Affiliation: Stockholm University
- Bayesian gene/species tree reconciliation and orthology analysis using MCMCLars 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...
- A bayesian method for analyzing lateral gene transferJoel Sjöstrand
Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden, Department of Numerical Analysis and Computer Science, Stockholm University, Sweden, McGill Centre for Bioinformatics, 4th Floor, Bellini Building, Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada, H3G 0B1, UMR CNRS 5558 LBBE, Biometrie et Biologie Evolutive, UCB Lyon 1 Bât Grégor Mendel, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, Department of Mechanics, Osquars backe 18, KTH, SE 100 44 Stockholm, Sweden, Karolinska University Hospital, CMM L8 03, Solna, SE 171 76 Stockholm, Sweden and The School of Computer Science and Communication, Lindstedtsvägen 3, 5, KTH CSC, SE 100 44 Stockholm, Sweden
Syst Biol 63:409-20. 2014..Bayesian; gene duplication; gene loss; horizontal gene transfer; lateral gene transfer; MCMC; phylogenetics.]. ..
- primetv: a viewer for reconciled treesBengt 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...
- GenPhyloData: realistic simulation of gene family evolutionJoel 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...
- Genome-wide survey for biologically functional pseudogenesOrjan 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...
- Efficient methods for estimating amino acid replacement ratesLars Arvestad
Stockholm Bioinformatics Center, AlbaNova University Center, Royal Institute of Technology KTH, SE 100 44, Stockholm, Sweden
J Mol Evol 62:663-73. 2006....
- DLRS: gene tree evolution in light of a species treeJoel 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...
- Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstructionVolker 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...
- Excap: maximization of haplotypic diversity of linked markersAndré Kahles
KTH Royal Institute of Technology, Stockholm Bioinformatics Center, School of Computer Science and Communication, Stockholm, Sweden
PLoS ONE 8:e79012. 2013..Additionally, we evaluated the quality of the estimation with an artificial dataset of mtDNA. The heuristic is shown to provide extensive speedup at little cost in accuracy. ..
- The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genesSoraya 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...
- Evolution after gene duplication: models, mechanisms, sequences, systems, and organismsChristian 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...