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Publications ,Talks, Reports


Book Chapters

1.
Alexandros Stamatakis: ``Parallel and Distributed Computation of Large Phylogenetic Trees''. To be published in Albert E. Zomaya, editor, Parallel Computing for Bioinformatics and Computational Biology, John Wiley & Sons.

Journal Papers

1.
Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``RAxML-III: A Fast Program for Maximum Likelihood-based Inference of Large Phylogenetic Trees''. To be published in Bioinformatics. (PDF)

2.
Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``RAxML-II: A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees''. To be published in Concurrency and Computation: Practice and Experience (CCPE).(PDF)

3.
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)

4.
Alexandros Stamatakis, Michael Ott, Thomas Ludwig, and Harald Meier: ``DRAxML@home: A Distributed Program for Computation of Large Phylogenetic Trees''. To be published in Future Generation Computer Systems (FGCS). (PDF)

5.
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)

6.
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)

7.
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.

8.
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)

Reviewed Conference Papers

1.
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)

2.
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)

3.
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)

4.
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)

5.
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)

6.
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)

7.
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)

8.
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)

9.
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)

10.
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)

11.
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)

Non-Reviewed Publications & Technical Reports

1.
Alexandros Stamatakis, Thomas Ludwig, and Harald Meier: ``RAxML: A Parallel Program for Phylogenetic Tree Inferrence''. Poster abstract in Proceedings of 2nd European Conference on Computational Biology (ECCB2003), Paris, France, September 2003. (PDF)

2.
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)

3.
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)

4.
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)

5.
Alexandros Stamatakis: ``Advanced Work on the Highly Interactive Problem Solver (HIPS)''. Report, Eurocontrol Experimental Center, Bretigny sur Orge, France, July 1999.(PDF)

6.
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.
Talk: ``Future technical and algorithmic solutions for inference of very large phylogenetic trees'', KONWIHR Result Workshop, Technical University of Munich, Germany, October 2004.

2.
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.

3.
Talk: ``Parallel Inference of a 10.000-taxon Phylogeny with Maximum Likelihood'', Euro-Par 2004 conference, Pisa, Italy, September 2004.

4.
Talk: ``Computing Large Phylogenies with Statistical Methods: Problems & Solutions'', BGRS2004 conference, Novosibirsk, Russia, July 2004.

5.
Talk: ``New Fast and Accurate Heuristics for Inference of Large Phylogenetic Trees'', IPDPS2004 conference, Santa Fe, New Mexico, April 2004.

6.
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.

7.
Talk: ``A Fast Program for Maximum Likelihood-based Inferrence of Large Phylogenetic Trees'', SAC2004 conference, Nicosia, Cyprus, March 2004.

8.
Talk: ``Phylogenetic Tree Inference with RAxML2'', Biology Seminar, Radjabazaar Science College, Calcutta, India, February 2004.

9.
Talk: ``Parllel & Distributed Phylogenetic Tree Inference with RAxML2'', Bioinformatik-Kolloquium der Fakultät für Informatik, Munich, Germany, February 2004.

10.
Talk: ``DAxML: A Program for Distributed Computation of Phylogenetic Trees Based on Load Managed CORBA'', PaCT2003 conference, Nizhni Novgorod, Russia, September 2003.

11.
Guest lecture: ``Applications of Cluster Computing: An Example from Bioinformatics'' within the framework of the course ``Cluster Computing'' (Prof. Ludwig), Heidelberg, Germany, July 2003.

12.
Talk: ``Phylogenetic Tree Inference on PC Architectures with AxML/PAxML'', IPDPS2003 conference, High Performance Computational Biology Workshop, Nice, France, April 2003.

13.
Talk: ``Current State of the ParBaum Project'', Laboratoire de l'Informatique du Parallelisme, Ecole Normale Superieure de Lyon, France, February 2003.

14.
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.

15.
Talk: ``Accelerating Parallel Maximum Likelihood-based Phylogenetic Tree Calculations using Subtree Equality Vectors'', SC2002 conference, Baltimore, Maryland, November 2002.

16.
Talk: ``Adapting PAxML to the Hitachi SR8000-F1 Supercomputer'', 1st Joint HLRB and KONWIHR Status and Reviewing Workshop, Munich, Germany, October 2002.

17.
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.

18.
Talk: ``Presentation of the ParBaum Project'', 7th School Graduate Orientation Day, Munich, Germany, March 2002.

19.
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.

Grants

1.
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.

2.
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 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.

2.
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.

       

Alexandros Stamatakis, 6 May 04