Statistical and computational challenges in molecular phylogenetics and evolution

Monday 28 and Tuesday 29 April 2008
Organised by Dr Nick Goldman and Professor Ziheng Yang FRS

Dr Richard Emes, Keele University, Chair

Richard Emes was appointed lecturer in bioinformatics at the institute for science and technology in medicine at Keele University in 2007. He initially studied Zoology at the University of Wales and molecular parasitology, at Glasgow University. He then undertook post-doctoral positions at Oxford University and the Sanger Institute applying bioinformatics and comparative genomics approaches to investigate the evolution of genes and genomes. In 2004 he was awarded a MRC Special Training Fellowship in Bioinformatics to study molecular evolution of parasite genomes at University College London. His research interests are in bioinformatics and comparative genomics.

Dr Nicolas Galtier, Universite Montpellier 2, Speaker

Nicolas Galtier is a french researcher interested in many aspects of molecular evolution, including theoretical and bioinformatic developments in molecular phylogeny and population genetics. he was born in 1970, did his PhD in Lyon (France) with Manolo Gouy, and a post-doc in Edinburgh (UK) with Nick Barton. he is now CNRS Directeur de Recherches in Institut des Sciences de l'Evolution de Montpellier (France). He is married with two kids, yet trying to do some research. At the moment, he is excited by the following biological/methodological questions: (i) how much have GC-biased gene conversion impacted genome evolution in eukaryotes? (ii) How could we detect position-specific changes of evolutionary rate during protein evolution, and how much does this relate to adaptive processes? (iii) is mitochondrial DNA a neutral, clonal, clock-like genetic marker? (iv) why is mitochondrial DNA hypermutable in animals, and why more in some species than in others? (v) how should we deal with phylogenetic conflicts between genes in phylogenomic reconstructions?

Professor Olivier Gascuel, Centre National de la Recherche Scientifique, LIRMM, Speaker

Olivier Gascuel first studied mathematics. His PhD was in computer science, and he started working in bioinformatics in the 80's, at the very beginning of the genomic era and of the rapid development of interactions between mathematicians, computer scientists and molecular biologists. His first interests were in sequence analysis and protein structure prediction, using machine learning approaches. Since the mid of the 90's, Olivier Gascuel is mostly concerned by evolution and phylogenetics, with focus on the mathematical and computational tools and concepts. Olivier Gascuel leads a research group at the Centre National de la Recherche Scientifique, Montpellier (France). He is an associate editor of Systematic Biology and belongs to the editorial board of several bioinformatics journals. He published 110 papers and book chapters, and authored several widely used computer programs in phylogenetics and bioinformatics.

Professor von Haeseler, Center for Integrative Bioinformatics Vienna, Speaker

Arndt von Haeseler was appointed scientific director of the Center for Integrative Bioinformatics Vienna (CIBIV) in
September 2005 and professor for bioinformatics. He studied biology and mathematics and received his PhD in Mathematics at the University of Bielefeld.
Then he did his post-doc at the University of Southern California (Los Angeles) with Mike Waterman. Subsequently he was
an assistant professor at the University of Munich, an associate professor at the Max Planck Institute for evolutionary Anthropology,
and full professpr for Bioinformatics at the University of Düsseldorf.

His research interests are: phylogenetic tree reconstruction, modelling evolution, and population genetics, algorithms for bioinformatics, biodiversity.

Dr Mark Holder, Florida State University, Speaker

Mark Holder received a PhD from the University of Texas at Austin where he worked with Dr. David Hillis. He continued to pursue his interests in statistical and computational issues in systematics during two postdoctoral positions: one at the University of Connecticut (with Dr. Paul Lewis), and the other at Florida State University (with Dr. David Swofford). Since August, 2007 Dr. Holder has been an assistant professor in the Department of Ecology and Evolutionary Biology at the University of Kansas (Lawrence, Kansas).

Professor John Huelsenbeck, University of California Berkeley, Speaker

John Huelsenbeck is professor of Integrative Biology at the University of California, Berkeley. He received his B.A. in Paleontology from UC Berkeley, and his Ph.D. in Zoology at the University of Texas, Austin, where he worked with Dr. David Hillis and Dr. Jim Bull. His research is in statistical phylogenetics and the genetics of adaptation.

Dr Ari Löytynoja, EMBL - European Bioinformatics Institute, Speaker

Ari Löytynoja studied biology at the Oulu University in Finland, did his Ph.D. at the Free University of Brussels in Belgium, and now works as a postdoctoral fellow at the EMBL-European Bioinformatics Institute in the UK. His main interests are in evolutionary and comparative sequence analysis.

Professor Vincent Moulton, University of East Anglia, Chair

Vincent Moulton is Professor in Computational Biology at University of East Anglia. He completed his PhD in 1994 at Duke University, USA, after which he worked as a visiting researcher at University of Bielefeld, DE, and University of Canterbury/Massey University, NZ. In 1999 he moved to Sweden, where he was employed as Senior Lecturer at Mid Sweden University and, as of 2002, as Professor in Bioinformatics at Uppsala University. He took up his position at University of East Anglia in 2004.

Professor Mark Pagel, University of Reading, Speaker

Mark Pagel is Professor of Evolutionary Biology at the University of Reading.  He works on models for inferring phylogenetic trees, on the detection of historical signatures of evolution from comparative data, and on aspects of cultural evolution.  Recent work includes inferring characteristics of dinosaur genomes, inferring rates of linguistic evolution, and identifying punctuational bursts of change in genes and in human languages.

Dr Tal Pupko, Tel-Aviv University, Speaker

RESEARCH INTERESTS:

My research interests are concerned with various fields of Bioinformatics:
" Functional genomics: Studying the evolutionary selection forces shaping genes and genomes and the in-silico predictions of these forces.
" Molecular evolution and phylogeny: Inferring evolutionary relationships and evolutionary dynamics: biological, statistical and computational aspects. Developing probabilistic evolutionary models.
" Computational virology and immunology: inference of functional sites in HIV and predicting anti-viral drug resistance sites, epitope binding-site prediction.

EDUCATION:

1990  B.Sc. in Biology, Tel Aviv University
1995    M.Sc. in Biochemistry, Tel Aviv University, magna cum laude
1997    B.Sc. in Mathematics, Tel Aviv University, summa cum laude
2001    Ph.D. in Zoology, Tel Aviv University

PROFESSIONAL EXPERIENCE:

2000-2002 Post Doctorate, The Institute of Statistical Mathematics, Tokyo, Japan   Supervisor: Prof. Masami Hasegawa.
2002-2003 Post Doctorate, School of Computational Science & Information Technology, Tallahassee Florida. Supervisor: Prof. David Swofford.
2003-2007 Lecturer, Tel Aviv University
2007- Senior Lecturer, Tel Aviv University

Professor Bruce Rannala, University of California Davis, Speaker

Bruce Rannala is a Professor in the Genome Center and the Evolution and Ecology Section at the University of California, Davis. He was formerly on the faculties of the Department of Medical Genetics at the University of Alberta and the Department of Ecology and Evolution at the State University of New York, Stony Brook.

Originally from Vancouver Island, Dr. Rannala earned his B.Sc. (Honours) from the University of British Columbia, his M.Sc. from the University of Toronto, and his Ph.D. in Mathematical Population Genetics from Yale University. He went on to do his postdoctoral training at the University of California, Berkeley. He became a member of CIAR's Evolutionary Biology Program in 2002.

Dr Allen Rodrigo, University of Auckland, Speaker

Allen Rodrigo is Professor of Computational Biology and Bioinformatics, and the Director of New Zealand's Bioinformatics Institute at the University of Auckland.  His research interests are in bioinformatics and computational biology, phylogenetics and evolutionary genetics, and the molecular evolution of viruses.  

Dr Alexandros Stamatakis, Swiss Federal Institute of Technology , Speaker

Alexandros Stamatakis received his Diploma in Computer Science in March 2001 from the Technische Universität München. His studies included internships at the Ecole Normale Superieure de Lyon, France (9 months), at the Eurocontrol Experimental Center near Paris, France (4 months) and at the Instituto de Salud Carlos III/Universidad Politecnica de Madrid, Spain (3 months). In October 2004 he received his Ph.D. for research on Distributed and Parallel Algorithms and Systems for Inference of Huge Phylogenetic Trees based on the Maximum Likelihood Method" from the Technische Universität München. From January 2005 to June 2006 he worked as postdoctoral researcher at the Institute of Computer Science in Heraklion, Greece. In July 2006 he joined Bernard Moret's group at the Swiss Federal Institute of Technology at Lausanne as a PostDoc. His main research interest is on technical and algorithmic solutions for inference of huge phylogenetic trees.

Dr Marc Suchard, UCLA School of Public Health, Speaker

Marc Suchard, MD, PhD (Biomathematics) is helping to develop the nascent field of evolutionary medicine. This field harnesses the power of methods and theory from evolutionary biology to advance our understanding of human disease processes. Just as phylogenetic approaches have stimulated the field of evolution at large, they posses the potential to revolutionize evolutionary medicine, particularly in the study of rapidly evolving pathogens. To bridge the gap between phylogenetics and human-pathogen biology, Dr Suchard's interests focus on the development of novel reconstruction methods drawing heavily on statistical, mathematical and computation techniques. Some of his current projects involve jointly estimating alignments and phylogenies from molecular sequence data and mapping recombination hot-spots in the HIV genome.

Dr Max Telford, University College London, Chair

Max Telford completed his D.Phil at the University of Oxford in 1993.  After a year working in Paris he spent 6 years as a research fellow at the Natural History Museum before taking up a Wellcome Trust Research Career Development Fellowship in Cambridge in 2000.  He moved back to London in 2003 and is now Reader in Zoology in the Department of Biology, University College London.  He has two principle related research interests; in metazoan molecular systematics, which provides the essential evolutionary framework for all comparative zoology and in comparative developmental (Evo-devo) studies principally in the arthropods.

Professor Jeff Thorne, North Carolina State University, Speaker

Jeff Thorne is a Professor in the Genetics and Statistics departments of North Carolina State University. He spent most of his childhood in Wisconsin. His undergraduate degrees were in Molecular Biology and in Mathematics (University of Wisconsin-Madison). In 1991, he received a Ph.D. in Genetics from the University of Washington. His research concentrates on the development of statistical techniques for studying DNA sequence evolution.

Dr Simon Whelan, University of Manchester, Speaker

Simon Whelan completed his PhD at the University of Cambridge in 2000. After spending the following six years in or around Cambridge at the Department of Zoology and EMBL-European Bioinformatics Institute he moved to the Faculty of Life Sciences at the University of Manchester in 2006. He works solely on computers and his research mostly focuses on two threads: (i) advancing our understanding of how biological molecules evolve and (ii) how to take this understanding and use it to improve our understanding of evolutionary relationships. His other research uses evolution as a tool for investigating other aspects of biology, including comparative genomics.