Miklos Csuros

Summary

Country: Canada

Publications

  1. pmc Joint genotype inference with germline and somatic mutations
    Eric Bareke
    Department of Computer Science and Operations Research, University of Montreal, QC, Canada
    BMC Bioinformatics 14:S3. 2013
  2. doi request reprint Non-identifiability of identity coefficients at biallelic loci
    Miklos Csuros
    Department of Computer Science and Operations Research, University of Montreal, C P 6128 Succursale Centre Ville, Montreal, Quebec H3C 3J7, Canada Electronic address
    Theor Popul Biol 92:22-9. 2014
  3. pmc Origin and evolution of spliceosomal introns
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
    Biol Direct 7:11. 2012
  4. pmc 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
  5. pmc 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
  6. pmc 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
  7. doi request reprint 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
  8. pmc 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
  9. pmc 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
  10. doi request reprint 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

Collaborators

Detail Information

Publications16

  1. pmc Joint genotype inference with germline and somatic mutations
    Eric Bareke
    Department of Computer Science and Operations Research, University of Montreal, QC, Canada
    BMC Bioinformatics 14:S3. 2013
    ..We implemented the methods in an open-source software package (QUADGT) that uses the standard file formats of the 1000 Genomes Project. Our method's utility is illustrated on quartets from the ALL cohort...
  2. doi request reprint Non-identifiability of identity coefficients at biallelic loci
    Miklos Csuros
    Department of Computer Science and Operations Research, University of Montreal, C P 6128 Succursale Centre Ville, Montreal, Quebec H3C 3J7, Canada Electronic address
    Theor Popul Biol 92:22-9. 2014
    ....
  3. pmc Origin and evolution of spliceosomal introns
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
    Biol Direct 7:11. 2012
    ....
  4. pmc 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...
  5. pmc 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...
  6. pmc 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...
  7. doi request reprint 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
    ..It implements popular methods employed in gene content analysis such as Dollo and Wagner parsimony, propensity for gene loss, as well as probabilistic methods involving a phylogenetic birth-and-death model...
  8. pmc 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...
  9. pmc 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...
  10. doi request reprint 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...
  11. ncbi request reprint 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...
  12. ncbi request reprint In search of lost introns
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Quebec, Canada
    Bioinformatics 23:i87-96. 2007
    ..The study yields the surprising result that ancestral eukaryotes were fairly intron-rich. For example, the bilaterian ancestor is estimated to have had more than 90% as many introns as vertebrates do now...
  13. ncbi request reprint 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...
  14. ncbi request reprint 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...
  15. ncbi request reprint 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...
  16. ncbi request reprint 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...