The Exelixis Lab


Enabling Research in Evolutionary Biology

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.

Copyright Notice: The documents accessible through these links are included by the authors as a means to ensure convenient electronic dissemination of technical work on a non-commercial basis. Copyright and all rights therein are maintained by the copyright holders (the authors or the publishers), notwithstanding that they have offered their works here electronically. It is understood that all persons copying this information will adhere to the terms and constraints invoked by each author's and publisher's copyright. In particular, these works may not be re-posted without permission of the copyright holders.

Exelixis rapid research dissemination reports

The technical reports made available here are mostly papers that are currently under review or about to be submitted. They are provided here prior to publication to allow for rapid dissemination of research conducted at the Exelixis lab. Emails with comments and suggestions on this work will be greatly appreciated. The documents below are only available for private non-commercial use, i.e., you are not allowed to modify or re-distribute them in any form, without prior explicit written permission by the authors. In case you want to cite the work below please cite it as technical report using the respective number, i.e., Exelixis-RRDR-20XY-Z.

  1. William D. Pearse, Andy Purvis, David B. Roy, Alexandros Stamatakis: "Modelling ecological communities as if they were DNA", Heidelberg Institute for Theoretical Studies, Exelixis-RRDR-2014-2, April 2014. PDF and on arxiv
  2. C. Hadjinikolis, C.S. Iliopoulos, S.P. Pissis, A. Stamatakis: "Minimising processor communication in parallel approximate string matching", Heidelberg Institute for Theoretical Studies, Exelixis-RRDR-2012-8, August 2012. PDF Source code and data: provided freely for academic use under the terms of the GNU General Public License here
  3. T. Flouris, A. Stamatakis: "An Improvement to DPPDIV", Heidelberg Institute for Theoretical Studies, Exelixis-RRDR-2012-7, August 2012. PDF
  4. S.A. Berger, A. Stamatakis: "PaPaRa 2.0: A Vectorized Algorithm forProbabilistic Phylogeny-Aware Alignment Extension", Heidelberg Institute for Theoretical Studies, Exelixis-RRDR-2012-5, March 2012. PDF

Phd theses

  • A. 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
  • M. Ott: "Inference of Large Phylogenetic Trees on Parallel Architectures", Ph.D. thesis, Technische Universität München, Germany, October 2010. PDF
  • N. Alachiotis: "Algorithms and Computer Architectures for Evolutionary Bioinformatics", Ph.D. thesis, Technische Universität München, Germany, November 2012. PDF
  • S. Berger: "Phylogeny-Aware Placement and Alignment Methods for Short Reads", Ph.D. thesis, Karlsruhe Institute of Technology, Karlsruhe, Germany, January 2013. PDF
  • F. Izquierdo-Carrasco: "Inference of Many-Taxon Phylogenies", Ph.D thesis, Karlsruhe Institute of Technology, Karlsruhe, Germany, June 2014. PDF

Master & Bachelor theses

  • A. Stamatakis: ``Interoperable Tool Deployment for the Late Development Phases of Distributed Object-Oriented Programs''. Diploma thesis, Technische Universität München, Germany, February 2001. PDF
  • S.A. Berger: "Protonation State and Enzyme/Substrate Interaction". Diploma thesis, LMU/TU Munich, München, Germany, July 2008 (thesis not conducted at Exelixis lab). 
  • N. Alachiotis: "Analysis, Design, and Implementation of the Phylogenetic Likelihood Function on Reconfigurable Logic", Technical University of Crete, Chania, Greece, September 2008 (thesis not conducted at Exelixis lab). PDF
  • Andre J. Aberer: "Advanced Methods for Phylogenetic Post-Analysis", Master's thesis, Technische Universität München/Heidelberg Institute for Theoretical Studies, Germany, January 2011.  PDF
  • Jörg Hauser: "Algorithms for Model Assignment in Multi-Gene Phylogenetics", Master's thesis, Heidelberg University/Heidelberg Institute for Theoretical Studies, Germany, August 2012 (co-supervised with Prof. Gertz at Heidelberg University). PDF
  • David Dao: "Automated Plausibility Analysis of Large Phylogenies", Bachelor thesis, Institute of Theoretical Computer Science, Karlsruhe Institute of Technology, Germany, January 2014. PDF
  • Patrick Flick: "Analysis of human tissue-specific protein-protein interaction networks", Master thesis, Institute of Theoretical Computer Science, Karlsruhe Institute of Technology, Germany, May 2014. PDF

Book chapters

  • D. Dao, T. Flouri, A. Stamatakis: "Automated Plausibility Analysis of Large Phyolgenies". Book chapter, to appear 2014. preprint
  • S. A. Smith, A. Stamatakis: "Inferring and Postprocessing Huge Phylogenies". In M. Elloumi, A.Y. Zomaya, editors. Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data, pages 1049-1072, John Wiley & Sons, Inc., 2014.
  • A. Stamatakis: "Phylogenetics". Encyclopedia of Parallel Computing: 1545-1554, David Padua editor in chief, Springer, 2011.
  • A. Stamatakis: "Phylogenetic Search Algorithms for Maximum Likelihood". In M. Elloumi, A.Y. Zomaya, editors. Algorithms in Computational Biology: techniques, Approaches and Applications, 547-577, John Wiley and Sons, 2011.
  • A. Stamatakis: "Orchestrating the Phylogenetic Likelihood Function on Emerging Parallel Architectures". In B. Schmidt, editor, Bioinformatics: High Performance Parallel Computer Architectures, 85-115, CRC Press, Taylor & Francis, 2010.
  • A. Stamatakis: "Parallel Phylogenetic Inference by Example of RAxML", Reinhard Leidl, Alexander K. Hartmann editors. Modern computational science 10: Lecture notes from the 2nd International Summer School Oldenburg, August 9-20, 2010, BIS-Verlag der Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany, 261-291, 2010.
  • D. Bader, U. Roshan, A. 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.
  • O.R.P. Bininda-Emonds, A. 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, 77-95, Volume 72, Special Volume for the Systematics Association, CRC Press. PDF
  • A. 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

2014

  • T. Flouri, K. Kobert, S.P. Pissis, A. Stamatakis: "An optimal algorithm for computing all subtree repeats in trees". In Phil. Trans. R. Soc. A 372:2016, 2014, open access.
  • R. Lanfear, B. Calcott, D. Kainer, C. Mayer, A. Stamatakis: "Selecting optimal partitioning schemes for phylogenomic datasets". In BMC Evolutionary Biology 14:1, 82, 2014, on-line access.
  • R.S. Peters, K. Meusemann, M. Petersen, C. Mayer, J. Wilbrandt, T. Ziesmann, A. Donath, K.M. Kjer, U. Aspöck, H. Aspöck, A. Aberer, A. Stamatakis, F. Friedrich, F. Hünefeld, O. Niehuis, R.G. Beutel, B. Misof: "The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data". In BMC Evolutionary Biology, 14:52, 2014, on-line access.
  • L. Salichos, A. Stamatakis, A. Rokas: "Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees". In Molecular Biology and Evolution, 2014, on-line access.
  • F. Izquierdo-Carrasco, J. Cazes, S.A. Smith, A. Stamatakis: "PUmPER: Phylogenies Updated Perpetually". In Bioinformatics, 2014, on-line access.
  • M. Dunthorn, J. Otto, S.A. Berger, A. Stamatakis, F. Mahé, S. Romac, C. de Vargas, S. Audic, A. Stock, F. Kauff, T. Stoeck, BioMarKs Consortium: "Placing environmental next generation sequencing amplicons from microbial eukaryotes into a phylogenetic context". In Molecular Biology and Evolution, 2014, on-line access.
  • A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". In Bioinformatics, 2014, open access.
  • M. Valle, H. Schabauer, C. Pacher, H. Stockinger, A. Stamatakis, M. Robinson-Rechavi, N. Salamin: "Optimisation strategies for fast detection of positive selection on phylogenetic trees". In Bioinformatics, 2014, advance on-line access.
  • K. Kobert, J. Hauser, A. Stamatakis: "Is the Protein Model Assignment Problem NP-hard?". In Theoretical Computer Science, 2014, on-line access.

2013

  • Amborella Genome Project (with the contribution of Solon S. Pissis): "The Amborella Genome and the Evolution of Flowering Plants". In Science 342(6165) on line access.
  • O. Gokcumen, V. Tischler, J. Tica, Q. Zhu, R.C. Iskow, E. Lee E, M.H. Fritz, A. Langdon, A.M. Stütz, P. Pavlidis, V. Benes, R.E. Mills, P.J. Park, C. Lee C, J.O. Korbel: "Primate genome architecture influences structural variation mechanisms and functional consequences". In PNAS 110:15764-15769, 2013 on line access.
  • M. Kiefer, R. Schmickl, D.A. German, T. Mandakova, M.A. Lysak, I.A. Al-Shehbaz, A. Franzke, K. Mummenhoff, A. Stamatakis, M.A. Koch: "BrassiBase: Introduction to a Novel Knowledge Database on Brassicaceae Evolution". In Plant and Cell Physiology, 2013, advance on-line access.
  • N. Alachiotis, S. Berger, T. Flouri, S.P. Pissis, A. Stamatakis: "libgapmis: extending short-read alignments". In BMC Bioinformatics 14(Suppl 11):S4. 2013. open access
  • J. Zhang, K. Kobert, T. Flouri, A. Stamatakis: "PEAR: a fast and accurate Illumina Paired-End reAd mergeR". In Bioinformatics, 2013, advance on-line access.
  • S. Sunagawa, D.R. Mende, G. Zeller, F. Izquierdo-Carrasco, S.A. Berger, J.R. Kultima, M. Arumugam, J. Tap, MetaHIT consortium, H.B. Nielsen, S. Brunak, D. Ehrlich, A. Stamatakis, P. Bork: "Metagenomic species profiling using universal phylogenetic marker genes". In Nature Methods, 2013, advance on-line access.
  • E. Dell’Ampio, K. Meusemann, N.U. Szucsich, R.S. Peters, B. Meyer, J. Borner, M. Petersen, A.J. Aberer, A. Stamatakis, M.G. Walzl, B.Q. Minh, A. von Haeseler, I. Ebersberger, G. Pass, B. Misof: "Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects". In Molecular Biology and Evolution, 2013, advance on-line access.
  • J. Zhang, P. Kapli, P. Pavlidis, A. Stamatakis: "A General Species Delimitation Method with Applications to Phylogenetic Placements". In Bioinformatics, 2013. advance on-line access.
  • C.S. Iliopoulos, S.P. Pissis "Verifying an enhanced cover array in linear time". In Formal Aspects of Computing, Essays dedicated to Derrick Kourie on the occasion of his 65th birthday, S. Gruner, B. Watson, Eds., Shaker Verlag, pages 111 - 123, 2013.
  • T. Flouri, C.S. Iliopoulos, T. Kociumaka,S. Pissis S.J. Puglisi, W.F. Smyth, W. Tyczynski: "Enhanced string covering". InTheoretical Computer Science, 506(0):102-114, 2013.
  • A.J. Aberer, A. Stamatakis: "Rapid Forward-in-Time Simulation at the Chromosome and Genome Level". In BMC Bioinformatics, 14:216, 2013.
  • P. Pavlidis, D. Zivkovic, A. Stamatakis, N. Alachiotis: "SweeD: Likelihood-based detection of selective sweeps in thousands of genomes''. In Molecular Biology and Evolution, doi:10.1093/bioinformatics/btt499, 2013.
  • C. Barton, C.S. Iliopoulos, I. Lee, L. Mouchard, K. Park, S.P. Pissis: "Extending alignments with k-mismatches and l-gaps". Journal of Theoretical Computer Science, 2013. Elsevier, in press.
  • H.Fang, M. Oates, R.Pethica, J.Greenwood, A.Sardar, O.Rackham, P.Donoghue, A.Stamatakis, D.A.de Lima Morais, J.Gough: "A daily-updated tree of (sequenced) life as a reference for genome research", Scientific Reports, 3, Article number: 2015 doi:10.1038/srep02015, 2013.
  • M. Christou,T. Flouri, C.S. Iliopoulos, J. Janousek, B. Melichar,S.P. Pissis, J. Zdarek: "Tree template matching in unranked ordered trees". InJournal of Discrete Algorithms, 20:51-60, 2013
  • C. Barton, M. Giraud, C.S. Iliopoulos, T. Lecroq, L. Mouchard, S.P. Pissis: "Querying Highly Similar Sequences", International Journal of Computational Biology and Drug Design, 6(1-2): 119-130, 2013.
  • J. Fuller, P. Khoueiry, H. Dinkel, K. Forslund, A. Stamatakis, J. Barry, A. Budd, T. Soldatos, K. Linssen, A. Rajput, and HUB participants: "Biggest Challenges in Bioinformatics". In EMBO reports, 14(4):302-304, 2013.
  • N. Alachiotis, E. Vogiatzi, P. Pavlidis, A. Stamatakis: "ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection". In Computational and Structural Biotechnology Journal, 6(7), 2013. PDF
  • N. Alachiotis, S. Berger, T. Flouri, S.P. Pissis, A. Stamatakis:  "libgapmis: extending short-read alignments". InBMC Bioinformatics, 14:S4, 2013,on-line access

2012

  • K. Frousios, C.S. Iliopoulos, G. Tischler, S. Kossida, S.P. Pissis, S. Arhondakis: "Transcriptome map of mouse isochores in embryonic and neonatal cortex", in press, Genomics, 2012.
  • A.J. Aberer, D. Krompass, A. Stamatakis: "Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice". In Systematic Biology, 62(1):162-166, 2012. ADVANCE ON-LINE ACCESS
  • M. Christou, M. Crochemore, T. Flouri, C.S. Iliopoulos, J. Janousek, B. Melichar, S.P. Pissis: "Computing all subtree repeats in ordered trees", accepted for publication in Information Processing Letters, 2012.
  • M. Piednoël, A.J. Aberer, G.M. Schneeweiss, J. Macas, P. Novak, H. Gundlach, E.M. Temsch, S.S. Renner: "Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae", Molecular Biology and Evolution, 2012. ON-LINE
  • N. Alachiotis, S. Berger, A. Stamatakis: "Coupling SIMD and SIMT Architectures to Boost Performance of a Phylogeny-aware Alignment Kernel". In BMC Bioinformatics, 13:196, 2012. OPEN ACCESS
  • N. Alachiotis, A. Stamatakis, P. Pavlidis: "OmegaPlus: A Scalable Tool for Rapid Detection of Selective Sweeps in Whole-Genome Datasets''. In Bioinformatics, 28(17):2274-2275, 2012.
  • A. Stamatakis,  A.J. Aberer, C. Goll, S.A. Smith, S.A. Berger, F. Izquierdo-Carrasco: "RAxML-Light: A Tool for computing TeraByte Phylogenies". In Bioinformatics, 28(15):2064-2066, 2012. On-Line Access PDF SUPPLEMENT
  • P. Pavlidis, J.D. Jensen, W. Stephan, A. Stamatakis: "A Critical Assessment of Story-Telling: Gene Ontology categories and the importance of validating genomic scans". In Molecular Biology and Evolution, 29(10):3237-3248, 2012. ADVANCE ON-LINE ACCESS
  • T. Flouri, K. Frousios, C.S. Iliopoulos, K. Park, S.P. Pissis, G. Tischler: "GapMis: a tool for pairwise sequence alignment with a single gap". Recent Patents on DNA and Gene Sequence Journal: Pattern Finding in Computational Molecular Biology, 2012. Bentham Science, accepted for publication.
  • F.A. Matsen, N. Hoffman, A. Gallagher, A. Stamatakis: "A format for phylogenetic placements". PLoS ONE 7(2): e31009, 2012. OPEN ACCESS

2011

  • S.A. Smith, N.G. Wilson, F.E. Goetz, C. Feehery, S.C.S. Andrade, G.W. Rouse, G. Giribet, C.W. Dunn: "Resolving the evolutionary relationships of molluscs with phylogenomic tools". Nature doi:10.1038/nature10526, 2011.
  • D.E. Soltis, S.A. Smith, N. Cellinese, et al.: "Angiosperm phylogeny: 17 genes, 640 taxa". American J. of Botany.98:704, 2011.
  • S. Siebert, M. Robinson, S. Tintori, F. Goetz, R. Helm, S.A. Smith, N. Shaner, S. Haddock, C. Dunn: "Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows". PLoS ONE 6(7): e22953. doi:10.1371/journal.pone.0022953, 2011.
  • F. Izquierdo-Carrasco, S.A. Smith, A. Stamatakis: "Algorithms, Data Structures, and Numerics for Likelihood-based Phylogenetic Inference of Huge Trees". BMC Bioinformatics 12:470 2011. OPEN ACCESS
  • S.S. Saminadin-Peter, C. Kemkemer, P. Pavlidis, J. Parsch: "Selective Sweep of a cis-Regulator y Sequence in a Non-African Population of Drosophila melanogaster", accepted for publication in Molecular Biology and Evolution, November 2011.
  • B.M. von Reumont, R.A. Jenner, M.A. Wills, E. Dell’Ampio, G. Pass,I. Ebersberger, B. Meyer, S. Koenemann, T.M. Iliffe, A. Stamatakis, O. Niehuis, K. Meusemann, B. Misof:  "Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda", Molecular Biology and Evolution, advance on-line access, November 2011.
  • E. Lee, A. Cibrián-Jaramillo, S.-O. Kolokotronis, M. Katari, A. Stamatakis, M. Ott, J. Chiu, D. Little, D. Stevenson, W.R. McCombie, R. Martienssen, G. Coruzzi, R. DeSalle: "A Functional Phylogenomic View of the Seed Plants" PLOS Genetics 7(12): e1002411. doi:10.1371/journal.pgen.1002411, 2011.
  • A. Bousios, Y. Kourmpetis, P. Pavlidis, E. Minga, A. Tsaftaris, N. Darzentas: "The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story", accepted for publication in The PLant Journal.
  • Aurélien Tellier, Stefan J.Y. Laurent, Hilde Lainer, Pavlos Pavlidis, Wolfgang Stephan: "Inference of Seed Bank Parameters in Two Wild Tomato Species Using Ecological and Genetic Data", accepted for publication in PNAS.
  • Stephen A Goff, Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E Stapleton, Damian Gessler, Naim Matasci, Liya Wang, Matthew Hanlon, Andrew Lenards, Andy Muir, Nirav Merchant, Sonya Lowry, Stephen Mock, Matthew Helmke, Adam Kuback, Martha Narro, Nicole Hopkins, Uwe Hilgert, Michael Gonzales, Chris Jordan, Edwin Skidmore, Rion Dooley, John Cazes, Robert McLay, Zhenyuan Lu, Shiran Pasternak, Lars Koesterke, William H Piel, Ruth Grene, Christos Noutsos, Karla Gendler, Xin Feng, Chunglao Tang, Monica Lent, Seung-jin Kim, Val Tannen, Alexandros Stamatakis, Michael Sanderson, Stephen M Welch, Karen Cranston, Pamela Soltis, Douglas Soltis, Brian O'Meara, Cecile Ane, Tom Brutnell, Daniel J Kleibenstein, Jeffrey W White, Jim Leebens-Mack, Michael J Donoghue, Edgar P Spalding, Kristian Kvilekval, B.S. Manjunath, Todd J Vision, Brian J Enquist, Brad Boyle, David Lowenthal, Ali Akoglu, David Micklos, Greg Andrews, Sudha Ram, Doreen Ware, Lincoln Stein, Dan Stanzione: "The iPlant Collaborative: Cyberinfrastructure for Plant Biology". Frontiers in Plant Genetics and Genomics 2011 on-line access.
  • S.A. Berger, A. Stamatakis: "Aligning Short Reads to Reference Alignments and Trees".Bioinformatics; doi: 10.1093/bioinformatics/btr320, 2011. PDF  SUPPLEMENT
  • Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko: "Fine-grain Parallelism using Multi-Core, Cell/BE, and GPU Systems", in Parallel Computing38: 365-390, 2012.
  • S.A. Berger, A. Stamatakis, R. Lücking: "Morphology-based phylogenetic binning of the lichen genera Allographa and Graphis via molecular site weight calibration", in Taxon 60(5):1450-1457, 2011.
  • Victoria I. Siarkou, Alexandros Stamatakis, Ilias Kappas, Paul Hadweh, Karine Laroucau: "Evolutionary Relationships amond Chmlamydophila abortus Variant Strains Inferred by rRNA Secondary Structure-based Phylogeny", accepted for publication in PLoS ONE, 2011.
  • Stephen A. Smith, Jeremy Beaulieu, Alexandros Stamatakis, Michael J Donoghue: "Understanding angiosperm diversification using small and large phylogenetic trees", accepted for publication in American Journal of Botany, special issue on Biodiversity.
  • Marc Gottschling, Markus Göker, Alexandros Stamatakis, Olaf R.P. Bininda-Emonds, Ingo Nindl, Ignacio G. Bravo: "Quantifying the phylodynamic forces driving papillomavirus evolution". In Molecular Biology and Evolution 28(7):2101-2113, 2011.
  • S.A. Berger, D. Krompaß, A. Stamatakis: "Performance, Accuracy and Web-Server for Evolutionary Placement of Short Sequence Reads under maximum-likelihood". In Systematic Biology 60(3):291-302, 2011. PDF
  • N. Alachiotis, A. Stamatakis: "A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm". International Journal of Reconfigurable Computing, vol. 2011, Article ID 341510, 12 pages, 2011. OPEN ACCESS
  • N.D. Pattengale, A.J. Aberer, K.M. Swenson, A. Stamatakis, B.M.E. Moret : "Uncovering Hidden Phylogenetic Consensus in Large Datasets". IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press 2011.
  • R.K. Luecking, B.P. Hodkinson, A. Stamatakis, R.A. Cartwright: "PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination". BMC Bioinformatics 12:10, 2011. OPEN ACCESS
  • A. Stamatakis, F. Izquierdo-Carrasco: "Result Verification, Code Verification, and Computation of Support Values in Phylogenetics". Briefings in Bioinformatics, Special Issue on Validation in Bioinformatics and Molecular Medicine 12(3):270-279, 2011. PDF

2010 and before

  • M. Stark, S.A. Berger, A. Stamatakis, C.v. Mering: "MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies". BMC Genomics 2010, 11:461. OPEN ACCESS
  • N. Poulakakis, A. Stamatakis: "Recapitulating the evolution of Afrotheria: 57 genes and rare genomic changes (RGCs) consolidate their history". Systematics and Biodiversity 8(3):395-408, 2010. LINK
  • A. Aberer, N. Pattengale, A. Stamatakis: "Parallelized phylogenetic post-analysis on multi-core architectures". Journal of Computational Science 1, 107-114, 2010. OPEN ACCESS
  • A. Stamatakis, M. Göker, G. Grimm: "Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling". Evolutionary Bioinformatics 2010:6 73-90 OPEN ACCESS.
  • N. Pattengale, M. Alipour, O.R.P. Bininda-Emonds, B.M.E. Moret, E.J. Gottlieb, A. Stamatakis "How many Bootstrap Replicates are necessary?".  Journal of Computational Biology 17(3):337-354, 2010.
  • A. Hejnol, M. Obst, A. Stamatakis, M. Ott, G. Rouse, G. Edgecombe, P. Martinez, J. Baguna, U. Jondelius, M. Wiens, W. Mueller, E. Seaver, W. Wheeler, M. Martindale, G. Giribet, C. Dunn: "Assessing the root of bilaterian animals with scalable phylogenomic methods". In Proc. R. Soc. B 276:4261-4270, 2009. PDF
  • H. Stockinger, A. Auch, M. Göker, J. Meier-Kolthoff, A. Stamatakis: “Large-Scale Co-Phylogenetic Analysis on the Grid”. International Journal of Grid and High Performance Computing, IGI Publishing, 1(1):39-54, 2009. PDF
  • A. Stamatakis, P. Hoover, J. Rougemont: “A Fast Bootstrapping Algorithm for the RAxML Web-Servers”. In Systematic Biology, 57(5): 758-771, 2008. PDF most frequently cited papers in Systematic Biology
  • A. Stamatakis, M. Ott: “Efficient Computation of the Phylogenetic Likelihood Function on Multi-Gene Alignments and Multi-Core Architectures”. In Philosophical Transactions of the Royal Society B, 363: 3977-3984, 2008.  PDF
  • M. Ott, J. Zola, S. Aluru, A.D. Johnson, D. Janies, A. Stamatakis: “Large-scale Phylogenetic Analysis on Current HPC Architectures”. In Scientific Programming, 16(2-3):255-270, 2008.  PDF
  • F. Blagojevic, D.S. Nikolopoulos, A. Stamatakis, C.D. Antonopoulos, M. Curtis-Maury: “Runtime Scheduling of Dynamic Parallelism on Accelerator-Based Multi-core Systems”.  In Parallel Computing, 33(10-11): 700–719, 2007.  PDF
  • A. Stamatakis, A. Auch, J. Meier-Kolthoff, M. Göker: “AxPcoords & Parallel AxParafit: Statistical Co-Phylogenetic Analyses on Thousands of Taxa”. In BMC Bioinformatics, 8:405, 2007.  PDF
  • A. Stamatakis,  F. Blagojevic, C.D. Antonopoulos, D.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.  PDF
  • M. Gottschling, A. Stamatakis, I. Nindl, E. Stockfleth, Á. Alonso, L. Gissmann, I.G. Bravo: ``Multiple evolutionary mechanisms drive papillomavirus diversification”. In Molecular Biology and Evolution, 24(5):1242-1258, 2007.  PDF
  • G. Grimm, S. Renner, A. Stamatakis, V. Hemleben: ``A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences”. In Evolutionary Bioinformatics 2:7-22, 2006.  PDF
  • A. Stamatakis: ``RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models”. In Bioinformatics 22(21):2688-2690, 2006.  PDF most frequently cited papers in Bioinformatics
  • A. Stamatakis, T. Ludwig, H. 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
  • A. Stamatakis:  ``Phylogenetics: Applications, Software and Challenges''. In Cancer Genomics & Proteomics 2(5):301-305, 2005.  PDF
  • A. Stamatakis, M. Ott, T. Ludwig, H. Meier: ``DRAxML@home: A Distributed Program for Computation of Large Phylogenetic Trees''. In Future Generation Computer Systems (FGCS) 21(5):725-730, 2005. PDF
  • A. Stamatakis, T. Ludwig, H. Meier: ``RAxML-III: A Fast Program for Maximum Likelihood-based Inference of Large Phylogenetic Trees''. In Bioinformatics 21(4):456-463, 2005.  PDF
  • M. Rafecas, B. Mosler, M. Dietz, M. Pögl, A. Stamatakis, D.P. McElroy, S.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
  • A. Stamatakis, T. Ludwig: ``The AxML Program Family for phylogenetic Tree Inference''. In Concurrency and Computation: Practice and Experience (CCPE), 16:975-988, 2004.  PDF
  • W. Ludwig, O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A.W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüssmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode,  K.-H. Schleifer: ``ARB: a software environment for sequence data''. In Nucleic Acids Research, 32(4):1363-1371, 2004. PDF
  • T. Ludwig, M. Lindermeier, A. Stamatakis, G. Rackl:``Tool environments in CORBA-based medical high-performance computing''. In Future Generation Computer Systems (FGCS), 18(6):841-847, 2002.  PDF
  • G. Rackl, T. Ludwig, M. Lindermeier, A. Stamatakis: ``Efficiently Building On-Line Tools for Distributed Heterogeneous Environments''. In Scientific Programming, 10(1):67-74, 2002.  PDF

Peer-reviewed conference papers

2014

  • T. Flouri, A. Stamatakis, K. Kobert, A.J. Aberer: "The divisible load balance problem and its application to phylogenetic inference". In Proceedings of WABI 2014, Wroclaw, Poland, September 2014, accepted for publication. PDF
  • A.M. Kozlov, C. Goll, A. Stamatakis: "Efficient Computation of the Phylogenetic Likelihood Function on the Intel MIC Architecture". In Proceedings of HICOMB workshop, held in conjunction with IPDPS 2014, Phoenix, Arizona, May 2014, accepted for publication. PDF

2013

  • C. Barton, T. Flouri, C.S. Iliopoulos, S.P. Pissis: "GapsMis: flexible sequence alignment with a bounded number of gaps", accepted for publication at ACM BCB 2013, Washington DC, USA, September 2013.
  • S. Pissis, A. Stamatakis, P. Pavlidis: "MoTeX: an HPC word-based tool for MoTif eXtraction", ACM BCB 2013, Washington DC, USA, September 2013. PDF link
  • C. Barton, C.S. Iliopoulos, S.P. Pissis: "Circular string matching revisited". Fourteenth Italian Conference on Theoretical Computer Science (ICTCS 2013), pages 200-205, 2013.
  • M. Crochemore, C.S. Iliopoulos, T. Kociumaka, M. Kubica, A. Langiu, S.P. Pissis, J. Radoszewski, W. Rytter, T. Walen: "Order-preserving incomplete suffix trees and order-preserving indexes", accepted at 20th String Processing and Information Retrieval Symposium (SPIRE 2013), Springer Lecture Notes in Computer Science, 2013.
  • S. Pissis, C. Goll, P. Pavalidis, A. Stamatakis: "Accelerating string matching on MIC architecture for motif extraction", accepted for publication at 10th International Conference on Parallel Processing and Applied Mathematics, Warsaw, Poland, September 2013.
  • K. Kobert, T. Flouri, S.P. Pissis, A. Stamatakis: "An optimal algorithm for computing all subtree repeats in trees", accepted for publication at IWOCA 2013, Rouen, France, July 2013. PDF
  • T. Kociumaka, S.P. Pissis, J. Radoszewski, W. Rytter, T. Walen: "Fast algorithm for partial covers in words". In Proceedings of the 24th Annual Symposium on Combinatorial Pattern Matching (CPM 2013), Lecture Notes in Computer Science, 2013. Springer
  • J. Hauser, K. Kobert, F. Izquierdo-Carrasco, K. Meusemann, B. Misof, M. Gertz, A. Stamatakis: "Heuristic Algorithms for the Protein Model Assignment Problem", accepted for publication at ISBRA 2013, Charlotte, USA, May 2013. PDF
  • F. Izquierdo-Carrasco, N. Alachiotis, S. Berger, T. Flouri, S.P. Pissis, A. Stamatakis: "A generic Vectorization Scheme and a GPU kernel for the Phylogenetic Likelihood Library", accepted for publication at IPDPS 2013, Boston, USA, 2013. PDF
  • D. Darriba, A.J. Aberer, T. Flouri, T.A. Heath, F. Izquierdo-Carrasco, A. Stamatakis: "Boosting the performance of Bayesian divergence time estimation with the Phylogenetic Likelihood Library", accepted for publication at IPDPS 2013, Boston, USA, 2013. PDF
  • A. Stamatakis, A. J. Aberer: "Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference", accepted for publication at IPDPS 2013, Boston, USA, 2013. PDF

2012

  • N. Alachiotis, S. Berger, A. Stamatakis: "A Versatile UDP/IP based PC-FPGA Communication Platform". Proceedings of ReConFig 2012, Cancun, Mexico, 2012. PDF   IEEEexplore link
  • T. Flouri, K. Kobert, S.P. Pissis, A. Stamatakis: "A simple method for computing all subtree repeats in unordered trees in linear time", Festschrift for Borivoj Melichar, Czech Technical University in Prague, 145-152, 2012.
  • M. Elloumi, P. Hayati, C.S. Iliopoulos, S.P. Pissis, A. Shah. Detection of fixed length web spambot using REAL (REad ALigner). In Proceedings of the International Information Technology Conference (CUBE 2012), pp.820-825, 2012. ACM Digital Library
  • T. Flouri, C.S. Iliopoulos, T. Kociumaka, S.P. Pissis, S.J. Puglisi, W. F. Smyth, W. Tyczynski: "New and efficient approaches to the quasiperiodic characterisation of a string", In Proceedings of the Prague Stringology Conference (PSC2012), pp.75-88, 2012.
  • N. Alachiotis, S. Berger, T. Flouri, S. Pissis, A. Stamatakis: "libgapmis: an ultrafast library for short-read single-gap alignment", accepted for publication at Next Generation Sequencing workshop in conjunction with IEEE BIBM 2012.
  • N. Alachiotis, P. Pavlidis, A. Stamatakis: ``Exploiting Multi-grain Parallelism for efficient Selective Sweep Detection'', accepted for publication at 12th International Conference on Algorithms and Architectures for Parallel Programming (ICA3PP-2012), Fukuoka, Japan, September 2012, to appear in Springer LNCS.
  • T. Flouri, C.S. Iliopoulos, K. Park, S.P. Pissis: "GapMis-OMP: pairwise short-read alignment on multi-core architectures." In Proceedings of the 8th Artificial Intelligence Applications and Innovations Conference (AIAI 2012), IFIP Advances in Information and Communication Technology, 2012. Springer LNCS, accepted for publication.
  • S.A. Berger, N. Alachiotis, A. Stamatakis: "An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood on DNA Data", accepted for publication at IEEE RAW workshop (in conjunction with IPDPS 2012). PDF
  • H. Schabauer, M. Valle, C. Pacher, H. Stockinger, A. Stamatakis, M. Robinson-Rechavi, Z. Yang, N. Salamin: "SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model", accepted for publication at 11th IEEE HICOMB workshop (in conjunction with IPDPS 2012).
  • J. Zhang, A. Stamatakis: "The Multi-Processor Scheduling Problem in Phylogenetics", accepted for publication at 11th IEEE HICOMB workshop (in conjunction with IPDPS 2012).  PDF
  • F. Izquierdo-Carrasco, J. Gagneur, A. Stamatakis: "Trading Memory for Running Time in Phylogenetic Likelihood Computations", 2012 Bioinformatics conference, Vilamoura, Portugal. PDF supplementary material

2011

  • Andre J. Aberer, Alexandros Stamatakis: "A Simple and Accurate Method for Rogue Taxon Identification", accepted for publication as short paper at IEEE BIBM 2011, Atlanta, Georgia, USA, November 2011. Long Version PDF
  • Madeleine Seeland, Simon A. Berger, Alexandros Stamatakis, Stefan Kramer: "Parallel Structural Graph Clustering", accepted for publication at ECML PKDD 2011, to appear in Springer LNAI.  PDF
  • N. Alachiotis, A. Stamatakis: "FPGA Acceleration of the Phylogenetic Parsimony Kernel?", accepted for publication at FPL 2011.  PDF
  • Nikos Alachiotis, Simon A. Berger, Alexandros Stamatakis: "Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs", accepted for publication at IEEE FCCM, Salt Lake City, Utah, USA, May 2011. PDF
  • Fernando Izquierdo-Carrasco, Alexandros Stamatakis: "Computing the Phylogenetic Likelihood Function Out-of-Core", accepted for publication at IEEE HICOMB 2011 workshop (held in conjunction with IPDPS 2011), Anchorage, USA, May 2011.  PDF
  • Nikos Alachiotis, Alexandros Stamatakis: "FPGA Optimizations for a Pipelined Floating-Point Exponential Unit", accepted for publication, 7th International Symposium on Applied Reconfigurable Computing (ARC 2011), Belfast, United Kingdom, March 2011. PDF

2010 and before

  • N. Alachiotis, A. Stamatakis: "A Generic and Versatile Architecture for Inference of Evolutionary Trees under Maximum Likelihood", Conference Record of the 44th IEEE Asilomar Conference on Signals, Systems and Computers (ASILOMAR) Studies, pp 829-835, November 2010. PDF
  • S.A. Berger, A. Stamatakis: "Assessment of Barrier Implementions for Fine-Grain Parallel Regions on Current Multi-core Architectures" accepted for publication at IEEE Cluster workshop on Parallel Programming and Applications on Accelerator Clusters, Heraklion, Greece, September 2010.  PDF
  • N. Alachiotis, S.A. Berger, A. Stamatakis: "Efficient PC-FPGA Communication over Gigabit Ethernet", accepted for publication at IEEE ICESS 2010, June/July 2010.  PDF
  • A. Stamatakis, N. Alachiotis: "Time and memory efficient likelihood-based tree searches on gappy phylogenomic alignments", Proceedings of ISMB 2010, Boston, Massachusetts, July 2010. In Bioinformatics, 26(12):i132-i139. OPEN ACCESS PDF
  • A. Aberer, N. Pattengale, A. Stamatakis: "Parallel Computation of Phylogenetic Consensus Trees", accepted for publication at ICCS 2010 conference, Emerging Parallel Architectures Workshop, Amsterdam, The Netherlands, May 2010. BEST PAPER FINALIST PDF
  • W. Pfeiffer, A. Stamatakis: "Hybrid MPI/Pthreads Parallelization of the RAxML Phylogenetics Code". Accepted for publication at HICOMB workshop, held in conjunction with IPDPS 2010, Atlanta, Georgia, April 2010. PDF
  • N. Alachiotis, A. Stamatakis: "Efficient Floating-Point Logarithm Unit for FPGAs". Accepted for publication at RAW workshop, held in conjunction with IPDPS 2010, Atlanta, Georgia, April 2010. PDF
  • S.A. Berger, A. Stamatakis: "Accuracy of Morphology-based Phylogenetic Fossil Placement under Maximum Likelihood". Accepted for publication at 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10), Hammamet, Tunisia, May 2010. PDF
  • A. Stamatakis, Z. Komornik, S.A. Berger: "Evolutionary Placement of Short Sequence Reads on Multi-Core Architectures". Accepted for publication at 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10), Hammamet, Tunisia, May 2010. PDF
  • S.A. Berger, A. Stamatakis: "Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction". P. Wyrzykowski et al. (Eds.): PPAM 2009, Part II, Springer LNCS 6068, pp. 270-279, 2010. PDF
  • N. Alachiotis, E. Sotiriades, A. Dollas, A. Stamatakis: "A Reconfigurable Architecture for the Phylogenetic Likelihood Function". Proceedings of FPL 2009, accepted for publication as short paper, Prague, Czech Republic, September 2009. PDF  PDF LONG VERSION
  • A. Stamatakis, M. Ott:"Load Balance in the Phylogenetic Likelihood Kernel". Proceedings of ICPP 2009, accepted for publication, Vienna, Austria, September 2009.  PDF
  • F. Pratas, P. Trancoso, A. Stamatakis, L. Sousa:  "Fine-grain parallelism using Multi-core, Cell/BE, and GPU systems: Accelerating the Phylogenetic Likelihood Function". Proceedings of ICPP 2009, accepted for publication, Vienna, Austria, September 2009.  PDF
  • N. Alachiotis, E. Sotiriades, A. Dollas, A. Stamatakis: "Exploring FPGAs for accelerating the Phylogenetic Likelihood Function". Proceedings of HICOMB 2009 (in conjunction with IPDPS 2009), accepted for publication, Rome, Italy, May 2009.  PDF
  • N.D. Pattengale, M. Alipour, O.R.P. Bininda-Emonds, B.M.E. Moret, A. Stamatakis: "How Many Bootstrap Replicates are Necessary?". Proceedings of RECOMB 2009, accepted for publication, Tucson, Arizona, May 2009.  PDF
  • A. Stamatakis, V. Rousset: "Phylogenetic Bootstrapping under Resource Constraints: Higher Model Accuracy or more Replicates?". Proceedings of the 3rd conference of the Hellenic Society for Computational Biology and Bioinformatics HSCBB08 pp 36-40, Thessaloniki, Greece, October 2008.  PDF
  • A. Stamatakis, M. Ott: “Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study”. Accepted for publication, Pattern Recognition in Bioinformatics (PRIB 2008).  Volume 5265 of Springer Lecture Notes in Computer Science pp 424-435, 2008. PDF
  • M. Ott, J. Zola, S. Aluru, A. Stamatakis: “Large-scale Maximum Likelihood-based Phylogenetic Analysis on the IBM BlueGene/L”. In Proceedings of IEEE/ACM Supercomputing (SC2007) conference, Reno, Nevada, November 2007. BEST PAPER FINALIST  PDF
  • F. Blagojevic, D.S. Nikolopoulos, A. Stamatakis, C.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
  • F. Blagojevic, D.S. Nikolopoulos, A. Stamatakis, C.D. Antonopoulos: “Dynamic Multigran Parallelization on the Cell Broadband Engine”. In Proceedings of ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming 2007 (PPoPP 2007), 90-100, San Jose, California, March 2007. BEST PAPER AWARD  PDF
  • A. Stamatakis: “Inferring Phylogenies with RAxML-VI-HPC” (software demonstration abstract). In Proceedings of German Conference of Bioinformatics 2006 (GCB2006), Tü̈bingen, Germany, September 2006.  PDF
  • A. 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, Rhodos, Greece, April 2006.   PDF
  • A. Arvelakis, M. Reczko, A. Stamatakis, A. Symeonidis, I.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
  • Z. Du, A. Stamatakis, F. Lin, U. Roshan, L. 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
  • M. Charalambous, P. Trancoso, A. 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, November 2005.  PDF
  • A. Stamatakis, M. Ott, T. 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
  • A. 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, Abstract on page 198, Denver, Colorado, April 2005.  PDF
  • A. Stamatakis, T. Ludwig, H. 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
  • A. Stamatakis, T. Ludwig, H. 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
  • A. Stamatakis, T. Ludwig, H. 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, Abstract on page 193, Santa Fe, New Mexico, April 2004.  PDF
  • A. Stamatakis, T. Ludwig, H. Meier: “A Fast Program for Maximum Likelihood-based Inference of Large Phylogenetic Trees”. In Proceedings of 19th ACM Symposium on Applied Computing (SAC2004), 197–201, Nicosia, Cyprus, March 2004.  PDF
  • A. Stamatakis, M. Lindermeier, M. Ott, T. Ludwig, H. 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
  • A. Stamatakis, T. 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, Abstract on page 157, Nice, France, April 2003.  PDF
  • A. Stamatakis, T. Ludwig, H. Meier, M.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
  • A. Stamatakis, T. Ludwig, H. Meier, M.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
  • T. Ludwig, M. Lindermeier, A. Stamatakis, G. 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 and technical reports

  • Nikolaos Alachiotis, Emmanouella Vogiatzi, Pavlos Pavlidis, Alexandros Stamatakis: "ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection", poster at the 7th Conference of the Hellenic Society for Computational Biology and Bioinformatics (HSCBB 2012), Heraklion, Crete, October 2012.
  • Fernando Izquierdo-Carrasco, Alexandros Stamatakis: "Inference of Huge Trees under Maximum Likelihood", Poster at IPDPS PhD forum, Shanghai, China, May 2012.
  • Pavlos Pavlidis: "Selective Sweeps in Multi-Locus Models", Poster at ESEB 2011, Tübingen, Germany, August 2011.
  • R.A. Cartwright, B. Hodkinson, A. Stamatakis, R. Lücking: "Extracting Phylogenetic Information from Ambiguous Regions", Evolution meeting, Portland, USA, June 2010.
  • N. Alachiotis, A. Stamatakis: "Future Reconfigurable Architectures for Phylogenetic Inference", 4th conference of the Hellenic Society for Computational Biology and Bioinformatics HSCBB09, Athens, Greece, December 2009.  PDF
  • M. Ott, A. Stamatakis: "Preparing RAxML for the SPEC MPI Benchmark Suite", Proceedings of HLRB09 reviewing workshop, Garching, Germany, December 2009.
  • N. Alachiotis, E. Sotiriades, A. Dollas, A. Stamatakis: "A Reconfigurable Architecture for the Phylogenetic Likelihood Function", Poster presentation at FPL 2009 (short paper), Prague, Czech Republic, September 2009.
  • M. Gottschling, I.G. Bravo, A. Stamatakis, E. Stockfleth, I. Nindl: “Human papillomavirus classification from a dermatological perspective”, Poster at 18th ADO (Arbeitsgemeinschaft für Dermatologische Onkologie, German society for dermatological oncology) conference & 4th German Cancer Congress, Berlin, Germany, 2008.
  • M. Ott, J. Zola, S. Aluru, A. Stamatakis: “ParBaum: Large-scale Maximum Likelihood-based Phylogenetic Analysis”. In High Performance Computing in Science and Engineering, Garching 2007, Springer Verlag, in press.
  • I.G. Bravo, A. Stamakis, I. Nindl, M. Gottschling: “Multiple driving forces of papillomavirus evolution”, Abstract/Talk Systematics Congress 2008, Gö̈ttingen, Germany, 2008.                                                                        
  • A. Johnson, M. Ott, J. Zola, S. Aluru, A. Stamatakis, D. 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
  • M. Gottschling, E. Schulz, I.G. Bravo, A. Stamatakis, U. Wittstatt, R. Deaville, E. Stockfleth, I. Nindl: “Phylogenomics of papillomaviruses and identification of novel types”, Abstract/Talk, 24th IPV Conference and Clinical Workshop, Beijing, China, 2007.
  • M. Gottschling, I.G. Bravo, A. Stamatakis, E. Stockfleth, I. Nindl: “Mechanisms of papillomavirus evolution and identification of novel types”, Abstract/Poster, 3rd European Congress of Virology, N ürnberg, Germany, 2007.              
  • M. Gottschling, I.G. Bravo, A. Stamatakis, A. Alonso, L. Gissmann, E. Stockfleth, I. Nindl: “Phylogenomics of papillomavirus and the biological interpretations”, Abstract/Talk, 9th annual meeting of the GfBS (German Society for Biological Systematics), Vienna, Austria, 2007.
  • M. Göker, A. Stamatakis: “Maximum Likelihood Phylogenetic Inference: An Empirical Assessment of Search Algorithms on a Multi-Gene Dataset”, German Conference on Bioinformatics (GCB 2006), Tübingen, Germany, September 2006.
  • A. Stamatakis: “RAxML-VI: A Program for Phylogenetic Analyses with Thousands of Taxa”, CIPRES (Cyberinfrastructure for Phylogenetic Research) project All Hands Meeting 2006, University of Texas at Austin, Texas, February 2006.
  • A. Stamatakis, T. Ludwig, H. 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, 278–287, Springer Verlag, 2005.
  • A. Stamatakis, M. Ott: “Algorithmic & Technical Concepts in RAxML-V”. Poster presented at MEP2005 conference, Paris, France, June 2005.
  • A. Stamatakis: “Computation of large phylogenetic trees: Algorithmic and technical solutions”. Abstracts of the 1st International Conference of the Hellenic Proteomics Society, in Cancer Genomics & Proteomics 2(3):176, 2005.
  • A. Stamatakis: “Computation of the first 10,000-organism Phylogeny with Maximum Likelhood on the RRZE PC Cluster”. In RRZE Aktuell, BI 72:34–35, October 2004.
  • A. Stamatakis, T. Ludwig, H. 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.
  • A. Stamatakis, T. Ludwig, H. Meier: “RAxML: A Parallel Program for Phylogenetic Tree Inference”. Poster abstract in Proceedings of 2nd European Conference on Computational Biology (ECCB2003), 325–326, Paris, France, September 2003.
  • A. Stamatakis, T. Ludwig, H. 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.
  • A. Stamatakis, T. Ludwig, H. 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.
  • G.H. Lopez-Campos, A. Stamatakis, F. 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.
  • A. Stamatakis: “Advanced Work on the Highly Interactive Problem Solver (HIPS)”. Report, Eurocontrol Experimental Center, Bretigny sur Orge, France, July 1999. PDF
  • A. Stamatakis: “Analysis of the Automation Potential of an Air Traffic Control Sector”. Report, National Technical University of Athens, Athens, Greece, July 1998.

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