Alexandros Stamatakis

Summary

Country: Switzerland

Publications

  1. ncbi request reprint RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
  2. 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
  3. pmc AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa
    Alexandros Stamatakis
    Ecole Polytechnique Federale de Lausanne, School of Computer and Communication Sciences, Laboratory for Computational Biology and Bioinformatics STATION 14, CH 1015 Lausanne, Switzerland
    BMC Bioinformatics 8:405. 2007
  4. 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
  5. pmc Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice
    Andre J Aberer
    Exelixis Laboratory, Scientific Computing Group, Heidelberg Institute for Theoretical Studies HITS gGmbH, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Germany
    Syst Biol 62:162-6. 2013
  6. 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
  7. pmc SweeD: likelihood-based detection of selective sweeps in thousands of genomes
    Pavlos Pavlidis
    Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies HITS gGmbH, Schloss Wolfsbrunnenweg, Heidelberg, Germany
    Mol Biol Evol 30:2224-34. 2013
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications17

  1. ncbi request reprint RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
    ..The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively...
  2. 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...
  3. pmc AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa
    Alexandros Stamatakis
    Ecole Polytechnique Federale de Lausanne, School of Computer and Communication Sciences, Laboratory for Computational Biology and Bioinformatics STATION 14, CH 1015 Lausanne, Switzerland
    BMC Bioinformatics 8:405. 2007
    ..We present AxParafit and AxPcoords (Ax stands for Accelerated) which are highly optimized versions of Parafit and DistPCoA respectively...
  4. 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...
  5. pmc Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice
    Andre J Aberer
    Exelixis Laboratory, Scientific Computing Group, Heidelberg Institute for Theoretical Studies HITS gGmbH, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Germany
    Syst Biol 62:162-6. 2013
    ....
  6. 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...
  7. pmc SweeD: likelihood-based detection of selective sweeps in thousands of genomes
    Pavlos Pavlidis
    Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies HITS gGmbH, Schloss Wolfsbrunnenweg, Heidelberg, Germany
    Mol Biol Evol 30:2224-34. 2013
    ..We compare SweeD results with results from a linkage-disequilibrium-based approach and identify common outliers. ..
  8. 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...
  9. 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...
  10. 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...
  11. pmc 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...
  12. pmc 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...
  13. pmc Biggest challenges in bioinformatics
    Jonathan C Fuller
    Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
    EMBO Rep 14:302-4. 2013
    ..HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Café' style event...
  14. 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...
  15. doi request reprint Result verification, code verification and computation of support values in phylogenetics
    Alexandros Stamatakis
    Heidelberg Institute for Theoretical Studies, Germany
    Brief Bioinform 12:270-9. 2011
    ..Program verification represents a largely underestimated problem in computational science that can have fatal effects on scientific conclusions...
  16. 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...
  17. ncbi request reprint Multiple evolutionary mechanisms drive papillomavirus diversification
    Marc Gottschling
    Skin Cancer Center Charite, University Hospital of Berlin, Berlin, Germany
    Mol Biol Evol 24:1242-58. 2007
    ..The molecular data globally supports a complex evolutionary scenario for PVes, which is driven by multiple mechanisms but not exclusively by coevolution with corresponding hosts...