Group leader „Scientific Computing“ at HITS Professor for High Performance Computing at the Karlsruhe Institute of Technology (KIT) Research Interests Algorithms, …

Group leader „Scientific Computing“ at HITS
Professor for High Performance Computing at the Karlsruhe Institute of Technology (KIT)

Research Interests

Algorithms, parallel computing, parallel architectures and evolutionary bioinformatics.

About me

I grew up in Athens and moved to Germany in 1995 to study computer science. During my studies in Munich I also spent quite time abroad in Lyon, Paris, Madrid and Athens. Prior to getting involved in Bioinformatics with the start of my PhD I mostly worked in the area of prototype software development for air traffic controllers.

Curriculum Vitae

Since 2012    Adjunct professor at the Department of Ecology and Evolutionary Biology at the University of Arizona at Tucson, US
Since 2012    Full professor for High Performance Computing at the Karlsruhe Institute of Technology (KIT), Germany
Since 2010    Leader “Scientific Computing” group at HITS, Germany
2008-2010    Head of an DFG Emmy-Noether junior research group at the Ludwig Maximilian University of Munich and the Technical University of Munich
2006-2008    PostDoc at the Swiss Federal Institute of Technology at Lausanne, Switzerland
2005-2006    PostDoc at the Institute for Computer Science, Foundation of Research and Technology Hellas, Heraklion, Greece
2001-2004    PhD at the Technical University of Munich, Germany
1995-2001    Study of computer science at the Technical University of Munich, Germany, and at the University of Lyon, France

Memberships

Teaching Awards

2016:     Received a certificate for teaching excellence from the dean of the faculty at the Karlsruhe Institute of Technology for their programming practical” Hands-on Bioinformatics Practical” tought in summer 2015 based on the practical evaluation by the students.
2015     Received a certificate for teaching excellence from the dean of the CS faculty at the Karlsruhe Institute of Technology for the course “Introduction to Bioinformatics for Computer Scientists” taught in winter 2014/15 based on the course evaluation by the students.

Publications

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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