Gruppenleiter „Scientific Computing“ am HITS
Professor für High Performance Computing am Karlsruher Institut für Technologie (KIT)

Forschungsinteresse

Algorithmen, Parallelcomputing, Parallel Architectures und Evolutionary Bioinformatik.

Über mich

Ich bin in Athen aufgewachsen und 1995 nach Deutschland gezogen, um Informatik zu studieren. Während meines Studiums in München verbrachte ich auch mehrere Auslandsaufenthalte in Lyon, Paris, Madrid und Athen. Vor meinem PhD und meiner Arbeit in der Bioinformatik, habe ich vor allem im Bereich der Entwicklung von Software für Fluglotsen gearbeitet.

Curriculum Vitae

Seit 2012     Adjunct professor am Department of Ecology and Evolutionary Biology an der University of Arizona at Tucson, USA
Seit 2012     Professor für High Performance Computing am Karlsruher Institut für Technologie (KIT)
Seit 2010     Leiter der “Scientific Computing” Gruppe am HITS
2008-2010    Leiter einer DFG Emmy-Noether Junior Forschungsgruppe an der Ludwig-Maximilians-Universität München und der Technischen Universität München
2006-2008    PostDoc an der Eidgenössischen Technische Hochschule Lausanne, Schweiz
2005-2006    PostDoc am Institute for Computer Science, Foundation of Research and Technology Hellas, Heraklion, Griechenland
2001-2004    PhD an der der Technischen Universität München
1995-2001    Studium der Informatik an der Technischen Universität München und der Universität Lyon, Frankreich

Mitgliedschaften

Lehrpreise

2016: Für den Kurs „Hands-on Bioinformatics Practical“ am Karlsruher Institut für Technologie (KIT) im Sommersemester 2015
2015: Für den Kurs „Introduction to Bioinformatics for Computer Scientists“ am Karlsruher Institut für Technologie (KIT) im Wintersemester 2014/15

Publikationen

2020

  • David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P.F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth (2020). Eleven grand challenges in single-cell data science, Genome Biol 21(1) 1093
  • Ben Bettisworth, Alexandros Stamatakis (2020). RootDigger : a root placement program for phylogenetic trees, biorxiv;2020.02.13.935304v2,[Preprint] 1094

2019

2018

  • Diego Darriba, Tomáš Flouri, Alexandros Stamatakis (2018). The state of software for evolutionary biology, Molecular Biology and Evolution, 35(5):1037–1046 322
  • Diep Thi Hoang, Le Sy Vinh, Tomáš Flouri, Alexandros Stamatakis, Arndt von Häseler, Bui Quang Minh (2018). MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation, BMC Evolutionary Biology, 18(1):11 323
  • Nikolaos Psonis, Aglaia Antoniou, Emmanouela Karameta, Adam D Leaché, Panayiota Kotsakiozi, Diego Darriba, Alexey Kozlov, Alexandros Stamatakis, Dimitris Poursanidis, Oleg Kukushkin, others (2018). Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system, Molecular Phylogenetics and Evolution, 125:100–115 324
  • Pierre Barbera, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences, Systematic Biology 68(2):365-369 325
  • Lucas Czech, Alexandros Stamatakis (2018). Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement, Bioinformatics, pp. advance online access 332
  • Lucas Czech, Alexandros Stamatakis (2018). Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements, bioRxiv, p. 346353 333
  • Benoit Morel, Alexey M Kozlov, Alexandros Stamatakis (2018). ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes., Bioinformatics 35(10):1771-1773 334
  • Alexandros Stamatakis (2018). Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges, In Population Genomics, Springer 335
  • Axel Trefzer, Alexandros Stamatakis (2018). Compressing Streams of Phylogenetic Trees, bioRxiv, p. 440644 336
  • Alexey Kozlov, Diego Darriba, Tomas Flouri, Benoit Morel, Alexandros Stamatakis (2018). RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference, bioRxiv, p. 447110 337

2017

2016

  • Frédéric Mahé, Colomban de Vargas, David Bass, Lucas Czech, Alexandros Stamatakis, Enrique Lara, David Singer, Jordan Mayor, John Bunge, Sarah Sernaker, Tobias Siemensmeyer, Isabelle Trautmann, Sarah Romac, Cédric Berney, Alexey Kozlov, Edward A.D. Mitchell, Christophe V. W. Seppey, Elianne Egge, Guillaume Lentendu, Rainer Wirth, Gabriel Trueba, Micah Dunthorn (2016). Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites, biorxiv;050997v3,[Preprint] 114
  • Constantin Scholl, Kassian Kobert, Tomá Flouri, Alexandros Stamatakis (2016). The divisible load balance problem with shared cost and its application to phylogenetic inference, In Parallel and Distributed Processing Symposium Workshops, 2016 IEEE International, pp. 408–417 115
  • Diego Darriba, Michael Weiß, Alexandros Stamatakis (2016). Prediction of missing sequences and branch lengths in phylogenomic data, Bioinformatics, 32(9):1331–1337 116
  • Michael Hoff, Stefan Orf, Benedikt Riehm, Diego Darriba, Alexandros Stamatakis (2016). Does the choice of nucleotide substitution models matter topologically?, BMC Bioinformatics, 17(1):143 117
  • Kassian Kobert, Alexandros Stamatakis, Tomáš Flouri (2016). Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations, Systematic Biology 122
  • Alexey M Kozlov, Jiajie Zhang, Pelin Yilmaz, Frank Oliver Glöckner, Alexandros Stamatakis (2016). Phylogeny-aware identification and correction of taxonomically mislabeled sequences, Nucleic Acids Research, 44(11):5022–5033 124
  • P. Kapli, S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis, T. Flouri (2016). Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo, biorxiv;063875v1,[Preprint] 125
  • Diep Thi Hoang, Le Sy Vinh, Tomas Flouri, Alexandros Stamatakis, Arndt von Häseler, Bui Quang Minh (2016). A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation, In Knowledge and Systems Engineering (KSE), 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE), Hanoi, 2016, pp. 1–6 127

2015

2013

  • Jonathan C Fuller, Pierre Khoueiry, Holger Dinkel, Kristoffer Forslund, Alexandros Stamatakis, Joseph Barry, Aidan Budd, Theodoros G Soldatos, Katja Linssen, Abdul Mateen Rajput (2013). Biggest challenges in bioinformatics, EMBO Rep 14(4):302-304 739

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