Alexandros Stamatakis

Summary

Affiliation: TU Munich
Country: Germany

Publications

  1. pmc Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling
    Alexandros Stamatakis
    The Exelixis Lab, Dept of Computer Science, Technische Universitat Munchen, Germany
    Evol Bioinform Online 6:73-90. 2010
  2. ncbi request reprint RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
    A Stamatakis
    Department of Computer Science, Technical University of Munich Boltzmannstrasse 3, D 85748 München, Germany
    Bioinformatics 21:456-63. 2005
  3. pmc Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data
    Alexandros Stamatakis
    The Exelixis Lab I12, Department of Computer Science, Technische Universitat Munchen, Boltzmannstr 3, D 85748, Garching b München, Germany
    Bioinformatics 26:i132-9. 2010
  4. pmc Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood
    Simon A Berger
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Germany
    Syst Biol 60:291-302. 2011
  5. pmc Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel
    Nikolaos Alachiotis
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Germany
    BMC Bioinformatics 13:196. 2012
  6. doi request reprint Aligning short reads to reference alignments and trees
    Simon A Berger
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, D 69118 Heidelberg, Germany
    Bioinformatics 27:2068-75. 2011
  7. doi request reprint A rapid bootstrap algorithm for the RAxML Web servers
    Alexandros Stamatakis
    Exelixis Lab, Teaching and Research Unit Bioinformatics, Department of Computer Science, Ludwig Maximilians University Munich, Munich, Germany
    Syst Biol 57:758-71. 2008
  8. ncbi request reprint PEAR: a fast and accurate Illumina Paired-End reAd mergeR
    Jiajie Zhang
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Graduate School for Computing in Medicine and Life Sciences, Institut für Neuro und Bioinformatik, University of Lubeck, 23538 Lübeck and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Germany
    Bioinformatics 30:614-20. 2014
  9. pmc A general species delimitation method with applications to phylogenetic placements
    Jiajie Zhang
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, D 68159 Heidelberg, Germany, Graduate School for Computing in Medicine and Life Sciences, University of Lubeck, Institut für Neuro und Bioinformatik, University of Lubeck, 23538 Lubeck, Germany, Natural History Museum of Crete, University of Crete, GR 71409 Irakleio, Crete, Greece and Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas FORTH, GR 70013 Heraklion, Crete, Greece
    Bioinformatics 29:2869-76. 2013
  10. pmc Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees
    Fernando Izquierdo-Carrasco
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Germany
    BMC Bioinformatics 12:470. 2011

Detail Information

Publications14

  1. pmc Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling
    Alexandros Stamatakis
    The Exelixis Lab, Dept of Computer Science, Technische Universitat Munchen, Germany
    Evol Bioinform Online 6:73-90. 2010
    ..Moreover, the newly implemented taxon subsampling procedure can be beneficial for inferring higher level relationships and interpreting bootstrap support from comprehensive analysis...
  2. ncbi request reprint RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
    A Stamatakis
    Department of Computer Science, Technical University of Munich Boltzmannstrasse 3, D 85748 München, Germany
    Bioinformatics 21:456-63. 2005
    ..Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa...
  3. pmc Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data
    Alexandros Stamatakis
    The Exelixis Lab I12, Department of Computer Science, Technische Universitat Munchen, Boltzmannstr 3, D 85748, Garching b München, Germany
    Bioinformatics 26:i132-9. 2010
    ..We also introduce a set of algorithmic rules to efficiently conduct tree searches via subtree pruning and re-grafting moves using this mechanism...
  4. pmc Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood
    Simon A Berger
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Germany
    Syst Biol 60:291-302. 2011
    ..We are also actively developing a Web server that offers a freely available service for computing read placements on trees using the EPA...
  5. pmc Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel
    Nikolaos Alachiotis
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Germany
    BMC Bioinformatics 13:196. 2012
    ..The algorithm needs to perform an immense number of pairwise alignments. Therefore, we explore vector intrinsics and GPUs to accelerate the PaPaRa alignment kernel...
  6. doi request reprint Aligning short reads to reference alignments and trees
    Simon A Berger
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, D 69118 Heidelberg, Germany
    Bioinformatics 27:2068-75. 2011
    ..It has also not been assessed if the reference phylogeny can be deployed in conjunction with the reference alignment to improve alignment accuracy in this context...
  7. doi request reprint A rapid bootstrap algorithm for the RAxML Web servers
    Alexandros Stamatakis
    Exelixis Lab, Teaching and Research Unit Bioinformatics, Department of Computer Science, Ludwig Maximilians University Munich, Munich, Germany
    Syst Biol 57:758-71. 2008
    ..These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources...
  8. ncbi request reprint PEAR: a fast and accurate Illumina Paired-End reAd mergeR
    Jiajie Zhang
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Graduate School for Computing in Medicine and Life Sciences, Institut für Neuro und Bioinformatik, University of Lubeck, 23538 Lübeck and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Germany
    Bioinformatics 30:614-20. 2014
    ..Therefore, a robust tool is needed to merge paired-end reads that exhibit varying overlap lengths because of varying target fragment lengths...
  9. pmc A general species delimitation method with applications to phylogenetic placements
    Jiajie Zhang
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, D 68159 Heidelberg, Germany, Graduate School for Computing in Medicine and Life Sciences, University of Lubeck, Institut für Neuro und Bioinformatik, University of Lubeck, 23538 Lubeck, Germany, Natural History Museum of Crete, University of Crete, GR 71409 Irakleio, Crete, Greece and Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas FORTH, GR 70013 Heraklion, Crete, Greece
    Bioinformatics 29:2869-76. 2013
    ..Coalescent-based species delimitation approaches often rely on Bayesian statistics and Markov Chain Monte Carlo sampling, and can therefore only be applied to small datasets...
  10. pmc Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees
    Fernando Izquierdo-Carrasco
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Germany
    BMC Bioinformatics 12:470. 2011
    ..The three main computational challenges are: numerical stability, the scalability of search algorithms, and the high memory requirements for computing the likelihood...
  11. pmc Rapid forward-in-time simulation at the chromosome and genome level
    Andre J Aberer
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, Heidelberg D 69118, Germany
    BMC Bioinformatics 14:216. 2013
    ..Forward simulation represents the most powerful, but, at the same time, most compute-intensive approach for simulating the genetic material of a population...
  12. ncbi request reprint A critical assessment of storytelling: gene ontology categories and the importance of validating genomic scans
    Pavlos Pavlidis
    The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies HITS gGmbH, Heidelberg, Germany
    Mol Biol Evol 29:3237-48. 2012
    ..Results are compared with a recent polymorphism data set from Drosophila melanogaster...
  13. ncbi request reprint PUmPER: phylogenies updated perpetually
    Fernando Izquierdo-Carrasco
    Scientific Computing Group, Heidelberg Institute for Theoretical Studies HITS gGmbH, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Baden Wurttemberg, Germany, Texas Advanced Computing Center, University of Texas, Austin, TX, 78758, USA, University of Michigan, Ann Arbor Department of Ecology and Evolutionary Biology, 48109, MI, USA and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, 76128 Karlsruhe, Baden Wurttemberg, Germany
    Bioinformatics 30:1476-7. 2014
    ..Using our framework, large phylogenetic trees can be perpetually updated without human intervention. Importantly, resulting phylogenies are not statistically significantly worse than trees inferred from scratch...
  14. pmc ARB: a software environment for sequence data
    Wolfgang Ludwig
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 853530 Freising, Germany
    Nucleic Acids Res 32:1363-71. 2004
    ..Currently, the package is used by numerous working groups worldwide...