Lecturers |
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| Lecturers | Lecturers (evening) | Teaching Assistants | |||
| LECTURERS | |||
| Aidan | Budd | EMBL, Heidelberg, Germany | |
Aidan Budd is a member of staff at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, where he works as a computational biologist in the group of Toby Gibson. He is interested in the evolution and prediction of short protein linear motifs, and in the evolution of individual gene families. Additionally, Aidan is involved in teaching and organising practical courses for researchers, mostly focusing on multiple sequence alignment, phylogenetics, and exploration of protein modular architecture - along with introductory courses for secondary school teachers in bioinformatics. After studying for his undergraduate degree in Zoology at Cambridge University, Aidan worked as a research assistant with Torsten Krude in the lab of Ron Laskey at the Gurdon Institute in Cambridge. He went on to obtain his PhD at EMBL Heidelberg focusing on the evolution of gene families expected to have similar evolutionary histories. Between completing his PhD and rejoining EMBL, Aidan worked as the commissioning editor for life science books at Wiley-VCH in Weinheim, Germany. |
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| Olivier | Gascuel | LIRMM Montpellier, France | |
| Olivier Gascuel first studied mathematics although his PhD was in computer science, and he started working in bioinformatics in the 80's at the verybeginning 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-90's Olivier Gascuel has concentrated on evolution and phylogenetics, with particular focus on the mathematical and computational tools and concepts. He now 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 has published 120 papers and book chapters, and authored several widely used computer programs in phylogenetics and bioinformatics. He has recently started a new adventure fighting pathogens, especially in Africa and endemic countries. |  |
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| Nick | Goldman | EBI, Hinxton, UK | |
| Nick Goldman is a Research Group Leader at the EMBL-European Bioinformatics Institute (EBI) in Hinxton, UK, where his research group studies methods for the analysis of DNA and amino acid sequences to study evolution. Nick studied Mathematics at the University of Cambridge, and has a PhD on statistical methods for studying sequence evolution. He worked at the Natural History Museum, London, the MRC National Institute for Medical Research, London, and the Departments of Genetics and Zoology, Cambridge, before joining EBI in 2002. Contributions to molecular evolution include papers on various statistical methods in phylogenetics, codon models to describe the evolution of protein-coding DNA, the relationships between protein sequence and structure, experimental design in phylogenetics and evolutionary multiple sequence alignment. Further information is available at http://www.ebi.ac.uk/goldman. |  |
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| Javier | Herrero | EBI, Hinxton, UK | |
Javier Herrero is the coordinator of the Ensembl Compara team, the Ensembl sub-group focused on comparative genomics. The Ensembl Compara team is part of the Vertebrate Genomics Team at the EBI. He graduated from the Universidad Complutense de Madrid in Chemistry (specialised in Biochemistry) and completed a PhD in Molecular Biology at the Universidad Autonoma de Madrid under the supervision of Joaquin Dopazo. Javier started his research work at GlaxoWellcome (now GlaxoSmithKline) and moved to the CNIO in 2000. His thesis focused on functional genomics, namely on the analysis of expression array data. He joined the Ensembl Compara team at the EBI in 2004. Most of his work has focused on the multiple genome alignments. He is coordinating the team since 2007. |
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| John | Huelsenbeck | University of California, Berkeley, USA | |
John Huelsenbeck is a Professor of Integrative Biology at the University of California, Berkeley. He received his Ph.D. in Zoology from the University of Texas at Austin in 1995. His research interests are in theoretical phylogenetics and molecular evolution. He is a coauthor of the program MrBayes, a program that is widely used for the Bayesian estimation of phylogeny. |
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| Giorgos | Kotoulas | IMBG-HCMR, Heraklion, Greece | |
| Giorgos Kotoulas is a principal investigator in the Institute of Marine Biology and Genetics (IMBG) at the Hellenic Centre for Marine Research (HCMR) in Iraklio, Crete. He got a bachelor degree in Biology at the Aristotle University of Thessaloniki, Greece, a MSc in Evolution and PhD in population genetics at the University of Montpellier II, France. At IMBG he got involved in intra-specific biogeography of vertebrates and has motivated a team towards interdisciplinary approaches in the study of biodiversity, by means of comparative mapping, functional genomics and genetics. Recent research comprises exploitation of new generation sequencing technologies in the study of structure and function of biodiversity. |
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| Tim | Massingham | EBI, Hinxton, UK | |
| Tim is a Senior Research Officer in the Goldman group (phylogenetic methods and models of sequencing), at the European Bioinformatics Institute. While doing a BA in mathematics, Tim did a summer project on experimental design in phylogenetics and was introduced to the statistical modelling of sequence evolution. After spending a further year gaining a postgraduate qualification in Statistics, he did a PhD at the Department of Zoology, Cambridge, studying methods to detect positive selection in protein-coding sequence. In 2003, Tim joined the Thornton group at the European Bioinformatics Institute, producing annotation of the putative function of proteins as part of the eProtein project; he moved to the Goldman group in 2006 and is currently working on improving the sequence quality produced "next-generation" sequencing machines but maintains a lively interest in evolution and selection, contributing to international consortium such as Encode, 2xMammals and the 1000 Genomes projects. |  |
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| Rasmus | Nielsen | University of California, Berkeley, USA | |
| Rasmus Nielsen is a Professor at the Department of Biology, University of Copenhagen and and Associate professor of Computational Biology at the Departments of Integrative Biology and Statistics, UC-Berkeley. He received his PhD from UC-Berkeley in 1998, worked as a postdoc at Harvard University 1998-2000, and as an assistant professor at Cornell University 2000-2004. His work focuses on development and applications of statistical methods in genetics, particularly evolutionary genetics. He works on problems in population genetics, molecular evolution, molecular ecology and disease genetics. |  |
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| Bill | Pearson | University of Virginia, USA | |
| William Pearson is a Professor of Biochemistry and Molecular Genetics at the University of Virginia School of Medicine, working the area of computational biology and protein evolution. He was the co-author of FASTA, one of the first widely used computer programs for identifying distantly related protein sequences, an approach that is widely used to annotate newly sequenced genomes. His current research focusses on improving methods for identifying distantly related proteins, and quantifying how often nature "reinvents the wheel" through convergent evolution. |  |
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| Mikkel | Schierup | Aahrus University, Denmark | |
| Mikkel H. Schierup is professor in Bioinformatics at the Bioinformatics Research Center at the University of Aarhus, Denmark. He presently heads a group of 4 post. docs., 3 PhD students and 2 student programmers. The research is focused on applying population genetics principles and coalescent theory to comparative genomics and association mapping. Presently, the group is involved in several genome projects, e.g. orangutan, gorilla, bonobo with the aim of understanding the speciation processes and the population genetics of ancestral species by combing phylogenetics and coalescent theory using hidden Markov models. |
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| Alexandros | Stamatakis | Technical University of Munich, Germany | |
Alexandros (Alexis) Stamatakis is a junior research group leader (equivalent to assistant professor) in the Computer Science Department of the Technical University of Munich. In 2004, he received a Ph.D. in Computer Science from the Technical University of Munich. His research concentrates on algorithms, emerging parallel architectures, and high performance computing for evolutionary biology. Alexis is the main developer of RAxML, a code for large-scale phylogeny reconstruction under Maximum Likelihood. |
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| Ziheng | Yang |
Yang, University College London, UK |
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| Ziheng Yang is Professor of Statistical Genetics at Department of Genetics, Evolution, and Environment at UCL. He develops statistical methods and writes computer programs for phylogenetic and population genetic analyses of sequence data. He developed a number of models and methods that are widely used. His current research focuses on dating species divergences incorporating uncertainties in fossil calibrations, coalescent-based statistical methods for analysis of phylogeographic data from several closely related species, and models of protein evolution. He is a Fellow of the Royal Society of London. His book Computational Molecular Evolution has been translated into Chinese and Japanese |  |
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Evening Lecturers |
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| Michail | Averof | IMBB-FORTH, Heraklion, Greece | |
| Michalis Averof is a principal investigator in the Institute of Molecular Biology and Biotechnology (IMBB) in Iraklio, Crete. He obtained a degree in Biology at Trinity College, Dublin, with a thesis in molecular evolution. He turned his interests to comparative developmental biology (evo-devo) during his PhD at the University of Cambridge (1990-94) and post-doc at EMBL Heidelberg (1995-97). He established his own research group at IMBB in 1999, focusing on the evolution of development and morphology in arthropods. |  |
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| Martin | Embley | Newcastle University, UK |
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| Martin is Professor of molecular evolutionary biology at the University of Newcastle in England. His research focuses on the evolution of eukaryotes, their genomes and organelles using computational approaches combined with molecular cell biology. He has a particular interest in the evolution of parasitic protists and the evolution and functions of their minimal mitochondria. |  |
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| Carolin | Kosiol | Veterinary Mdeical University, Vienna, Austria | |
| Carolin Kosiol completed her PhD in Molecular Phylogeny on "Markov process models for protein sequence evolution" at the European Bioinformatics Institute and the University of Cambridge in 2006. During her PhD she estimated the first empirical codon model using Maximum Likelihood techniques. She then pursued a 2-year postdoc at Cornell University working on the detection of natural selection and conducted various inter- and intraspecific scans for signatures of selection in mammals. Recently she started her own research group at the Institute of Population Genetics at the University of Veterinary Medicine Vienna. Her main interest is to study the evolution of protein coding sequences by merging population genetic and phylogentic approaches. |
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| Aoife | McLysaght | University of Dublin, Ireland | |
| Aoife McLysaght is a lecturer in Genetics in Trinity College Dublin where she also leads a molecular evolution research group focussing on vertebrate comparative genomics. http://www.gen.tcd.ie/molevol |
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| Antonis | Rokas | Vanderbilt University, USA |
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| Antonis Rokas in an Assistant Professor in the Department of Biological Sciences at Vanderbilt University. He received his Ph.D. in 2001 from Edinburgh University for research on the evolutionary ecology of oak-feeding gallwasps. Before joining Vanderbilt, he worked at the Broad Institute of MIT and Harvard as a Research Scientist, and at the University of Wisconsin-Madison as a postdoctoral fellow. Research in the Rokas lab combines computational and experimental approaches to investigate the factors influencing phylogenetic accuracy and their usefulness in obtaining more robust phylogenies,the molecular origins of multicellularity in fungi and animals, and the molecular foundations of the fungal lifestyle. Further information is available at http://people.vanderbilt.edu/~antonis.rokas/ |  |
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| Jeff | Thorne | North Carolina State University, USA |
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| 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. iin Genetics from the University of Washington. His research concentrates on the development of statistical techniques for studying DNA sequence evolution. |  |
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| Ken | Wolfe | University of Dublin, Ireland | |
| Ken Wolfe is Professor of Genome Evolution in the Smurfit Institute of Genetics, Trinity College Dublin, Ireland. His PhD research (1989) included the discovery that, in plants, mitochondrial DNA evolves more slowly than nuclear DNA, with chloroplast DNA having an intermediate rate. As a postdoc at Indiana University, Wolfe switched from dry-lab to wet-lab research and sequenced the plastid genome of a non-photosynthetic plant. Returning to Dublin in 1992 as a faculty member, he joined the international collaborative project to sequence the /Saccharomyces cerevisiae/ genome and stumbled upon evidence for an ancient whole-genome duplication in this organism. His laboratory's subsequent research has been focused on genome evolution in eukaryotes, on gene duplication and loss, and on the evolution of gene order within genomes. |  |
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Teaching Assistants |
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| Maria | Anisimova | ETH Zurich, Switzerland | |
Maria Anisimova is a senior research fellow at the Computational Biochemistry Research |
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| Natalie | Cusimano | University of Munich, Germany | |
| Natalie Cusimano is a graduate student in the Lab Group of Prof. Susanne S. Renner at the Ludwig-Maximilians University in Munich. Her PhD thesis is on intron evolution, diversification analyses, phylogenetics and taxonomy of the plant family Araceae. She is scheduled to defend early next year and will then continue on as a postdoctoral researcher with a project investigating karyotype evolution in closely related Araceae taxa. Phylogenetic analyses of molecular data with state-of-the-art programs are the basis for all of her work; she also utilizes and writes programs in the R computational language |  |
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| Clemens | Lakner | Florida State University, USA | |
| Clemens is a biology PhD candidate in Gavin Naylor's group at Florida State University (FSU). He obtained his Masters degree in biology at the University of Vienna in Austria. During an ERASMUS year in Uppsala, Sweden he became interested in problems relating to molecular evolution. Subsequently, he started working with Fredrik Ronquist on problems in Bayesian phylogenetics. For his Masters thesis Clemens implemented and tested different tree update mechanisms for MCMC inference. He participated in the Woods Hole workshop on Molecular Evolution and has been a teaching assistant in Bioinformatics courses at FSU. In 2007 he spent six months at the European Bioinformatics Institute in Hinxton as a Marie Curie fellow in Nick Goldman's group. Currently his main research interest lies in modeling the evolution of proteins. For his PhD project he is further developing stochastic models of evolution that explicitly incorporate protein structural information. Hopefully this can improve our estimates of phylogenetic trees and our understanding of molecular evolution in general. |  |
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