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


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.


  • Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson Bd, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder Jd, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A (2020). Eleven grand challenges in single-cell data science, Genome Biol 21(1) 1093
  • Bettisworth B, Stamatakis A (2020). RootDigger : a root placement program for phylogenetic trees, biorxiv;2020.02.13.935304v2,[Preprint] 1094



  • Darriba D, Flouri T, Stamatakis A (2018). The state of software for evolutionary biology, Molecular Biology and Evolution, 35(5):1037–1046 322
  • Hoang DT, Vinh LS, Flouri T, Stamatakis A, Häseler Av, Minh BQ (2018). MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation, BMC Evolutionary Biology, 18(1):11 323
  • Psonis N, Antoniou A, Karameta E, Leaché AD, Kotsakiozi P, Darriba D, Kozlov A, Stamatakis A, Poursanidis D, Kukushkin O, 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
  • Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences, Systematic Biology 68(2):365-369 325
  • Czech L, Stamatakis A (2018). Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement, Bioinformatics, pp. advance online access 332
  • Czech L, Stamatakis A (2018). Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements, bioRxiv, p. 346353 333
  • Morel B, Kozlov AM, Stamatakis A (2018). ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes., Bioinformatics 35(10):1771-1773 334
  • Stamatakis A (2018). Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges, In Population Genomics, Springer 335
  • Trefzer A, Stamatakis A (2018). Compressing Streams of Phylogenetic Trees, bioRxiv, p. 440644 336
  • Kozlov A, Darriba D, Flouri T, Morel B, Stamatakis A (2018). RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference, bioRxiv, p. 447110 337



  • Mahé F, Vargas Cd, Bass D, Czech L, Stamatakis A, Lara E, Singer D, Mayor J, Bunge J, Sernaker S, Siemensmeyer T, Trautmann I, Romac S, Berney C, Kozlov A, Mitchell EA, Seppey CVW, Egge E, Lentendu G, Wirth R, Trueba G, Dunthorn M (2016). Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites, biorxiv;050997v3,[Preprint] 114
  • Scholl C, Kobert K, Flouri T, Stamatakis A (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
  • Darriba D, Weiß M, Stamatakis A (2016). Prediction of missing sequences and branch lengths in phylogenomic data, Bioinformatics, 32(9):1331–1337 116
  • Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A (2016). Does the choice of nucleotide substitution models matter topologically?, BMC Bioinformatics, 17(1):143 117
  • Kobert K, Stamatakis A, Flouri T (2016). Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations, Systematic Biology 122
  • Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A (2016). Phylogeny-aware identification and correction of taxonomically mislabeled sequences, Nucleic Acids Research, 44(11):5022–5033 124
  • Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T (2016). Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo, biorxiv;063875v1,[Preprint] 125
  • Hoang DT, Vinh LS, Flouri T, Stamatakis A, Häseler Av, Minh BQ (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



  • Fuller JC, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos TG, Linssen K, Rajput AM (2013). Biggest challenges in bioinformatics, EMBO Rep 14(4):302-304 739

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