Lars Arvestad

Summary

Affiliation: Stockholm University
Country: Sweden

Publications

  1. ncbi request reprint Bayesian gene/species tree reconciliation and orthology analysis using MCMC
    Lars Arvestad
    SBC and Center for Genomics and Bioinforamtics, Karolinska Instituet, SE 171 77, Stockholm, Sweden
    Bioinformatics 19:i7-15. 2003
  2. pmc primetv: a viewer for reconciled trees
    Bengt Sennblad
    Stockholm Bioinformatics Center and Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
    BMC Bioinformatics 8:148. 2007
  3. pmc Genome-wide survey for biologically functional pseudogenes
    Orjan Svensson
    Stockholm Bioinformatics Centre, Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
    PLoS Comput Biol 2:e46. 2006
  4. ncbi request reprint Efficient methods for estimating amino acid replacement rates
    Lars Arvestad
    Stockholm Bioinformatics Center, AlbaNova University Center, Royal Institute of Technology KTH, SE 100 44, Stockholm, Sweden
    J Mol Evol 62:663-73. 2006
  5. pmc GenPhyloData: realistic simulation of gene family evolution
    Joel Sjöstrand
    Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden
    BMC Bioinformatics 14:209. 2013
  6. doi request reprint DLRS: gene tree evolution in light of a species tree
    Joel Sjöstrand
    Science for Life Laboratory, Stockholm University, SE 17121, Solna, Sweden
    Bioinformatics 28:2994-5. 2012
  7. ncbi request reprint Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction
    Volker Hollich
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Mol Biol Evol 22:2257-64. 2005
  8. ncbi request reprint The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes
    Soraya Djerbi
    Royal Institute of Technology, Department of Biotechnology, AlbaNova University Center, 10691, Stockholm, Sweden
    Planta 221:739-46. 2005
  9. ncbi request reprint Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms
    Christian Roth
    Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
    J Exp Zool B Mol Dev Evol 308:58-73. 2007

Collaborators

Detail Information

Publications9

  1. ncbi request reprint Bayesian gene/species tree reconciliation and orthology analysis using MCMC
    Lars Arvestad
    SBC and Center for Genomics and Bioinforamtics, Karolinska Instituet, SE 171 77, Stockholm, Sweden
    Bioinformatics 19:i7-15. 2003
    ..For orthology analysis, uncertainty has recently been addressed using parsimonious reconciliation combined with bootstrap techniques. However, until now no probabilistic methods have been available...
  2. pmc primetv: a viewer for reconciled trees
    Bengt Sennblad
    Stockholm Bioinformatics Center and Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
    BMC Bioinformatics 8:148. 2007
    ..However, there exists a plethora of biologically relevant non-parsimonious reconciliations. Illustrations of these general reconciliations may not be achieved without manual editing...
  3. pmc Genome-wide survey for biologically functional pseudogenes
    Orjan Svensson
    Stockholm Bioinformatics Centre, Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
    PLoS Comput Biol 2:e46. 2006
    ..To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios...
  4. ncbi request reprint Efficient methods for estimating amino acid replacement rates
    Lars Arvestad
    Stockholm Bioinformatics Center, AlbaNova University Center, Royal Institute of Technology KTH, SE 100 44, Stockholm, Sweden
    J Mol Evol 62:663-73. 2006
    ....
  5. pmc GenPhyloData: realistic simulation of gene family evolution
    Joel Sjöstrand
    Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden
    BMC Bioinformatics 14:209. 2013
    ..The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock...
  6. doi request reprint DLRS: gene tree evolution in light of a species tree
    Joel Sjöstrand
    Science for Life Laboratory, Stockholm University, SE 17121, Solna, Sweden
    Bioinformatics 28:2994-5. 2012
    ..PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters...
  7. ncbi request reprint Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction
    Volker Hollich
    Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
    Mol Biol Evol 22:2257-64. 2005
    ..We also assessed the recently developed Scoredist measure, which performed equally well as more complex methods...
  8. ncbi request reprint The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes
    Soraya Djerbi
    Royal Institute of Technology, Department of Biotechnology, AlbaNova University Center, 10691, Stockholm, Sweden
    Planta 221:739-46. 2005
    ..The newly identified copies of CesA genes in P. trichocarpa give rise to a number of new questions concerning the mechanism of cellulose synthesis in trees...
  9. ncbi request reprint Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms
    Christian Roth
    Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
    J Exp Zool B Mol Dev Evol 308:58-73. 2007
    ..single gene duplication. Lastly, the role that these processes may have played in driving speciation is examined...