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Dr. Alexandros Stamatakis |
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Postdoctoral Researcher |
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PUBLICATIONS |
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Information for Biologists: CS Conference Publications Unlike in Biology, conference publications are much more important in computer science. We normally submit full papers to conferences which are then peer-reviewed and appear in printed conference proceedings or on CDs. If you look at the publication record of CS professors (for a representative example have a look at the homepage of Dimitris Nikolopoulos) you will find that they typically have much more conference than journal publications. Theses 1. Alexandros Stamatakis: ``Distributed and Parallel Algorithms and Systems for Inference of Huge Phylogenetic Trees based on the Maximum Likelihood Method ''. Ph.D. thesis, Technische Universität München, Germany, October 2004.(PDF) 2. Alexandros Stamatakis: ``Interoperable Tool Deployment for the Late Development Phases of Distributed Object-Oriented Programs''. Master's thesis, Technische Universität München, Germany, February 2001.(PDF) Book Chapters 1. David Bader, Usman Roshan, Alexandros Stamatakis: `` Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions''. In Chau-Wen Tzeng, editor, Advances in Computers, Volume 68, 128-170, Elsevier, 2006. 2. Olaf R.P. Bininda-Emonds, Alexandros Stamatakis: ``Taxon Sampling versus Computational Complexity and their Impact on obtaining the Tree of Life''. In Trevor Hodkinson, John Parnell, and Steve Waldren, editors, Towards the Tree of Life: taxonomy and systematics of large and species rich clades, pp 77-95, Volume 72, Special Volume for the Systematics Association, CRC Press. 3. Alexandros Stamatakis: ``Parallel and Distributed Computation of Large Phylogenetic Trees''. Published in Albert E. Zomaya, editor, Parallel Computing for Bioinformatics and Computational Biology, 327-346, John Wiley & Sons, 2006. Journal Papers 1. Filip Blagojevic, Dimitrios S. Nikolopoulos, Alexandros Stamatakis, Christos D. Antonopoulos, Matthew Curtis-Maury: “Runtime Scheduling of Dynamic Parallelism on Accelerator-Based Multi-core Systems”. Accepted for publication in Parallel Computing, 2007. 2. Alexandros Stamatakis, Alexander Auch, Jan Meier-Kolthoff, Markus Göker: 3. Alexandros Stamatakis, Filip Blagojevic, Christos D. Antonopoulos, Dimitrios S. Nikolopoulos: "Exploring new Search Algorithms and Hardware for Phylogenetics: RAxML meets the IBM Cell". In Journal of VLSI Signal Processing Systems, 48(3):271-286, 2007. 4. Marc Gottschling, Alexandros Stamatakis, Ingo Nindl, Eggert Stockfleth, Ángel Alonso, Lutz Gissmann, Ignacio G. Bravo: ``Multiple evolutionary mechanisms drive papillomavirus diversification”. In Molecular Biology and Evolution, 24(5):1242-1258, 2007. (on-line access) 5. Guido Grimm, Susanne Renner, Alexandros Stamatakis, Vera Hemleben: ``A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences”. In Evolutionary Bioinformatics On-Line 2:279-294, 2006. (PDF) 6. Alexandros Stamatakis: ``RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models”. In Bioinformatics 22(21):2688-2690, 2006. (PDF, on-line access) 7. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``RAxML-II: A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees''. In Concurrency and Computation: Practice and Experience (CCPE) 17:1705-1723. (PDF) 8. Alexandros Stamatakis: ``Phylogenetics: Applications, Software and Challenges''. In Cancer Genomics & Proteomics 2(5):301-305, 2005. 9. Alexandros Stamatakis, Michael Ott, Thomas Ludwig, and Harald Meier: ``DRAxML@home: A Distributed Program for Computation of Large Phylogenetic Trees''. In Future Generation Computer Systems (FGCS) 21(5):725-730, 2005. (PDF) 10. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``RAxML-III: A Fast Program for Maximum Likelihood-based Inference of Large Phylogenetic Trees''. In Bioinformatics 21(4):456-463, 2005.(PDF) 11. Magdalena Rafecas, Brygida Mosler, Melanie Dietz, Markus Pögl, Alexandros Stamatakis, David P. McElroy, Sibylle I. Ziegler: ``Use of a Monte-Carlo based probability matrix for 3D iterative reconstruction of MADPET-II data''. In IEEE Transactions on Nuclear Sciences 51(5):2597-2605, 2004. (PDF) 12. Alexandros Stamatakis and Thomas Ludwig: ``The AxML Program Family for phylogenetic Tree Inference''. In Concurrency and Computation: Practice and Experience (CCPE), 16:975-988, 2004. (PDF) 13. Wolfgang Ludwig, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier, Yadhukumar, Arno Buchner, Tina Lai, Susanne Steppi, Gangolf Jobb, Wolfram Förster, Igor Brettske, Stefan Gerber, Anton W. Ginhart, Oliver Gross, Silke Grumann, Stefan Hermann, Ralf Jost, Andreas König, Thomas Liss, Ralph Lüssmann, Michael May, Björn Nonhoff, Boris Reichel, Robert Strehlow, Alexandros Stamatakis, Norbert Stuckmann, Alexander Vilbig, Michael Lenke, Thomas Ludwig, Arndt Bode, and Karl-Heinz Schleifer: ``ARB: a software environment for sequence data''. In Nucleic Acids Research, 32(4):1363-1371, 2004. (PDF) 14. Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis, and Günther Rackl:``Tool environments in CORBA-based medical high-performance computing''. In Future Generation Computer Systems (FGCS), 18(6):841-847, 2002. 15. Günther Rackl, Thomas Ludwig, Markus Lindermeier, and Alexandros Stamatakis: ``Efficiently Building On-Line Tools for Distributed Heterogeneous Environments''. In Scientific Programming, 10(1):67-74, 2002. (PDF) Peer-Reviewed Conference Papers 1. Michael Ott, Jaroslaw Zola, Srinivas Aluru, Alexandros Stamatakis: “Large–scale Maximum Likelihood–based Phylogenetic Analysis on the IBM BlueGene/L”. In Proceedings of ACM/IEEE Supercomputing conference 2007. BEST PAPER FINALIST 2. Filip Blagojevic, Dimitrios S. Nikolopoulos, Alexandros Stamatakis, Christos D. Antonopoulos. "RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine". In Proceedings of 21st IEEE International Parallel & Distributed Processing Symposium (IPDPS2007), Proceedings on CD, Long Beach, California, USA, March 2007. (PDF) 3. Filip Blagojevic, Dimitrios S. Nikolopoulos, Alexandros Stamatakis, and Christos D. Antonopoulos: “Dynamic Multigrain Parallelization on the Cell Broadband Engine”. In Proceedings of ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP'07), 90-100, San Jose, California, USA, March 2007. (PDF) BEST PAPER AWARD 4. Alexandros Stamatakis: ``Inferring Phylogenies with RAxML-VI-HPC” (software demonstration abstract). In Proceedings of German Conference of Bioinformatics 2006, to be published, Tuebingen, Germany, September 2006. (PDF) 5. Alexandros Stamatakis: ``Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective''. In Proceedings of 20th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2006), High Performance Computational Biology Workshop, Proceedings on CD, Rhodos, Greece, April 2006. (PDF) 6. Adam Arvelakis, Martin Reczko, Alexandros Stamatakis, Alkiviadis Symeonidis, Ioannis G.Tollis: ``Using Treemaps to Visualize Phylogenetic Trees''. In Proceedings of 6th International Symposium on Biological and Medical Data Analysis (ISBMDA 2005), Volume 3745 of Lecture Notes in Computer Science, 283-293, Springer Verlag, November 2005. (PDF) 7. Maria Charalambous, Pedro Trancoso, and Alexandros Stamatakis: ``Initial Experiences Porting a Bioinformatics Application to a Graphics Processor''. In Proceedings of 10th Panhellenic Conference on Informatics (PCI2005), Volume 3746 of Lecture Notes in Computer Science, 415-425, Springer Verlag, September 2005. (PDF) 8. Zhihua Du, Alexandros Stamatakis, Feng Lin, Usman Roshan, Luay Nakhleh: ``Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood''. In Proceedings of the 2005 International Conference on High Performance Computing and Communications (HPCC-05), Volume 3726 of Lecture Notes in Computer Science, 776-785, Springer Verlag, September 2005. (PDF) 9. Alexandros Stamatakis, Michael Ott, and Thomas Ludwig:``RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs''. In Proceedings of 8th International Conference on Parallel Computing Technologies (PaCT2005), Volume 3606 of Lecture Notes in Computer Science, 288-302, Springer Verlag, September 2005. (PDF) 10. Alexandros Stamatakis: ``An Efficient Program for phylogenetic Inference Using Simulated Annealing''. In Proceedings of 19th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2005), High Performance Computational Biology Workshop, Proceedings on CD, Denver, Colorado, April 2005. (PDF) 11. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``Parallel Inference of a 10.000-taxon Phylogeny with Maximum Likelihood''. In Proceedings of 10th International Euro-Par Conference (Euro-Par 2004), Volume 3149 of Lecture Notes in Computer Science, 997-1004, Springer Verlag, September 2004. (PDF) 12. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``Computing Large Phylogenies with Statistical Methods: Problems & Solutions''. In Proceedings of 4th International Conference on Bioinformatics and Genome Regulation and Structure (BGRS2004), 2:229-233, Novosibirsk, Russia, July 2004. (PDF) 13. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees''. In Proceedings of 18th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2004), High Performance Computational Biology Workshop, Proceedings on CD, Santa Fe, New Mexico, April 2004. (PDF) 14. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``A Fast Program for Maximum Likelihood-based Inferrence of Large Phylogenetic Trees''. In Proceedings of 19th ACM Symposium on Applied Computing (SAC2004), 197-201, Nicosia, Cyprus, March 2004. (PDF) 15. Alexandros Stamatakis, Markus Lindermeier, Michael Ott, Thomas Ludwig, and Harald Meier: ``DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA''. In Proceedings of 7th International Conference on Parallel Computing Technologies (PaCT2003), Volume 2763 of Lecture Notes in Computer Science, 538-548, Springer Verlag, September 2003. (PDF) 16. Alexandros Stamatakis and Thomas Ludwig: ``Phylogenetic Tree Inference on PC Architectures with AxML/PAxML''. In Proceedings of 17th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2003), High Performance Computational Biology Workshop, Proceedings on CD, Nice, France, April 2003. (PDF) 17. Alexandros Stamatakis, Thomas Ludwig, Harald Meier, and Marty J. Wolf: ``Accelerating Parallel Maximum Likelihood-based Phylogenetic Tree Calculations using Subtree Equality Vectors''. In Proceedings of 15th IEEE/ACM Supercomputing Conference (SC2002), Proceedings on CD, Baltimore, Maryland, November 2002. (PDF) 18. Alexandros Stamatakis, Thomas Ludwig, Harald Meier, and Marty J. Wolf: ``AxML: A Fast Program for Sequential and Parallel Phylogenetic Tree Calculations Based on the Maximum Likelihood Method''. In Proceedings of 1st IEEE Computer Society Bioinformatics Conference (CSB2002), 21-28, Palo Alto, California, August 2002. (PDF) 19. Thomas Ludwig, Markus Lindermeier, Alexandros Stamatakis, and Günther Rackl: `` Tool Environments in CORBA-based Medical High Performance Computing''. In Proceedings of 6th International Conference on Parallel Computing Technologies (PaCT2001), Volume 1067 of Lecture Notes in Computer Science, 447-455, Springer Verlag, September 2001. (PDF) Posters, Abstracts & Technical Reports 1. Andrew Johnson, Michael Ott, Jaroslaw Zola, Srinivas Aluru, Alexandros Stamatakis, and Daniel Janies: "Personal Phylogenomics: First Human Lineage Trees Based on Large HapMap Datasets", Abstract/Talk, Ohio Collaborative Conference on Bioinformatics, Miami University, Oxford, Ohio, 2007. PRIZE WINNING TALK BY ANDREW JOHNSON 2. Marc Gottschling, Eberhard Schulz, Ignacio G. Bravo, Alexandros Stamatakis, Ulrich Wittstatt, Robert Deaville, Eggert Stockfleth, Ingo Nindl: “Phylogenomics of papillomaviruses and identification of novel types”, Abstract/Talk, 24th IPV Conference and Clinical Workshop, Beijing, China, 2007. 3. Marc Gottschling, Ignacio G. Bravo, Alexandros Stamatakis, Eggert Stockfleth, Ingo Nindl: “Mechanisms of papillomavirus evolution and identification of novel types”, Abstract/Poster, 3rd European Congress of Virology, Nürnberg, Germany, 2007. 4. Marc Gottschling, Ignacio G. Bravo, Alexandros Stamatakis, Angel Alonso, Lutz Gissmann, Eggert Stockfleth, Ingo Nindl: “Phylogenomics of papillomavirus and the biological interpretations”, Abstract/Talk, 9th annual meeting of the GfBS (German Society for Biological Systematics), Vienna, Austria, 2007. 5. Markus Göker and Alexandros Stamatakis. “Maximum Likelihood Phylogenetic Inference: An Empirical Assessment of Search Algorithms on a Multi-Gene Dataset", Poster at German Conference on Bioinformatics (GCB 2006), Tübingen, Germany, September 2006.(PDF) 6. Alexandros Stamatakis, ``RAxML-VI: A program for Maximum Likelihood based Phylogenetic Analyses with Thousands of Taxa”. Poster at CIPRES All-Hands-Meeting 2006, Austin, Texas, February 2006. 7. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``ParBaum: A Fast Program for Phylogenetic Tree Inference with Maximum Likelihood''. In Arndt Bode and Franz Durst, editors, High Performance Computing in Science and Engineering, Garching 2004, 275-284, Springer Verlag, 2005. 8. Alexandros Stamatakis, Michael Ott:``Algorithmic & Technical concepts in RAxML-V”. Poster at MEP2005 conference, Paris, France, June 2005. 9. Alexandros Stamatakis: ``Computation of large phylogenetic trees: Algorithmic and technical solutions”, abstracts of 1st International Conference of the Hellenic Proteomics Society, in Cancer Genomics & Proteomics 2(3):176-177, 2005. 10. Alexandros Stamatakis: ``Computation of the first 10,000-organism Phylogeny with Maximum Likelihood on the RRZE PC Cluster”, RRZE Aktuell, BI 72, 34-35, October 2004. 11. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``A Fast Program for Phylogenetic Tree Inference with Maximum Likelihood''. In Siegfried Wagner, Werner Hanke, Arndt Bode, and Franz Durst, editors, High Performance Computing in Science and Engineering, Munich 2004, 273-283, Springer Verlag, March 2004. (PDF) 12. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``RAxML: A Parallel Program for Phylogenetic Tree Inference''. Poster abstract in Proceedings of 2nd European Conference on Computational Biology (ECCB2003), Paris, France, September 2003. (PDF) 13. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``Neues vom Projekt ParBaum ... Parallele und verteilte Systeme und Algorithmen zur Berechnung grosser phylogenetischer Bäume mit Maximum-Likelihood (Parallel and Distributed Systems and Algorithms for the Inference of big Phylogenetic Trees with Maximum Likelihood)''. In KONWIHR Quartl, 34(1):4-7, May 2003. (PDF) 14. Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``Adapting PAxML to the Hitachi SR8000-F1 Supercomputer''. In Siegfried Wagner, Werner Hanke, Arndt Bode, and Franz Durst, editors, High Performance Computing in Science and Engineering, Munich 2002, 453-466, Springer Verlag, October 2002. (PDF) 15. Guillermo H. Lopez-Campos, Alexandros Stamatakis, and Fernando Martin: ``AMANDA-II: A MIAME-compliant Array MAnagement Database and Representation Tool''. Poster abstract in Proceedings of III Jornadas de Bioinformatica (JBI2002), Salamanca, Spain, September 2002. (TXT, TIFF) 16. Alexandros Stamatakis: ``Advanced Work on the Highly Interactive Problem Solver (HIPS)''. Report, Eurocontrol Experimental Center, Bretigny sur Orge, France, July 1999.(PDF) 17. Alexandros Stamatakis: ``Analysis of the Automatisation Potential of an Air Traffic Control Sector''. Report, National Technical University of Athens, Athens, Greece, July 1998.(PDF) Talks 1. Invited Talk: “Large-Scale Phylogenetic Inference with Maximum Likelihood”, Royal Society Discussion Meetig on Statistical and computational challenges in molecular phylogenetics and evolution, London, UK, April 2008. 2. Invited Talk: “”, International workshop on ribosomal RNA technology, Bremen, Germany, April 2008. 3. Invited Talk: “Crunching Huge Phylogenies: A Rapid Bootstrap Algorithm, a Bootstopping Criterion, and Massive Parallelism on the IBM BlueGene”, ETH Zürich, Switzerland, December 2007. 4. Talk: “Large–scale Maximum Likelihood–based Phylogenetic Analysis on the IBM BlueGene/L”, IEEE/ACM Supercomputing 2007 conference, Reno, Nevada, November 2007. 5. Invited Talk: “Crunching Huge Phylogenies: A Rapid Bootstrap Algorithm and Massive Parallelism on the IBM BlueGene”, Phyloinformatics workshop, Edinburgh, UK, October 2007. 6. Talk: “Faster Algorithms for Support Value Computation & Parallel Computing for Large-Scale Phylogeny Reconstruction", Hellenic Bioinformatics & Medical Informatics Meeting, Athens, Greece, October 2007. 7. Talk: “Phylogenetic Inference: A Computational Perspective”, Ludwig-Maximilians University, Munich, Germany, September 2007. 8. Talk: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Karlsruhe, Germany, July 2007. 9. Talk: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, Ludwig-Maximilians University, Munich, Germany, May 2007. 10. Invited Talk: “Phylogenetics enter the High Performance Computing Era”, University of Kaiserslautern, Germany, May 2007. 11. Invited Lecture: “Phylogenetic Inference: Models, Algorithms, Parallel Computing, and Open Problems”, University of Cyprus, May 2007. 12. Invited Talk: “Faster Algorithms for Support Value Computation & Emerging Parallel Architectures for Phylogeny Reconstruction”, University of Texas at Austin, USA, April 2007. 13. Talk: “Potential Algorithmic Solutions for Large-Scale Maximum Likelihood Phylogeny Estimation”, Mathematical and Statistical Aspects of Molecular Biology (MASAMB 2007) Conference, Manchester, UK, March 2007. 14. Invited Talk: “Algorithmic and HPC Challenges for Large-scale Phylogeny Reconstruction ”, Virginia Tech, USA, March 2007. 15. Invited Talk: “Models, Algorithms, and High Performance Computing for Phylogenetic Inference: Current Work and Future Challenges”, DOE Joint Genome Institute, California, USA, March 2007. 16. Two Invited Talks and a Hands-on session: “RAxML: A Program for ML-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models: How it works and how to use it” & “Models, Algorithms, and HPC for Phylogeny Reconstruction: Current State and Future Challenges” & “RAxML Hands-On Session”, Ohio State University, USA, March 2007. 17. Talk: “Recent Improvements and Experimental Work with RAxML”, American Museum of National History, New York, USA, March 2007. 18. Invited Talk: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, State University of New York at Stony Brook, USA, February 2007. 19. Invited Talk: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Heidelberg, Germany, February 2007. 20. Invited Talk: “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. 21. Talk: “Models, Algorithms, and High Performance Computing for Evolutionary Biology”, University of Greifswald, Germany, February 2007. 22. Invited Talk: “Recent Improvements in RAxML, The Story of a Bug, and HPC Solutions for Phylogenetic Inference", Center for Integrative Bioinformatics, Vienna, Austria, November 2006. 23. Talk: “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. 24. Software Demonstration: ``Inferring Phylogenies with RAxML-VI-HPC”, German Conference of Bioinformatics 2006, Tuebingen, Germany, September 2006. 25. Summer School Lecture: ``Computation of large phylogenetic trees: algorithmic and technical solutions”, The 2006 BGRS International Summer School for young scientists: "Evolution, Systems Biology and High Performance Computing Bioinformatics", Novosibirsk, Russia, July 2006. 26. Invited Talk: ``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. 27. Invited Talk: ``Technical Challenges for Large-Scale Phylogeny Reconstruction”, Technical University of Munich, Department of Computer Science, Munich, Germany, May 2006. 28. Talk: ``Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective''. IPDPS2006 conference, Rhodos, Greece, April 2006. 29. Invited Talk: ``Inference of Large Phylogenetic Trees with RAxML”, Hellenic Center for Marine Research, Heraklion, Greece, March 2006. 30. Talk: ``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. 31. Invited Talk: ``RAxML-VI: A program for large-scale Maximum Likelihood-based analyses; How it works and how to use it”, Max-Planck Institute for Developmental Biology, Tübingen, Germany, February 2006. 32. Invited Talk: ``Using RAxML-VI in practice”, CIPRES All-Hands-Meeting 2006, Austin, Texas, February 2006. 33. Invited Talk: ``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. 34. Talk: ``Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood'', HPCC-05 conference, Sorrento, Italy, September 2005. 35. Invited Talk: ``Computation of large phylogenetic trees: Algorithmic and technical solutions”, 1st International Conference of the Hellenic Proteomics Society, Athens, May 2005. 36. Invited Talk: ``Technical & Algorithmic concepts in RAxML-V“, University of Düsseldorf, Germany, April 2005. 37. Talk: ``An Efficient Program for phylogenetic Inference Using Simulated Annealing'', IPDPS2005 conference, Denver, Colorado, April 2005. 38. Seminar: ``Using RAxML in practice”, Pace Laboratory, University of Colorado at Boulder, Colorado, April 2005. 39. Talk: ``Research Statement: High Performance Computing Bioinformatics“, Bioinformatics Seminar, Institute of Computer Science & Institute of Molecular Biology and Biotechnology, Heraklion, Greece, February 2005. 40. Talk: ``Future technical and algorithmic solutions for inference of very large phylogenetic trees'', KONWIHR Result Workshop, Technical University of Munich, Germany, October 2004. 41. Invited Talk: ``Future algorithms & computer systems for inference of large phylogenetic trees with statistical methods'', Center for Computational Science, Computational Biology Unit, Bergen, Norway, September 2004. 42. Talk: ``Parallel Inference of a 10.000-taxon Phylogeny with Maximum Likelihood'', Euro-Par 2004 conference, Pisa, Italy, September 2004. 43. Talk: ``Computing Large Phylogenies with Statistical Methods: Problems & Solutions'', BGRS2004 conference, Novosibirsk, Russia, July 2004. 44. Talk: ``New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees'', IPDPS2004 conference, Santa Fe, New Mexico, April 2004. 45. Talk: ``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. 46. Talk: ``A Fast Program for Maximum Likelihood-based Inferrence of Large Phylogenetic Trees'', SAC2004 conference, Nicosia, Cyprus, March 2004. 47. Talk: ``Phylogenetic Tree Inference with RAxML2'', Biology Seminar, Radjabazaar Science College, Calcutta, India, February 2004. 48. Talk: ``Parllel & Distributed Phylogenetic Tree Inference with RAxML2'', Bioinformatik-Kolloquium der Fakultät für Informatik, Munich, Germany, February 2004. 49. Talk: ``DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA'', PaCT2003 conference, Nizhni Novgorod, Russia, September 2003. 50. Guest lecture: ``Applications of Cluster Computing: An Example from Bioinformatics'' within the framework of the course ``Cluster Computing'' (Prof. Ludwig), Heidelberg, Germany, July 2003. 51. Talk: ``Phylogenetic Tree Inference on PC Architectures with AxML/PAxML'', IPDPS2003 conference, High Performance Computational Biology Workshop, Nice, France, April 2003. 52. Talk: ``Current State of the ParBaum Project'', Laboratoire de l'Informatique du Parallelisme, Ecole Normale Superieure de Lyon, France, February 2003. 53. Guest lecture: ``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. 54. Talk: ``Accelerating Parallel Maximum Likelihood-based Phylogenetic Tree Calculations using Subtree Equality Vectors'', SC2002 conference, Baltimore, Maryland, November 2002. 55. Talk: ``Adapting PAxML to the Hitachi SR8000-F1 Supercomputer'', 1st Joint HLRB and KONWIHR Status and Reviewing Workshop, Munich, Germany, October 2002. 56. Talk: ``DAxMl: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA'', 6th Workshop Systemintegrierte Verfahren zur Last- und Ressourcenverwaltung, Heidelberg, Germany, March 2002. 57. Talk: ``Presentation of the ParBaum Project'', 7th School Graduate Orientation Day, Munich, Germany, March 2002. 58. Talk: ``Interoperable Tool Deployment for the Late Development Phases of Distributed Object-Oriented Programs'', 5th Workshop Systemintegrierte Verfahren zur Last- und Ressourcenverwaltung, Munich, Germany, March 2001. Community Service Conference Organization Together with Sofia Kossida I initiated and organized the Hellenic Bioinformatics & Medical Informatics Meeting which was held at Biomedical Research Academy of Athens in October 2007 and gathered around 100 participants. Initiator & Coordinator of the 1st Cretan Bioinformatics Forum, Heraklion, Crete, 2006. CS Conference Program Committees & Reviewing Program Committee Member of IEEE/ACM 2008 Supercomputing conference. Program Committee Member of the 22nd Annual ACM Symposium on Applied Computing 2007 Bioinformatics Track (ACM SAC 2007). Program Committee Member (Biological Informatics and Computing Track) of IEEE 21th International Conference on Advanced Information Networking and Applications (AINA-07). Scientific Committee Member of Parallel Bio-Computing Workshop PBC 2005 and PBC 2007 Program Committee Member (Biological/Molecular Computing Track) of HPCC 05 and HPCC 06 Program Committee Member of HiCOMB 2006 and HiCOMB 2008 Scientific Committee Member of the 2005 and 2006 and 2008 BGRS International Summer School for young scientists on ``Evolution, Systems Biology and High Performance Computing Bioinformatics" Reviewer for Journals Bioinformatics, IEEE Transactions on Parallel and Distributed Systems, Journal of Molecular Evolution, Systematic Biology, BMC Bioinformatics, BMC Evolutionary Biology, Genome Biology, Evolutionary Bioinformatics Online, Parallel Computing Grants 1. Received 1-year Postdoc scholarship by the German Academic Exchange Service (DAAD) for the year 2005. 2. Received 1-year 3.130 EUR travel funding by the franco-bavarian center for academic cooperation (BFHZ/CCUFB). Together with researchers from the Laboratoire de l'Informatique du Parallelisme at the Ecole Normale Superieure de Lyon work was conducted on ``High Performance Bioinformatics on Grids of Supercomputers'' in 2003. 3. The position as research assistant (wissenschaftlicher Angestellter) at the Lehrstuhl für Rechnertechnik und Rechnerorganisation for the period 01.10.2001-31.12.2004 has been sponsored under the project ID ParBaum, within the framework of the ``Competence Network for Technical, Scientific High Performance Computing in Bavaria'' (KONWIHR). Tutorials 1. Joint half-day tutorial with David Bader and Usman Roshan on ``Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions''. Presented at EEE/ACM Supercomputing Conference (SC2005), Seattle, Washington State, November 2005. Abstract: PDF. 2. Joint half-day tutorial with Thomas Ludwig on ``High Performance Computing in Bioinformatics''. Presented at 4th International Conference on Bioinformatics and Genome Regulation and Structure (BGRS2004) in Novosibirsk, Russia, July 2004. Slides: PDF. Tutorial-Evaluation by the participants: PDF. 3. Joint half-day tutorial with Thomas Ludwig on ``High Performance Computing in Bioinformatics''. Presented at the German Conference on Bioinformatics (GCB 2004) in Bielefeld, Germany, October 2004. Slides: PDF.
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