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Laboratory for Computational
Biology and Bioinformatics
 
Welcome to the website of the Laboratory for Computational Biology and Bioinformatics.
The Laboratory was started in June 2006 by Professor Bernard Moret. Our main area of interest is the design of models and algorithms for problems arising in biology, mostly evolutionary biology (phylogenetics) and genomics (regulatory, comparative, and evolutionary genomics). We work mainly with large-scale simulations, but we also make use of published data, including most common databases in genomics and proteomics.

Objective
To design, implement, test, and assess models and algorithms for discrete problems arising in evolutionary molecular biology.

See the recent ACM Ubiquity interview with Prof. Moret on Experimental Algorithmics.

Latest Events

• December 13: Congratulations to Nishanth Nair and Mingfu Shao, who both won departmental teaching awards today.
• November 26: Congratulations to Yu Lin, who was granted a postdoctoral fellowship from the Swiss National Science Foundation to work in Dr. Pavel Pevzner's group at UC San Diego, starting early 2013.
• October 31-November 3: Bernard Moret travels to Washington DC to serve on an NSF panel.
• October 31: Yann Christinat leaves us today to start his postdoctoral fellowship at the ETHZ under the supervision of Prof. Wilhelm Krek.
• October 17-19: Mingfu Shao and Yu Lin travel to Rio de Janeiro to attend the RECOMB-CG'12 conference and present a paper.
• October 7-10: Bernard Moret travels to Orlando to attend the ACM-BCB'12 conference and give a keynote address.
• September 2012: Xiuwei Zhang started her postdoctoral work at the U. of Cambridge (in the Laboratory for Molecular Biology of the MRC) and at the EBI (the European Bioinformatics Institute, in nearby Hinxton), working under the supervision of Prof. Sarah Teichmann. We miss her terribly, but we are collaborating and so expect regular visits back and forth.
• August 27-29: Bernard Moret, Yu Lin, and Mingfu Shao travelled to St Petersburg to participate in the RECOMB-AB'12 conference, where Bernard Moret gave an invited address.
• August 21: Mingfu Shao passed his doctoral candidacy exam today. Congratulations, Mingfu!
• August 1-3: Bernard Moret travelled to Washington DC to serve on an NSF panel.
• July 13-15: Yann Christinat travelled to San Diego to present a poster at ISMB'12.
• July 1:: Lab alumnus (past postdoc) Alexandros Stamatakis was named a full professor in the Department of Computer Science at the Karlsruhe Institute of Technology (one of the top CS departments in Europe). Congratulations, Alexis!
• June 22-24: Yann Christinat, Cristina Ghiurcuta, and Nishanth Nair travel to Dublin to attend the SMBE meeting and present posters.
• June 20: Yu Lin successfully defended his PhD thesis today, in the presence of committee members Rachid Guerraoui (EPFL, jury president), John Maddocks (EPFL), Christos Papadimitriou (UC Berkeley), and Russell Schwartz (CMU). Congratulations Yu!!!
• June 18-19: Bernard Moret travels to Paris to serve on the HDR (Habilitation) examination committee for Guillaume Blin.
• May 22: Vaibhav Rajan left us today, flying to Bangalore to begin the next phase of his life, as a research staff member at the Xerox Research Center India. Our best wishes go with him and we hope to host him on a visit soon.
• May 19-24: Yann Christinat travelled to Dallas to participate in the 8th Int'l Symp. on Bioinformatics Research & Applications ISBRA'12, where he gave a paper.
• May 19-23: Bernard Moret travelled to Washington DC to attend a workshop on phylogenetic reconstruction at the Smithsonian Institute and conduct a program review.
• May: Congratulations to Yu Lin, who received a Chinese Government Fellowship for Outstanding Students Abroad.
• April 30: Congratulations to Xiuwei Zhang, who was granted a postdoctoral fellowship from the Swiss National Science Foundation to work in Dr. Teichmann's group at the Laboratory for Molecular Biology at the U. of Cambridge, starting this coming August.
• April 23: Yann Christinat successfully defended his PhD thesis today, in the presence of committee members Jean-Yves Le Boudec (EPFL, jury president), Paola Bonizzoni (U. di Milano), Philipp Bücher (EPFL), and Marc Robinson-Rechavi (U. Lausanne). Congratulations Yann!!!
• April 19: Vaibhav Rajan successfully defended his PhD thesis today, in the presence of committee members Arjen Lenstra (EPFL, jury president), Mona Singh (Princeton U.), Emre Telatar (EPFL), and Tandy Warnow (U. Texas). Congratulations Vaibhav!!!
• November 14: Congratulations to Yann Christinat, who won the Best Student Paper award at the 5th IEEE Conf. on Bioinformatics and Biomedicine BIBM'11.
• November 13-15: Yann Christinat and Bernard Moret travelled to Atlanta to attend the 5th IEEE Conf. on Bioinformatics and Biomedicine BIBM'11; Yann Christinat presented a paper and Bernard Moret gave an invited address.
• November: Xiuwei Zhang travelled to MIT (and the Broad Institute), Princeton (and the Lewis-Sigler Institute), and the US NIH, where she gave invited talks; she also attended the Cold Spring Harbor workshop on Genome Informatics.
• October: Xiuwei Zhang and Vaibhav Rajan travelled to Barcelona to attend some of the workshops in the RECOMB combined satellite meetings RECOMB-SB/RECOMB-RG/RECOMB-RICCI/DREAM
• October: Xiuwei Zhang and Bernard Moret visited Cambridge U. to initiate a collaboration with Prof. Sarah Teichmann; Bernard Moret gave an invited talk at the MRC.
• September: Jonas Helfer has been awarded a Fulbright Foreign Student fellowship, which will fully fund his initial year of PhD studies in the US.
• September 15: Jonas Helfer successfully defended his MS thesis today, presenting it from Beijing -- he worked with Prof. Rui Jiang at Tsinghua University.
• August 15: Avinash Das Sahu successfully defended his MS thesis today, presenting it from India -- he worked with Prof. William Noble at the U. of Washington. Avinash will start working on his PhD in Computer Science at the U. of Maryland in Fall 2011.
• August: Prof. Jijun Tang, from the U. of South Carolina, has joined our lab for the first half of his sabbatical. He will stay with us until the end of the year, working with everyone in the lab on phylogenetic reconstruction, rearrangements, and related topics.
• July 25:: Xiuwei Zhang successfully defended her PhD thesis today, in the presence of committee members Emre Telatar (EPFL, jury president), Manolis Kellis (MIT), Sarah Teichmann (Cambridge U.), and Matthias Seeger (EPFL). Congratulations Xiuwei!!!
  Xiuwei will stay this next year with our lab as a postdoctoral fellow.
• Nishanth Nair has been offered a fellowship for the fall program Mathematical and Computational Approaches in High-Throughput Genomics at the Institute for Pure and Applied Mathematics at UCLA, from mid-September to mid-December 2011.
• July: Bernard Moret travelled to Vienna to give an invited lecture at the 3rd RECOMB Conf. on Bioinformatics Education RECOMB-BE'11.
• Two international MS students joined us this summer under the Summer@EPFL program: Ms. Anastasiya Migunova and Mr. Vladislav Semipiatnyi, both from Moscow State U. (Russia).
• May: Yu Lin, Bernard Moret, Vaibhav Rajan, and Xiuwei Zhang travelled to Changsha (China) to give a keynote address and present papers at the 7th Int'l Symp. on Bioinformatics Research & Appls. ISBRA'11.
• March: Bernard Moret travelled to Raleigh-Durham to participate in a meeting on "Challenges with large-scale phylogeny estimation" at the National Evolutionary Synthesis Center NESCENT.
• Olga Ponomarova, who was a summer intern in our lab in 2010, was admitted to the PhD program of the European Molecular Biology Laboratory (EMBL) in Heidelberg. Congratulations to Olga!

Courses

We regularly teach the Master's level courses Computational Molecular Biology (Spring semesters, 5 EPFL credits) and Advanced Algorithms (Fall semesters, 7 EPFL credits). We occasionally teach the PhD level course Theory of Computation (5 EPFL credits). We have co-taught (with colleagues from the School of Life Sciences) courses in Bioinformatics at both Master's and PhD level. We will teach the second-year course Theoretical Computer Science in Spring 2012.

About EPFL

EPFL is consistently ranked among the top three (after Cambridge U. and with its sister institution ETHZ) in Europe and among the world's top 20 in Engineering and Computer Science; see, for instance, the Times Higher Education (#14), the Leiden Ranking (#13, using Impact + PP), the Shanghai Jiaotong Academic Ranking of World Universities (#18), and the QS World University Ranking (#17). (Note that most rankings of Computer Science departments are unusable, as they rely on ISI Web of Science, which is heavily biased towards journals, whereas most high-value outlets in Computer Science are conference proceedings.)