The Exelixis Lab


Enabling Research in Evolutionary Biology

Computational molecular evolution workshop series

Here is a link to a series of summer schools on computational molecular evolution in which our lab is actively involved: CoME

Photo below: Group picture of the 2010 EMBO summer school at HCMR-IMBG in Crete.

Typically PostDocs and PhD students from the Exelixis lab also contribute actively to the school as teaching assistants. Pavlos participated in 2011 and 2012. Simon helped as TA in 2012, Fernando and Tomas helped in 2013.

  • The 3rd course in 2011 course took place in Hinxton and was funded by the Wellcome Trust.
  • The 4th course took place in Crete again in 2012 and was funded by EMBO and co-sponsored by the Heidelberg Institute for Theoretical Studies.
  • The 5th course took us back to Hinxton again in 2013 from April 29 to May 10 thanks to the Wellcome trust.
  • The 6th course took place in Crete again in 2014 from May 5 - May thanks to EMBO, HITS, and the Astir beach hotel.
  • The 7th course will take us back to Hinxton again in 2015 from April 13 to April 24 thanks to the Wellcome trust.

Regular courses

Summer 2014

Course: Introduction to Bioinformatics for Computer Scientists. Introductory course (2 hours per week) to Bioinformatics for CS Master's students at the Karslruhe Institute of Technology. This course forms part of the Bioinformatics module which we teach at the CS department of KIT. Module web site.

Summer 2013

Seminar: Hot Topics in Bioinformatics

Exelixis lab members will organize a seminar on hot topics in the current Bioinformatics literature. This seminar forms part of the Bioinformatics module which we teach at the CS department of KIT. Module web site.

Winter 2012/2013

Course: Introduction to Bioinformatics for Computer Scientists

Alexis, Pavlos, Solon, and Thomas will give an introductory course (2 hours per week) to Bioinformatics for CS Master's students at the Karslruhe Institute of Technology. This course forms part of the Bioinformatics module which we teach at the CS department of KIT. Module web site.

Summer 2010

Course: High Performance Computing for Bioinformatics Students

Taught by Alexis (2 hours per week) at the CS department of TU Munich

Seminar:Biological and Computational Aspects of Phylogenetic Inference and Implications for the Evolution of Life on Earth

Taught by Alexis together with Gert W├Ârheide at LMU Munich. Course web site

Winter 2009/2010

Course: Computational Phylogenetics

Taught by Alexis (2 hours per week) within the framework of the EES school at Martinsried. Audience: Biology, Bioinformatics.

Summer 2009

Course: Pearls of Computer Science IV

taught by Alexis and all fellow Junior Research (Emmy-Noether) Group leaders at the CS department of TUM. "Pearls of Computer Science IV" is a special series of lectures for gifted undergraduate students.

Seminar: Biological and Computational Aspects of Phylogenetic Inference and Implications for the Evolution of Life on Earth

Joint interdisciplinary main seminar (Hauptseminar) taught by Alexis with Gert W├Ârheide at the LMU. The seminar was open to CS, Bioinformatics, and Biology students and the main goal was for Biologists and Computer Scientist to learn to talk to each other. Course web site

Winter 2008/2009

Course: High Performance Computing

Alexis taught a 2 hour per week course on high performance computing at LMU Munich. Course web-site


Summer school lectures & tutorials

  1. Alexis: "Large-scale phylogenetic inference", 17th international bioinformatics workshop, Belgrade, Serbia, August 2012.
  2. Fernando: "Lectures and practical excercises: Parallel Computing & Phylogenetic Inference" at Bioinformatics and systems biology school for young scientists,Institute of Cytology and Genetics, Novosibirsk, Russia, June 2012.
  3. Alexis: "RAxML hands-on tutorial", National Museum of Natural History, Stockholm, Sweden, May 2012.
  4. Alexis: "Parallel Computing in Phylogenetics", CoME summer school, Heraklion, Greece, April/May2012.
  5. Alexis: "Parallel Computing in Phylogenetics: Lectures and Practicals", training course on Basic Molecular Evolution and Phylogenetics, Sofia, Bulgaria, March 2012.
  6. Alexis: "HPC in Bioinformatics Lectures and Practicals", Cyprus Advanced HPC Workshop, Nicosia, Cyprus, February 2012.
  7. Pavlos: "Detecting positive selection: i) Machine-learning and Bayesian approaches ii) Selection in multiple-locus models", Genomics In Biodiversity workshop, Institute for Marine Biology and Genetics, Heraklion, Greece, September 2011.
  8. Alexis: "EES Phylogenetics summer-school", lectures, Frauenchiemsee, Germany, August 2011.
  9. Alexis: " Computational Molecular Evolution", CoME summer school, Wellcome Trust, Hinxton, UK, April 2011.
  10. Alexis: "Fast, Free Phylogenies: HPC for Phylogenetics Tutorial”, tutorial lectures, NIMBioS, Knoxville, Tennessee, October 2010.
  11. Alexis: "Phylogenetic Inference", summer school, Frauenchiemsee, Germany, September 2010.
  12. Alexis: "Phylogenetic Inference under Maximum Likelihood",  summer school, Milano, Italy, August 2010.
  13. Alexis: "Modern Computational Science", summer school, University of Oldenburg, Germany, August 2010.
  14. Alexis: "Computational Molecular Evolution", summer school, Institute of Marine Biology and Genetics - Hellenic Center for Marine Research, Heraklion, Greece, May 2010.
  15. Alexis: "Phylogenetic Inference & Identification",  TRACEability of Arbuscular Mycorrhizal fungi as plant-beneficial microorganisms in agro-environments Summer School, Munich, Germany, April 2009.
  16. Alexis: “Phylogenetic Inference”, Bernhard-Rensch Summer School 2008, Carolinensiel, Germany, July 2008.
  17. Alexis: “Computation of large phylogenetic trees: algorithmic and technical solutions”, The 2008 BGRS International Summer School for young scientists: “Evolution, Systems Biology and High Performance Computing Bioinformatics”, Novosibirsk, Russia, July 2008.
  18. Alexis: “Computation of large phylogenetic trees: algorithmic and technical solutions”, The 2006 BGRS International Summer School for young scientists: “Evolution, Systems Biology and High Performance Computing Bioinformatics”, Novosibirsk, Russia, July 2006.
  19. Alexis: “Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions” half-day tutorial with David Bader and Usman Roshan at 18th IEEE/ACM Supercomputing Conference (SC2005), Seattle, Washington, November 2005.
  20. Alexis: “High Performance Computing in Bioinformatics”, half-day tutorial with Thomas Ludwig at the German Conference on Bioinformatics (GCB’04) in Bielefeld, Germany, October 2004.
  21. Alexis: “High Performance Computing in Bioinformatics”, half-day tutorial with Thomas Ludwig at the 4th International Conference on Bioinformatics and Genome Regulation and Structure (BGRS2004) in Novosibirsk, Russia, July 2004.