The Exelixis Lab


Enabling Research in Evolutionary Biology

the gang in 2021

group leader

  • Tough day doing field work in Crete Tough day doing field work in Crete

  • Fighting the heat in Valencia

  • Very thirsty in latin america

Prof. Dr. Alexandros Stamatakis

E-mail: Alexandros.Stamatakis[at]h-its.org
GitHub: https://github.com/stamatak
Google scholar
Personal web page
Twitter

  • staff scientist

    Dr. Alexey Kozlov

    PhD in Computer Science, Karlsruhe Institute of Technology. After finishing his PhD in January 2018, Alexey now works with us as staff scientist.
    Phone: +49 (0)6221 - 533 - 291
    E-mail:
    GitHub: https://github.com/amkozlov
    Google scholar

  • postdoc

    Benoit Morel

    Diplôme d'ingénieur, Ecole Nationale Superieure d'Informatique et de Mathematiques Appliquees, started working on his PhD project in October 2016 and submitted his thesis in summer 2021.
    E-mail:

phd students

bachelor and master students

lab alumni

postdocs

  • Stephen A. Smith (PhD, Evolutionary Biology, Yale) worked as a shared PostDoc in the Exelixis Lab and the Dunn Lab  at Brown University from mid-2010 to the end of 2011. Stephen is now an assistant professor at the university of michigan.
  • Pavlos Pavlidis (Dr. rer. nat, LMU Munich) worked as a PostDoc with us from February 2011 to December 2012. He went back to Crete to commence a second PostDoc at IMBB since he had missed our beautiful island too much for too many years. More recently, he was appointed as Associate Researcher (equivalent to associate professor) in Bioinformatics at the Institute of Computer Science of the Foundation for research and technology, Hellas in Heraklion, Crete.
  • Solon Pissis (PhD, Computer Science, King's college London) worked as a shared PostDoc in the Soltis lab and the Exelixis lab from November 2011 until June 2013. He will start his new job as lecturer at King's college Londin in September 2013.
  • Paschalia Kapli (PhD, Biology, University of Crete) worked with us as PostDoc from January 2014 to December 2016. She then moved to University College London for a second PostDoc.
  • Tomas Flouri (PhD, Computer Science, Czech Techncal University in Prague) worked with us as PostDoc from May 2012 to April 2017. He is now doing a 2nd PostDoc with Ziheng Yang at University College London.
  • Diego Darriba (PhD, Universities of A Coruna/Vigo, Spain) worked with us as PostDoc from January 2014 to October 2017. He returned to Spain to start his new job as assitant professor in computer science at the University of A Coruna.

phd students

  • Michael Ott (Dr. rer. nat., TU Munich) has been co-supervised by Prof. Bode (chair of Computer Architectures and Computer Organization) and me and has succesfully defended his PhD thesis in October 2010. He did a PostDoc in Australia until fall 2011 with Lars Jermiin at CSIRO. He returned to Munich and is now working as staff scientist at the Munich supercomputing center.
  • Nikos Alachiotis (Dr. rer. nat, TU Munich) worked as PhD student in our group from February 2009 to December 2012. He received his PhD in November 2012 and initially went back to Greece to do his military service before continuing his scientific career as a PostDoc at Carnegie Mellon University in the US in 2014.
  • Simon Berger (Dr. ing., Karlsruhe Institute of Technology) worked as PhD student in our group from January 2009 to January 2013. He received his PhD in January 2013 and decided to start working in the automotive software industry. He now works for BMW in Munich.
  • Fernando Izquierdo-Carrasco (Dr. ing., Karlsruhe Institute of Technology) worked as PhD student in our group from January 2010 to December 2013. He received his PhD in June 2014 and has been working as Bioinformatician at Oxford Nanopore in the UK since February 2014.
  • Jiajie Zhang (Dr. rer. nat., University of Lübeck) worked as PhD student in our group from June 2012 to March 2015. He received his PhD in March 2015 and has joined his lab-mate Fernando at Oxford Nanopore in the UK as of mid-March 2015.
  • Andre J. Aberer (Dr. ing., Karlsruhe Institute of Technology) worked as master's and then PhD student in our group from 2009 to March 2015. He submitted his thesis in summer 2015 and defended it in winter 2015. He now works for Bloomberg in Frankfurt.
  • Kassian Kobert, (Dr. rer. nat., Karlsruhe Institute of Technology) worked as a PhD student in our group from October 2011 to November 2015. He succesfully defend his PhD thesis in May 2016 at KIT. He has already started working as a PostDoc with Bastien Bousseau in Lyon, France as of February 1st, 2016.
  • Lucas Czech, worked as PhD student in our group from July 2014 to June 2019. He succesfully defended his PhD thesis in January 2020.
  • Philipp Bongartz, worked as PhD student in another group at HITS, but was officially and then also essentially supervised by Alexis. He defended his PhD thesis in early 2020.
  • Sarah Lutteropp, worked on her PhD with us from May 2017 to August 2021 and will defend her thesis soon.
  • Pierre Barbera, worked on his PhD with us from September 2016 to March 2021. He succesfully defendied his PhD thesis in October 2021.
  • Benoit Morel, worked on his PhD with us from October 2016 to October 2021. He succesfully defended his PhD thesis in October 2021.
  • Ben Bettisworth, worked on his PhD with us from September 2018 to July 2023. He succesfully defended his PhD thesis in July 2023.

master and bachelor students

  • Jan Strehmel (MsC candidate Computer Science, Karlsruhe Institute of Technology), completed his Master's thesis with us in 2023.
  • Luise Hauser (MsC candidate Computer Science, Karlsruhe Institute of Technology), completed her Master's thesis with us in 2023.
  • Christoph Stelz (BsC candidate Computer Science, Karlsruhe Institute of Technology), completed his Bachelor thesis with us in April 2022.
  • Xinyi Zhang (BsC Computer Science, Karlsruhe Institute of Technology), completed her Master's thesis with us in February 2022.
  • Julia Haag (MSc in Computer Science, Karlsruhe Institute of Technology) did her Master's thesis with us and then joined the lab as PhD student in spring 2022.
  • Paul Schade (BsC Computer Science, Karlsruhe Institute of Technology), worked with us as a student programmer in early 2020 and completed his Master's thesis in November 2020.
  • Ivo Baar (BsC Computer Science, Karlsruhe Institute of Technology), worked with us as a student programmer from May 2018 until April 2020.
  • Adrian Zapletal (BsC Computer Science, Karlsruhe Institute of Technology), worked with us as a student programmer from June 2018 to November 2019.
  • Johanna Wegmann (MsC Computer Science, Karlsruhe Institute of Technology), started working with us as a student programmer in December 2018 and completed her Master's thesis with us in November 2019.
  • Paula Breitling (MsC in Information Engineering and Management, Karlsruhe Institute of Technology), worked with us as a student programmer from October - December 2018 and also completed her Master's thesis with us in June 2019.
  • Linda Rülicke (MsC Computer Science, University of Frankfurt), did her Master's thesis with us and our colleague Prof. Ulrich Meyer in Frankfurt. She completed her thesis work in August 2018.
  • Rudolf Biczok (MsC Computer Science, Karlsruhe Institute of Technology), worked with us as a student programmer from May 2017 - July 2018, and also did his Master's thesis with us which he finished in early 2019.
  • Sebastian Giesse, BsC Computer Science, Karlsruhe Institute of Technology, worked with us as a student programmer from November 2017 - January 2018, and then did his Master's thesis with us which he completed in July 2018.
  • Axel Trefzer, BsC Computer Science, Karlsruhe Institute of Technology, worked with us as a student programmer from May 2017 to April 2018.
  • Tobias Ribizel, BsC Computer Science, Karlsruhe Institute of Technology, worked with us as a student programmer from November 2017 to August 2018.
  • Fernando Ramirez was a computer science exchange student at KIT from Argentina and worked with us as an intern from November 2017 to March 2018. He returned to Argentine and is now working at an IT company in Buenos Aires.
  • Nico Schwaiger (MSc in Mathematics, Karlsruhe Institute of Technology) worked with us on his Master's thesis from January to July 2016. His topic was the development of MCMC algorithms for divergence time estimation. The thesis was co-advised with Prof. Tilmann Gneiting from the department of Mathematics at KIT and HITS. Nico is now working as programmer in industry.
  • Pierre Barbera (MSc in Computer Science, Karlsruhe Institute of Technology) did his Master's thesis with us and then joined the lab as PhD student in fall 2016.
  • Sarah Lutteropp (MSc in Computer Science, Karlsruhe Institute of Technology) worked with us as a student programmer, did her Master's thesis with us and then joined the lab as PhD student in spring 2017.
  • Constantin Scholl (BsC in Information Engineering and Management, Karlsruhe Institute of Technology) worked with us as on his Bachelor thesis from May to November 2015. His topic was to implement and assess data distribution heuristics for parallel likelihood calculations on partitioned alignments when the site repeats technique is being used for accelerating phylogenetic likelihood calculations. He will move to the US in August 2016 to do a Master's in CS at Cornell university.
  • David Dao (BSc Computer Science, Karlsruhe Institute of Technology) did his Bachelor's thesis with us, working on automated methods for assessing the plausibility of large phylogenies. Thereafter, he also worked as a student programmer with us for almost two years. He will move to the US soon, to work on his Master's thesis there.
  • Patrick Flick (MSc Computer Science, Karlsruhe Institute of Technology) did his Master's thesis with us, working on protein interaction networks. He moved to the US in the meantime and will do a PhD at Georgia Tech.
  • Sebas Mendez (MSc Computer Science, Karlsruhe Institute of Technology) worked with us from April 2013 - December 2013 as student programmer (HiWi) on GPUs.
  • Jörg Hauser (MSc Computer Science, Master's thesis, Heidelberg University) is now working at a software company in Munich.
  • Denis Krompaß (MSc Bioinformatics, TUM/LMU, project work) is now doing a PhD in Munich.
  • Pinar Özbay (MSc Computational Science and Engineering, TUM, project work)
  • Harald Kraft (with Prof. Bungartz and Prof. Kranzlmueller; Diploma student in Computer Science, LMU Munich, project work)
  • Jan Stutzki (with Prof. Bungartz and Prof. Kranzlmueller; Diploma student in Computer Science, LMU Munich, project work)
  • Roland Wittman (with Prof. Bungartz; BSc Computer Science, TUM, project work)
  • Valeriy Khakhutskyy (with Prof. Bungartz; Bachelor Thesis, Technical University of Munich)
  • Szymon Seliga (Student Programmer, Technical University of Munich)
  • Zsolt Komornik (Student Programmer, Technical University of Munich)
  • Nikos Alachiotis (with Prof. Dollas, Diploma Thesis, Technical University of Chania)
  • Masoud Alipur (Master Thesis, Ecole Polytechnique Federale de Lausanne)
  • Margarida Faria (Project Work, Ecole Polytechnique Federale de Lausanne)
  • Maria Charalambous (with Prof. Trancoso, Master Thesis, University of Cyprus)
  • Michael Ott (Diploma Thesis, Technical University of Munich)
  • Georg Hoesch (Diploma Thesis, Technical University of Munich)
  • Bert van Heukelom (Diploma Thesis, Technical University of Munich)
  • Christoph Lauter (Project Work, Technical University of Munich)
  • Michael Ott (Project Work, Technical University of Munich)
  • Cornel Babel (Project Work, Technical University of Munich)

former lab visitors

visiting faculty

  • Prof. Mark Holder from the University of Kansas spent his sabbatical with us at HITS from August 2014 to July 2015.

visiting postdocs

  • Dr. Josefin Stiller from the University of Copenhagen visited us in November 2018 to jointly work on a bird genome evolution project.
  • Dr. Emily Jane McTavish from the University of Kansas joined Mark Holder on his sabbatical via a Humboldt-Fellowship. She worked with us from december 2014 to August 2015.

visiting students and interns

  • Aggelos Koropoulis (Bachelor in CS, University of Crete) worked with us as an intern from October 2018 - January 2019.
  • Dora Serdari (MSc in Bioinformatics from the University of Athens) worked with us as an intern from February 2017 to December 2018.
  • Khouloud Madhbouh is a PhD student with Mourad Elloumi at the University of Tunis-El Manar, Tunisia. She worked with us in July/August 2016 and returned t Heidelberg for a second visit from mid-November 2016 to mid-February 2017.
  • Nikos Psonis was a PhD student with Nikos POulakakis at the University of Crete. He visited our lab from September to december 2016, shortly before finishing his PHd.
  • Rebecca Harris is a PhD student with Adam Leache at the University of Washington in Seattle. She spent three months working with us from October to December 2015.
  • Paschalia Kapli, a PhD student from the Biology department at the University of Crete spent 6 months with us from September 2012 to March 2013 and then another 6 months from September 2013 to March 2014.
  • Diego Darriba, a PhD student from the University of Vigo at david Posada's lab spent three months working with us in fall 2012.
  • Dilrini De Silva, a PhD student from Queens College London spent three months working with us in spring 2012.
  • William Pearse (MSc Biology), a PhD student from Imperial College London spent three months with us in fall 2011.

© The Exelixis Lab 2013 | Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg

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