Quebec, Canada
    Bioinformatics 23:i87-96. 2007
    ..AVAILABILITY: The Java implementations of the algorithms are publicly available from the corresponding author's site http://www.iro.umontreal.ca/~csuros/introns/. Data are available on request...
  10. ncbi Maximum-scoring segment sets
    Miklos Csuros
    Départment d informatique et de recherche opérationnelle, Universite de Montreal, C P 6128, Succ Centre Ville, Montreal, Que H3C 3J7, Canada
    IEEE/ACM Trans Comput Biol Bioinform 1:139-50. 2004
    ..The statement leads to fast algorithms for finding such segment sets. We apply our methods to the identification of noncoding RNA genes in thermophiles...
  11. ncbi Statistical alignment of retropseudogenes and their functional paralogs
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Succursale Centre Ville, Montreal, Quebec H3C 3J7, Canada
    Mol Biol Evol 22:2457-71. 2005
    ..We also describe how ancestral codons can be computed when the same gene produced multiple pseudogene homologs. We apply our methods to the evolution of human cytochrome c...
  12. ncbi Clone-array pooled shotgun mapping and sequencing: design and analysis of experiments
    Miklos Csuros
    Département d informatique et de recherche opérationnelle, Universite de Montreal, CP 6128 Succ Centre Ville, Montreal, Quebec H3C 3J7, Canada
    Genome Inform 14:186-95. 2003
    ..Both CAPSS and CAPS-MAP construct subclone libraries from pooled genomic BAC clones...
  13. ncbi A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Montreal, Quebec, Canada
    PLoS Comput Biol 7:e1002150. 2011
    ..The reconstruction shows that the entire line of descent from LECA to mammals was intron-rich, a state conducive to the evolution of alternative splicing...