The Exelixis Lab


Enabling Research in Evolutionary Biology

brief CV

Alexandros (Alexis) Stamatakis studied computer science at TU Munich and ENS Lyon (with internships in Athens, Paris, and Madrid). In 2001 he received his diploma in computer science from TU Munich.

In 2004 he received his PhD (also at TU Munich) for work on algorithms and parallel computing for phylogenetic inference (reconstruction of evolutionary trees using DNA data).

He continued working in the area of evolutionary Bioinformatics and parallel computing as a PostDoc at the Institute for Computer Science in Heraklion Greece (2005-2006) and at the Swiss Federal Institute of Technology at Lausanne (2006-2008).

In early 2008 he returned to Munich to start his own independent junior research group (DFG Emmy-Noether grant), initially at LMU and then at TU Munich.

In fall 2010 he moved to the Heidelberg Institute for Theoretical Studies (HITS) to start his new job as permanent research group leader of the scientific computing group that also entailed the management of the entire IT HPC infrastructure at HITS until July 2013.

In 2012 he was appointed as adjunct professor at the Dept. of Ecology and Evolutionary Biology at the University of Arizona at Tucson and as full professor at the faculty of computer science of the Karlsruhe Institute of Technology. Both appointments are in conjunction with his position at HITS.

His main research interests are algorithms, parallel computing, parallel architectures and evolutionary Bioinformatics.


trivia

Before getting involved in Bioinformatics and parallel computing, Alexis was primarily interested in writing aviation software, in particular everything related to Air Traffic Control. The technical report he produced back in the late 90ies while doing an internship at the Eurocontrol Experimental Center near Paris, France got recently cited, this is his favorite citation.

citation metrics

community service

phd committees

Alexis is/was a member of the PhD committees and a bit of a co-supervisor for the following students:

cs conference programme committees

    • IEEE HICOMB 2017
    • 4th International Conference on Algorithms for Computational Biology (AlCoB 2017), Aveiro, Portugal, June 2017.
    • CompHPC 2017, International Conference on Computational Methods and Algorithms on HPC Platforms and Accelerators, September 2017, Athens, Greece
    • 31st IEEE International Parallel & Distributed Processing Symposium (IPDPS 2017), May/June 2017, Orlando, USA
    • Supercomputing Conference (SC16), November 2016, Salt Lake City, USA
    • International Supercomputing Conference 2016 (ISC'16), June 2016, Frankfurt, Germany
    • Parallel Computational Biology 2015, Krakow, Poland
    • HIPC 2015, Bangalore, India
    • IEEE HICOMB 2015
    • International Supercomputing Conference 2015 (ISC'15), July 2015, Frankfurt, Germany
    • PRIB 2014 PC Member, August 2014, Stockholm, Sweden
    • ECBB'14 PC member, September 2014, Strasbourg, France
    • International Conference on Communication and Information Systems (ICICS 2014), April 2014, Ibrid, Jordan
    • International Supercomputing Conference 2014 (ISC'14), June 2014, Leipzig, Germany
    • IEEE HICOMB 2014
    • BIOIT 2013 conference, December 2013, Utah, US
    • ICPP 2013
    • Parallel Bio-Computing Workshop (PBC 2013) held in conjunction with PPAM, Warsaw Poland
    • International Supercomputing Conference 2013, Leipzig, Germany.
    • IEEE HICOMB 2013
    • BIOIT 2012 conference, October 2012, Utah, US
    • ECBB'12 PC member "Evolution, Phylogeny, and Comparative Genomics" & "Technology and Software" tracks, September 2012, Basel, Switzerland
    • IEEE HPCC 2012 PC member
    • PC member 18th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2012), December 2012, Singapore
    • PC member: 12th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP-12), September 2012, Fukuoka, Japan
    • 9th IEEE International Conference on Embedded Software and Systems IEEE (ICESS 2012)
    • Fourth Workshop on Parallel Emerging Architectures (in conjunction with ICCS 2012, Omaha, Nebraska)
    • co-chair IEEE IPDPS 2012 publicity committee
    • IEEE HICOMB 2012
    • 8th IEEE International Conference on Embedded Software and Systems IEEE (ICESS 2011)
    • Hellenic Society for Computational Biology Conference (HSCB 2011)
    • Workshop on Parallel Programming on Accelerator Clusters (PPAC11) in conjunction with IEEE Cluster 2011
    • IEEE HPCC 2011 PC member Biological Molecular Computing Track
    • 4th International Conference on Contemporary Computing, Noida, India, 2011
    • 2nd International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD'11) held in conjunction with 22nd International Conference on Database and Expert system Applications (DEXA'11)
    • Parallel Bio-Computing Workshop (PBC 2011)
    • Third Workshop on Parallel Emerging Architectures (in conjunction with ICCS 2011, Tsukuba, Japan)
    • 2011 ACS/IEEE International Conference on Computer Systems and Applications (AICCSA 2011)
    • IEEE HICOMB 2011
    • Hellenic Society for Computational Biology Conference (HSCB 2010)
    • IEEE HCPP 2010 PC member "Parallel and Distributed Algorithms Track"
    • IEEE HCPP 2010 PC member "High-Performance Scientific and Engineering Computing Track"
    • Reviewer for inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) 2010
    • co-chair IEEE Cluster 2010 conference workshop on "Parallel Programming and Applications on Accelerator Clusters
    • IEEE ICESS 2010
    • IEEE CEC 2010
    • IEEE HICOMB 2010
    • International Conference on Computational Science 2010 (ICCS 2010) Emerging Parallel Architectures Workshop
    • 2010 ACS/IEEE International Conference on Computer Systems and Applications (AICCSA 2010)
    • ACM Symposium on BioComputing 2010
    • co-chair Parallel Bio-Computing Workshop (PBC 2009)
    • ACM SAC 2009
    • Emerging Parallel Architectures Workshop at ICCS 2009
    • HPCC-09
    • Hellenic Society for Computational Biology (HSCB 2009)
    • IEEE CEC 2009
    • IEEE CSE-09
    • ICPADS 2009
    • WABI 2009
    • IEEE HICOMB 2009
    • Hellenic Society for Computational Biology (HSCB 2008)
    • ACM SAC 2008
    • PRIB 2008
    • ACM/IEEE Supercomputing Conference 2008
    • IEEE HICOMB 2008
    • ACM SAC 2007
    • PBC 2007
    • IEEE AINA-07
    • HPCC-06
    • IEEE HICOMB 2006
    • HPCC-05
    • PBC 2005

reviews for journals

    • PeerJ
    • Systematic Biology
    • Bioinformatics
    • BMC Bioinformatics
    • IEEE Transactions on Parallel and Distributed Systems
    • Journal of Molecular Evolution
    • BMC Evolutionary Biology
    • BMC Molecular Biology
    • BMC Research Notes
    • Evolutionary Bioinformatics Online
    • Parallel Computing
    • Molecular Biology and Evolution
    • Philosophical Transactions of the Royal Society
    • IBM Journal of Research and Development
    • Transactions on Computers
    • Nucleic Acids Research
    • IEEE Transactions on Computational Biology and Bioinformatics
    • Journal of Systems and Software
    • PLoS ONE
    • Journal of Computational Science
    • Environmental Microbiology and Environmental Microbiology Reports
    • Trends in Evolutionary Biology
    • Molecular Ecology Resources
    • Journal of Parallel and Distributed Computing
    • Organisms Diversity and Evolution
    • Genome Biology
    • Genome Biology and Evolution
    • Interface Journal of the Royal Society
    • IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
    • Journal of Integrative Bioinformatics
    • Infection, Genetics, and Evolution
    • Nature Methods
    • Future Generation Computer Systems
    • Computing (Springer)