The Exelixis Lab


Enabling Research in Evolutionary Biology

Invited talks

  1. Anastasis: "Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using dataset difficulty", Rencontres Bioinformatiques du Muséum National d'Histoire Naturelle 2023, Paris, France, May 2023. Talk slides
  2. Anastasis: "Parallel Inference of Phylogenetic Stands with Gentrius", 22nd IEEE International Workshop on High Performance Computational Biology (HiCOMB), IPDPS 2023, St. Petersburg, Florida, USA, May 2023. Talk slides
  3. Benoit: "AleRax: massively parallel species tree inference and gene tree reconciliation from gene tree distributions", Peder Sather/Invertomics Symposium “Progress and Development in Phylogenetic Methods”, University of Oslo, Norway, March 2023. Talk slides
  4. Anastasis: "Adaptive search heuristic for maximum likelihood phylogenetic tree inference based on the predicted difficulty of the dataset", Peder Sather/Invertomics Symposium “Progress and Development in Phylogenetic Methods”, University of Oslo, Norway, March 2023. Talk slides
  5. Julia: "Predicting the Difficulty of Phylogenetic Analyses", Peder Sather/Invertomics Symposium “Progress and Development in Phylogenetic Methods”, University of Oslo, Norway, March 2023. Talk slides
  6. Benoit: "Inferring gene trees and species trees in presence of gene duplication, loss, and transfer", EVOLCYP Workshop on Biodiversity Genomics, University of Cyprus, Cyprus, September 2022.
  7. Julia: "Predicting the Difficulty of a Phylogenetic Analysis", EVOLCYP Workshop on Biodiversity Genomics, University of Cyprus, Cyprus, September 2022.
  8. Alexey: "EcoFreq: compute with cleaner energy via carbon-aware power scaling", GSI ITEE-Palaver, Darmstadt, Germany (online), May 2022. Talk slides
  9. Adrian & Dimitri: "Das SoftWipe-Tool zur Analyse von Code-Qualität", CampusSource Herbsttagung 2021, University of Hagen, Germany, September 2021.
  10. Alexis: "Current and Future Research in Phylogenetics", on-line bioinformatics/genomics seminar by the Department of Computational Biology, Institut Pasteur, April 2021.
  11. Benoit: "Gene tree inference under gene duplication, transfer and loss with GeneRax", Sanger Institut Microbial Genomics Meetings, December 2020. Talk slides
  12. Alexey: "Random thoughts on GreenHPC", MPIA Sustainability meeting, December 2020. Talk slides
  13. Alexis & Alexey: "RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference", ISCBacademy webinar, September 2020. Talk slides
  14. Alexey: "New phylogenetic tools for genome-scale datasets: RAxML-NG, ParGenes and GeneRax", 2nd B10K Symposium and Workshop, Copenhagen, Denmark, February 2020.
  15. Alexis: "Hochleistungsrechnen könnte so schön sein ... wenn nur die Software nicht wäre", annual meeting of the DFN, sceience center Bonn, Germany, December 2019.
  16. Alexey: "RAxML-NG Introduction and Laboratory", 2019 Workshop on Phylogenomics, Český Krumlov, Czech Republic, January 2019. Talk slides
  17. Alexey: "Maximum-likelihood inference of cell phylogenies", Workshop: Single Cell Data Science: Making Sense of Data from Billions of Single Cells, Lorentz Center, Leiden, Netherlands, June 2018.
  18. Alexis: "Introduction to Phylogenetics ... in 12 Minutes", Workshop: Single Cell Data Science: Making Sense of Data from Billions of Single Cells, Lorentz Center, Leiden, Netherlands, June 2018.
  19. Alexis: "Supercomputing Challenges in Evolutionary Biology", International Supercomputing Conference (ISC2017), Frankfurt, Germany, June 2017.
  20. Alexis: "Designing next generation RAxML and Tales of Bugs in Bioinformatics Software & Algorithms", Max Planck Institute for Plant Breeding Research, Cologne, Germany, March 2017.
  21. Alexey: "Identification of taxonomically mislabeled sequences in large databases", 2nd EukREF workshop, Barcelona, Spain, November 2016.
  22. Alexis: "Challenges & problems in phylogenetic inference and bioinformatics", Max Planck Institute & University of Saarland, Saarbrücken, Germany, November 2016.
  23. Alexis: "Challenges & problems in phylogenetic inference and bioinformatics", Hellenic Bioinformatics 2016, Thessaloniki, Greece, November 2016.
  24. Alexis: "Maximizing the Number of Bugs in Bioinformatics Software", CLIMB 2016, retirement colloquium for Bernard Moret, EPFL, Lausanne, Switzerland, November 2016.
  25. Alexis: "Challenges & Problems in Phylogenetic Inference and Bioinformatics", JOBIM 2016, Lyon, France, June 2016.
  26. Alexis: "1KITE, a worldwide HPC Initiative: Challenges and Problems", HPC Forum, LRZ, Munich, Germany, October 2015.
  27. Alexis: "Evolutionsbiologie auf dem SuperMUC", Inauguration of the SuperMUC-2, LRZ, Munich, Germany, June 2015.
  28. Alexis: "Computational Biology as Computational Science: Challenges & Problems", Hennig XXXIV meeting, New York, USA, June 2015.
  29. Alexis: "Computational Biology as Computational Science: Challenges & Problems", COS Symposium 2015 - Darwin 2.0: New Tools to Go Through Time, University of Heidelberg, Germany, June 2015.
  30. Alexis: "Computational Biology as Computational Science: Challenges & Problems", CADMOS day, EPFL, Lausanne, Switzerland, June 2015.
  31. Jiajie & Alexey: "Models and Algorithms for Phylogenetic Marker Analysis", DNA Workshop of the German Ornithologists' Society, Heidelberg, Germany, February 2015.
  32. Tomas: "Merging Illumina paired-end reads", FEW/FAIR 22014, Stellenbosch, South Africa, December 2014.
  33. Alexis: "Inference and Post-Analysis of Huge Phylogenies", IWR seminar, Heidelberg, Germany, November 2014.
  34. Andre: "Big Computers for Big Trees: Challenges of Petascale Phyloinformatics", Pawsey Petascale Bioinformatics Symposium, Perth, Australia, November 2014.
  35. Alexis: "Inference and Post-Analysis of Huge Phylogenies", Annual Society for Bioinformatics in Northern Europe (SocBiN) conference, Oslo, Norway, June 2014.
  36. Alexis: "My personal view of Bioinformatics", Institut de Biologie Computationelle, Montpellier, France, May 2014.
  37. Alexis: "Using Supercomputers to build Evolutionary Trees from DNA data", Panhellenic Electrical and Computer Engineering Students Conference, Athens, Greece, April 2013.
  38. Alexis: "ExaML and ExaBayes: Maximum Likelihood and Bayesian Phylogenetic Inference on Exascale Supercomputers", Arizona State University, Phoenix, USA, March 2013.
  39. Solon: "Finding subtree repeats to slash the time for phylogenetic analyses", Theo Murphy International scientific meeting on Storage and Indexing of massive data, The Royal Society at Chicheley Hall, home of the Kavli Royal Society International Centre, Buckinghamshire, UK, February 2013.
  40. Alexis: "What's up at the Exelixis Lab", Museo Nacional de Ciencias Naturales, Madrid, Spain, January 2013.
  41. Pavlos: "Macroevolutionary processes of RNA viruses", 9. Jahrestagung: Deutsche Vereinte Gesellschaft für Klinische Chemie und Laboratoriumsmedizin, Mannheim, Germany, October 2012.
  42. Alexis: "Challenges in Biodiversity Informatics", Hellenic Socity for Computational Biology and Bioinformatics 2012 conference, Heraklion, Greece, October 2012.
  43. Alexis: "A Suite of new Tools for Large-Scale Analysis of Next-Generation Sequencing Data", MARBIGEN workshop, IMBG-HCMR Heraklion, Crete, October 2012.
  44. Simon: "Phylogeny-Aware Placement and Alignment Methods for Short Reads", COST workshop -  From Signals to Environmentally Tagged Sequences, IMBG-HCMR, Heraklion, Greece, September 2012.
  45. Alexis: "Reconstructing Huge Phylogenies", Workshop in Computational and Statistical Phylogenomics (CSPHYLO'12), Vigo, Spain, September 2012.
  46. Solon: "Single-gap & phylogeny-aware alignment of NGS reads", ICiS Summer Workshop on Developing a Next-Generation Systems Analysis Library, The Institute for Computing in Science (ICIS), Argonne National Laboratory, Utah, USA, August 2012.
  47. Alexis: "Phylogeny-Aware Analysis of Metagenomic Samples", SMBE conference, Dublin, Ireland, June 2012.
  48. Alexis: "High Performance Phylogenetics", Mathematical and Computational Evolutionary Biology Meeting, Hameau de l'Etoile, France, June 2012.
  49. Alexis: "Biodiversity Informatics: An Emerging Computational Science", Center for Organismal Studies, Heidelberg, Germany, June 2012.
  50. Alexis: "Biodiversity Informatics: An Emerging Computational Science", Natural History Museum, Stockholm, Sweden, May 2012.
  51. Pavlos: "The problem of detecting selective sweeps", Max Planck Institute for Developmental Biology, Tübingen, Germany, April 2012.
  52. Alexis: "Biodiversity Informatics: An Emerging Computational Science", Scottish Phylogeny Discussion Group Meeting, Glasgow, UK, March 2012.
  53. Alexis: "Biodiversity Informatics: An Emerging Computational Science", University of Glasgow, Glasgow, UK, March 2012.
  54. Stephen: "Life Sciences Colloquium", Smith College, Northampton, Massachusetts, USA, 2011.
  55. Stephen: "Biology 2011", University of Zurich, Switzerland, 2011.
  56. Stephen: "Large scale phylogenetics and the exploration of evolutionary patterns", MSU, Dept. Plant Biology, Lansing, Michigan, USA, 2011.
  57. Alexis: "Analyzing metagenomic data in a phylogenetic framework", Institute for Marine Biology and Genetics, Heraklion, Greece, December 2011.
  58. Alexis: "Disentangling Evolution on Supercomputers", University of Arizona, Tucson, Arizona, October 2011.
  59. Alexis: "Fishing in the dark: Trying to identify rogue taxa", Deep Metazoan Phylogeny Symposium, LMU Munich, October 2011.
  60. Pavlos: "Detecting positive selection in natural populations", Institut de biologia evolutiva, Universitat Pompeu Fabra, Barcelona, Spain, July 2011.
  61. Alexis: "Computing huge Phylogenies & Placing Short Reads", EMBL, Heidelberg, July 2011.
  62. Alexis: "Disentangling Evolution on Supercomputers", University of Bristol, UK, June 2011.
  63. Simon: "Aligning Short Reads to Reference Alignments and Trees", US Food and Drug Administration meeting on "Next Generation Sequencing: Enabling Transformative Technology for Biodiversity Science",  Colleg Park, MD, USA, April 2011.
  64. Alexis: "New Approaches for Identifying Rogue Taxa", Research Museum Koenig, Bonn, Germany, November 2010.
  65. Alexis: "Petascale Computing and Personalized Medicine Workshop", National Center for Supercomputing Applications, Urbana-Champaign, USA, October 2010. Video of this talk
  66. Alexis: "Using Phylogenetics to analyze Short Reads", Systematics Study Group Graduate Meeting of the German Zoological Society, Hamburg, Germany, September 2010.
  67. Alexis: "Evolutionary Placement and Alignment of Short Reads", European Bioinformatics Institute, Hinxton, UK, July 2010.
  68. Alexis: "Parallel Computing in RAxML: An Overview", University of Lausanne, Switzerland, July 2010.
  69. Alexis: "High Performance Computing for Phylogenetics", University of Vigo, Spain, May 2010.
  70. Alexis: "Current Research at the Exelixis Lab", University of Vigo, Spain, May 2010.
  71. Alexis: "High Performance Computing in Bioinformatics", University of Florida, USA, April 2010.
  72. Alexis: "RAxML hands-on session", University of Florida, USA, April 2010.
  73. Alexis: Sandia National Labs, USA, April 2010.
  74. Alexis: University of new Mexico, USA, April 2010.
  75. Alexis: "Rapid Sequential and Parallel Evolutionary Placement of Short Sequence Reads", LMU Munich, Germany, March 2010.
  76. Alexis: "Rapid Evolutionary Placement of Short Sequence Reads", Joint Genome Institute, California, USA, January 2010. Video of this talk
  77. Alexis: "Scaling up Tree Reconstruction Methods to 100K Taxa and Beyond", iPlant data assembly workshop, Phoenix, Arizona, November 2009.
  78. Alexis: "Rapid Evolutionary Placement of Short Sequence Reads", Department of Biology, TU Munich, Germany, November 2009.
  79. Alexis: "Tracing Evolution on Supercomputers", Department of Computer Science, University of Stuttgart, Germany, October 2009.
  80. Alexis: "Phylogenetic Inference is an Engineering Discipline", Botany & Mycology 2009 Conference, Salt Lake City, USA, July 2009.
  81. Alexis: “Algorithms for Rapid Phylogenetic Classification”, Evolution Meeting, Moscow, Idaho, USA, June 2009.
  82. Alexis: "Mapping the Phylogenetic Likelihood Kernel to Emerging Parallel Computer Architectures", Brown University, Providence, USA, June 2009.                               
  83. Alexis: "The Co-Evolution of Computer Architectures and Tree Search Algorithms", keynote speech within the framework of a two-week course on ”Molecular Evolution: Methods and Applications 2009”, European Bioinformatics Institute, Cambridge, UK, April 2009.
  84. Alexis: "Phylogenetic Engineering for the Data Flood", Center for Population Biology, Imperial College London, UK, March 2009.
  85. Alexis: “Mathematical and Biological Aspects of Phylogenetic Tree Reconstruction”, joint talk with Susanne Renner within the framework of the Munich Science Days, that intend to present and explain current research issues to the broad public, Munich, Germany, October 2008.
  86. Alexis: “The Evolution of Computer Architectures and how it affects Bioinformatics”, University of Vienna, Austria, October 2008.
  87. Alexis: “High Performance Computing in Evolutionary Bioinformatics”, Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece, June 2008.
  88. Alexis: “An Abstract Concept for Mapping the Phylogenetic Likelihood Function to FPGAs”, Technical University of Crete, Chania, Greece, June 2008.
  89. Alexis: “High Performance Computing for Evolutionary Biology”, NEC Labs, Princeton, USA, June 2008.
  90. Alexis: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Vienna, Austria, May 2008.
  91. Alexis: “High Performance Computing for Evolutionary Biology”, University of Potsdam, Volkswagen Foundation Meeting on Evolutionary Biology, Potsdam, Germany, May 2008.
  92. Alexis: “Efficient Computation of the Phylogenetic Likelihood Function on Multi-Gene Alignments and Multi-Core Architectures”, Royal Society Discussion Meetig on “Statistical and computational challenges in molecular phylogenetics and evolution”, London, UK, April 2008.
  93. Alexis: “Algorithms, High Performance Computing, and Challenges for Large-Scale Phylogenetic Inference”, International workshop on ribosomal RNA technology, Bremen, Germany, April 2008.
  94. Alexis: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Colorado at Boulder, Boulder, USA, April 2008.
  95. Alexis: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Göttingen, Gö̈ttingen, Germany, February 2008.
  96. Alexis: “Crunching Huge Phylogenies: A Rapid Bootstrap Algorithm, a Bootstopping Criterion, and Massive Parallelism on the IBM BlueGene”, ETH Zürich, Switzerland, December 2007.                                                         
  97. Alexis: “Crunching Huge Phylogenies: A Rapid Bootstrap Algorithm and Massive Parallelism on the IBM BlueGene”, Phyloinformatics Workshop, Edinburgh, UK, October 2007.
  98. Alexis: “Phylogenetics enter the High Performance Computing Era”, University of Kaiserslautern, Germany, May 2007.
  99. Alexis: “Phylogenetic Inference: Models, Algorithms, Parallel Computing, and Open Problems”, University of Cyprus, May 2007.
  100. Alexis: “Faster Algorithms for Support Value Computation & Emerging Parallel Architectures for Phylogeny Reconstruction”, University of Texas at Austin, USA, April 2007.
  101. Alexis: “Algorithmic and HPC Challenges for Large-scale Phylogeny Reconstruction”, Virginia Tech, USA, March 2007.
  102. Alexis: “Models, Algorithms, and High Performance Computing for Phylogenetic Inference: Current Work and Future Challenges”, DOE Joint Genome Institute, California, USA, March 2007.
  103. Alexis: “RAxML: A Program for ML-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models: How it works and how to use it”, Ohio State University, USA, March 2007.
  104. Alexis: “Models, Algorithms, and HPC for Phylogeny Reconstruction: Current State and Future Challenges”, Ohio State University, USA, March 2007.
  105. Alexis: “RAxML Hands-On Session”, Ohio State University, USA, March 2007.
  106. Alexis: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, State University of New York at Stony Brook, USA, February 2007.
  107. Alexis: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Heidelberg, Germany, February 2007.
  108. Alexis: “RAxML-VI: A Program for Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models: How it works and how to use it”, Department of Systematic Botany and Geobotany, Free University of Berlin, Germany, February 2007.
  109. Alexis: “Recent Improvements in RAxML, The Story of a Bug, and HPC solutions for Phylogenetic Inference”, Center for Integrative Bioinformatics, Vienna, Austria, November 2006.
  110. Alexis: “RAxML-VI: A Program for Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa: How it works and how to use it”, Botanic Garden of Munich, Germany, May 2006.
  111. Alexis: “Technical Challenges for Large-scale Phylogenetic Reconstruction”, Technical University of Munich, Department of Computer Science, Munich, Germany, May 2006.
  112. Alexis: “Inference of Large Phylogenetic Trees with RAxML”, Hellenic Center for Marine Research, Heraklion, Greece, March 2006.
  113. Alexis: “RAxML-VI: A program for large-scale Maximum Likelihood-based phylogenetic analyses; How it works and how to use it”, Max-Planck-Institute for Developmental Biology, Tü̈bingen, Germany, February 2006.
  114. Alexis: “Using RAxML in practice”, CIPRES (Cyberinfrastructure for Phylogenetic Research) project All Hands Meeting 2006, University of Texas at Austin, Texas, February 2006.
  115. Alexis: “Computing Huge Trees with Maximum Likelihood: An HPC Perspective”, Workshop on “The Problems of Phylogenetic Analysis of Large Datasets”, Mathematical Biosciences Institute, Columbus, Ohio, December 2005.
  116. Alexis: “Computation of large phylogenetic trees: Algorithmic and technical solutions”, 1st International Conference of the Hellenic Proteomics Society, Athens, Greece, May 2005.
  117. Alexis: “Technical & Algorithmic concepts in RAxML-V”, University of Düsseldorf, Germany, April 2005.
  118. Alexis: “Applications of Cluster Computing: An Example from Bioinformatics” within the framework of the course “Cluster Computing” (Prof. Ludwig), Heidelberg, Germany, July 2003.
  119. Alexis: “Current Research Issues by Example of the ParBaum Project” within the framework of the special course “Pearls of Computer Science” (Prof. Steger) for talented 1st and 2nd year students, Munich, Germany, January 2003.

Regular talks

  1. Jan: "Why you should swear more!! - Exploring the Correlation between the Use of Swearwords and Code Quality in Open Source Code", HITS Scientific Seminar, Germany, June 2023. Talk slides
  2. Lukas: "The Computatioal Stumbling Blocks: Fault-Tolerance and Reproducibility", Biodiversity Bioinformatics Workshop, Heraklion, Greece, May 2023. Talk slides
  3. Lukas: "ReStore: In-Memory REplicated STORagE for Rapid Recovery", Fault-Tolerance at eXtreme Scale, Dallas, United States, November 2022. Talk slides
  4. Pierre: "Phylogenetic Placement: Why the where of the what tells us the who and the why", University of Duisburg-Essen, Essen, Germany, February 2020.
  5. Adrian: "Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning", HICOMB workshop, IEEE IPDPS, Rio de Janeiro, Brasil, May 2019.
  6. Alexis: "Research Activities in the Exelixis Lab", Roche, Basel, Switzerland, November 2018.
  7. Benoit: "ParGenes: An integrated tool for model selection and maximum likelihood (ML) based phylogenetic inference on thousands of independent MSAs on clusters and supercomputers", 2018 Phylogenomics Symposium, Montpellier, France, October 2018.
  8. Alexey: "Maximum-likelihood inference of cell phylogenies", Workshop: Single Cell Data Science: Making Sense of Data from Billions of Single Cells, Lorentz Center, Leiden, Netherlands, June 2018.
  9. Pierre: "Analysis of microbial environments using phylogenetic placement", SBR, Roscoff, France, April 2018.
  10. Benoit: "A novel heuristic for data distribution in massively parallel phylogenetic inference using site repeats", The 19th International Conferences on High Performance Computing and Communications (HPCC), Bangkok, Thailand, December 2017.
  11. Alexey: "Tools for large-scale phylogenetic inference", Global Plant Phylogeny Synthesys Workshop 2017, London, UK, October 2017. Talk slides
  12. Lucas: "Do Phylogenetic Tree Viewers correctly display Support Values?", Hellenic Bioinformatics Conference (HBio) 2016, Thessaloniki, Greece, November 2016. Talk slides
  13. Constantin: "The divisible load balance problem with shared cost and its application to phylogenetic inference", 15th IEEE International Workshop on High Performance Computational Biology, in conjunction with IPDPS 2016, Chicago, Illinois, USA, May 2016.
  14. Lucas and Alexey: "Phylogenetic Placement of Short Reads: Visualization, Species Delimitation and Taxonomic Annotation", 1st UniEuks Implementation Meeting, Paris, France, May 2016. Talk slides
  15. Kassian: "Computing the Internode Certainty using partial gene trees", 25th Workshop on Mathematical and Statistical Aspects of Molecular Biology (MASAMB), Helsinki, Finland, April 2015.
  16. Kassian: "The divisible load balance problem and its application to phylogenetic inference", 14th Workshop on Algorithms in Bioinformatics (WABI), Wrocław, Poland, September 2014.
  17. Andre: "Bayesian Tree Inference on Whole-Genome Datasets is Possible!", Symposium of the SMBE, San Jose, USA, June 2014.
  18. Alexey: "Efficient Computation of the Phylogenetic Likelihood Function on the Intel MIC Architecture", IPDPS 2014, Phoenix, USA, May 2014. Talk slides
  19. Solon: "MoTeX: A word-based HPC tool for MoTif eXtraction", International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, Washington DC, September 2013.
  20. Solon: "Accelerating string matching on MIC architecture for motif extraction", International Conference on Parallel Processing and Applied Mathematics, Warsaw, October 2013.
  21. Tomas: "An optimal algorithm for computing all subtree repeats in trees", IWOCA, Rouen, France, July 2013.
  22. Fernando: "Heuristic Algorithms for the Protein Model Assignment Problem", ISBRA 2013, Charlotte, USA, May 2013.
  23. Andre: "Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference", IPDPS 2013, Boston, USA, May 2013.
  24. Alexis: "Software bugs and identification of mislabeled sequences", Symposium on detecting Errors in Phylogenies, BioSyst.EU 2013, Vienna, Austria, February 2013.
  25. Tomas: "A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library", HiCOMB (in conjuction with IPDPS 2012), Boston, USA, May 2013.
  26. Nikos: "A Versatile UDP/IP based PC-FPGA Communication Platform", ReConFig conference, Cancun, Mexico, December 2012.
  27. Solon: "A simple method for computing all subtree repeats in unordered trees in linear time", Prague Stringology Conference (PSC2012), Czech Technical University in Prague, August 2012.
  28. Solon: "New and efficient approaches to the quasiperiodic characterisation of a string", Prague Stringology Conference (PSC2012), Czech Technical University in Prague, August 2012.
  29. Simon: "Phylogeny-aware metagenomic analysis", Bertinoro Computational Biology meeting 2012, Bertinoro, Italy, October 2012.
  30. Nikos: "Exploiting Multi-grain Parallelism for efficient Selective Sweep Detection", ICA3PP-2012, Fukuoka, Japan, September 2012.
  31. Alexis: "Biodiversity Informatics: Problems and Challenges for an emerging Computational Science", Evolution Meeting 2012, Ottawa, Canada, July 2012.
  32. Nikos: "An Optimized Reconfigurable System for Computing the PhylogeneticLikelihood on DNA Data" RAW 2012, Shanghai, China, May 2012.
  33. Jiajie: "The Multi-Processor Scheduling Problem in Phylogenetics", 11th IEEE HICOMB workshop (in conjunction with IPDPS 2012), Shanghai, China, May 2012.
  34. Solon: "GapMis: a tool for pairwise sequence alignment with a single gap". London Stringology Days & London Algorithmic Workshop 2012 (LSD & LAW 2012), King's College London, London, UK, February 2012.
  35. Fernando: "Trading Memory for Running Time in Phylogenetic Likelihood Computations", 2012 Bioinformatics conference, Vilamoura, Portugal, February 2012.
  36. Andre: "A Simple and Accurate Method for Rogue Taxon Identification", IEEE BIBM 2011, Atlanta, Georgia, USA, November 2011.
  37. Nikos: "FPGA Acceleration of the Phylogenetic Parsimony Kernel?" FPL 2011, Chania, Greece, September 2011.
  38. Alexis: "What's new in RAxML?", Evolution Meeting 2011, Norman, Oklahoma, June 2011.
  39. Fernando: "Computing the Phylogenetic Likelihood Function Out-of-Core", IEEE HICOMB 2011 workshop (held in conjunction with IPDPS 2011), Anchorage, USA, May 2011.
  40. Nikos: "Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs", IEEE FCCM, Salt Lake City, Utah, USA, May 2011.
  41. Nikos: "FPGA Optimizations for a Pipelined Floating-Point Exponential Unit", 7th International Symposium on Applied Reconfigurable Computing (ARC 2011), Belfast, United Kingdom, March 2011.
  42. Nikos: "A Generic and Versatile Architecture For Inference of Evolutionary Trees under Maximum Likelihood", ASILOMAR 2010, Pacific Grove, USA, November 2010.
  43. Alexis: "Assessment of Barrier Implementions for Fine-Grain Parallel Regions on Current Multi-core Architectures", IEEE Cluster 2010, Heraklion, Greece, September 2010.
  44. Nikos: "Time and memory efficient likelihood-based tree searches on gappy phylogenomic alignments", ISMB 2010, Boston, Massachusetts, July 2010.
  45. Simon: "Efficient PC-FPGA Communication over Gigabit Ethernet", IEEE ICESS 2010, Bradford, UK, June/July 2010.
  46. Andre: "Parallel Computation of Phylogenetic Consensus Trees", ICCS 2010, Emerging Parallel Architectures Workshop, Amsterdam, The Netherlands, May 2010.
  47. Simon: "Accuracy of Morphology-based Phylogenetic Fossil Placement under Maximum Likelihood", 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10), May 2010.
  48. Simon: "Evolutionary Placement of Short Sequence Reads on Multi-Core Architectures", 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10), May 2010.
  49. Nikos: "Efficient Floating-Point Logarithm Unit for FPGAs", RAW workshop, held in conjunction with IPDPS 2010, April 2010.
  50. Alexis: "Computing Big Trees: Hardware, Parallelism, and Algorithms", Department of Bioengineering, Berkeley, California, January 2010.
  51. Nikos: "Future Reconfigurable Architectures for Phylogenetic Inference", 4th conference of the Hellenic Society for Computational Biology and Bioinformatics HSCBB09, Athens, Greece, December 2009.
  52. Michael: "Preparing RAxML for the SPEC MPI Benchmark Suite", HLRB review workshop, Garching, Germany, December 2009.
  53. Alexis: "Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction", Parallel Biocomputing Workshop, Wroclaw, Poland, September 2009.
  54. Michael: "Load Balance in the Phylogenetic Likelihood Kernel", ICPP 2009, Vienna, Austria, September 2009.
  55. Nikos: "Exploring FPGAs for accelerating the Phylogenetic Likelihood Function", HICOMB 2009, Rome, Italy, May 2009.
  56. Alexis: "Parallel Computation of the Phylogenetic Likelihood Kernel in HW and SW", Department of Electric and Electronical Engineering, Imperial College, London, UK, March 2009.
  57. Alexis: "Phylogenetic Bootstrapping under Resource Constraints: Higher Model Accuracy or more Replicates?", 3rd conference of the Hellenic Society for Computational Biology and Bioinformatics HSCBB08, Thessaloniki, Greece, October 2008.
  58. Michael: "Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study", PRIB 2008, Melbourne, Asutralia, October 2008.
  59. Alexis: “Emerging Processor Architectures and Associated Performance Problems for Phylogenetic Reconstruction”, Technical University of Delft, Netherlands, May 2008.
  60. Alexis: “Large-scale Maximum Likelihood-based Phylogenetic Analysis on the IBM BlueGene/L”, IEEE/ACM Supercomputing 2007 conference, Reno, Nevada, November 2007.
  61. Alexis: “Faster Algorithms for Support Value Computation & Parallel Computing for Large-Scale Phyllogeny Reconstruction”, Hellenic Bioinformatics & Medical Informatics Meeting, Athens, Greece, October 2007.
  62. Alexis: “Phylogenetic Inference: A Computational Perspective”, University of Munich, Germany, August 2007.
  63. Alexis: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Karlsruhe, Germany, July 2007.
  64. Alexis: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Munich, Germany, May 2007.
  65. Alexis: “Potential Algorithmic Solutions for Large-Scale Maximum Likelihood Phylogeny Estimation”, Mathematical and Statistical Aspects of Molecular Biology (MASAMB 2007) Conference, Manchester, UK, March 2007.
  66. Alexis: “Recent Improvements and Experimental Work with RAxML”, American Museum of National History, New York, USA, March 2007.
  67. Alexis: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Greifswald, Germany, February 2007.
  68. Alexis: “The Story of a Bug, its Impact on Phylogenetic Inference, and Open Problems in Phylogenetics”, 1st Lausanne Campus Bioinformatics Workgroup meeting, Lausanne, Switzerland, October 2006.
  69. Alexis: “Inferring Phylogenies with RAxML-VI-HPC”, GCB2006 conference, Tü̈bingen, Germany, September 2006.
  70. Alexis: “Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective”, IPDPS2006 conference, Rhodos, Greece, April 2005.
  71. Alexis: “Large-scale Inference of Phylogenetic Trees: A Talk for Biologists and Computer Scientists”, Bioinformatics Seminar, Institute of Computer Science & Institute of Molecular Biology and Biotechnology, Heraklion, Greece, March 2006.
  72. Alexis: “Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood”, HPCC05 conference, Sorrento, Italy, September 2005.
  73. Alexis: “An Efficient Program for Phylogenetic Inference Using Simulated Annealing”, IPDPS2005 conference, Denver, Colorado, April 2005.
  74. Alexis: “Using RAxML in practice”, Pace Laboratory, University of Colorado at Boulder, Colorado, April 2005.
  75. Alexis: “Research Statement: High Performance Computing Bioinformatics”, Bioinformatics Seminar, Institute of Computer Science & Institute of Molecular Biology and Biotechnology, Heraklion, Greece, February 2005.
  76. Alexis: “Future technical and algorithmic solutions for inference of very large phylogenetic trees”, KONWIHR Result Workshop, Technical University of Munich, Germany, October 2004.
  77. Alexis: “Future algorithms & computer systems for inference of large phylogenetic trees with statistical methods”, Center for Computational Science, Computational Biology Unit, Bergen, Norway, September 2004.
  78. Alexis: “Parallel Inference of a 10.000-taxon Phylogeny with Maximum Likelihood”, Euro-Par 2004 conference, Pisa, Italy, September 2004.
  79. Alexis: “Computing Large Phylogenies with Statistical Methods: Problems & Solutions”, BGRS2004 conference, Novosibirsk, Russia, July 2004.
  80. Alexis: “New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees”, IPDPS2004 conference, Santa Fe, New Mexico, April 2004.
  81. Alexis: “Parallel & Distributed Systems and Algorithms for Maximum Likelihood-based Phylogenetic Tree Inference”, Bioinformatics Seminar, Institute of Computer Science & Institute of Molecular Biology and Biotechnology, Heraklion, Greece, March 2004.
  82. Alexis: “A Fast Program for Maximum Likelihood-based Inference of Large Phylogenetic Trees”, SAC2004 conference, Nicosia, Cyprus, March 2004.
  83. Alexis: “Phylogenetic Tree Inference with RAxML-II”, Biology Seminar, Radjabazaar Science College, Calcutta, India, February 2004.
  84. Alexis: “Parallel & Distributed Phylogenetic Tree Inference with RAxML-II”, Bioinformatik-Kolloquium der Fakultä̈t fü̈r Informatik, Munich, Germany, February 2004.
  85. Alexis: “DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA”, PaCT2003 conference, Nizhni Novgorod, Russia, September 2003.“Phylogenetic Tree Inference on PC Architectures with AxML/PAxML”, IPDPS2003 conference, High Performance Computational Biology Workshop, Nice, France, April 2003.
  86. Alexis: “Current State of the ParBaum Project”, Laboratoire de l’Informatique du Parallelisme, Ecole Normale Superieure de Lyon, France, February 2003.
  87. Alexis: “Accelerating Parallel Maximum Likelihood-based Phylogenetic Tree Calculations using Subtree Equality Vectors”, SC2002 conference, Baltimore, Maryland, November 2002.
  88. Alexis: “Adapting PAxML to the Hitachi SR8000-F1 Supercomputer”, 1st Joint HLRB and KONWIHR Status and Reviewing Workshop, Munich, Germany, October 2002.
  89. Alexis: “DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA”, 6th Workshop on “Systemintegrierte Verfahren zur Last- und Ressourcenverwaltung”, Heidelberg, Germany, March 2002.
  90. Alexis: “Presentation of the ParBaum Project”, 7th School Graduate Orientation Day, Munich, Germany, March 2002.
  91. Alexis: “Interoperable Tool Deployment for the Late Development Phases of Distributed Object-Oriented Programs”, 5th Workshop on “Systemintegrierte Verfahren zur Last- und Ressourcenverwaltung”, Munich, Germany, March 2001.