Instructors

 

Andre J. Aberer

Heidelberg Institute for Theoretical Studies, Germany

Andre Aberer is a PhD student in Alexandros Stamatakis' research group. He obtained a Master's degree in bioinformatics from the Ludwig-Maximilians-University and Technical University of Munich. In his PhD project, he developed an efficient algorithm for rogue taxon identication (RogueNaRok) and a fast forward-in-time simulation tool for population genetic datasets (AnA-FiTS). Furthermore, he is interested in large-scale Bayesian sampling of phylogenetic trees.

Maria Anisimova
Institute of Applied Simulation, Zurich University of Applied Sciences, Switzerland

Maria Anisimova is an associate research fellow and lecturer at the Institute of Applied Simulations (Zurich University of Applied Sciences, ZHAW), where she is currently establishing a new research direction in applied computational genomics. Maria has a degree in mathematics from the Pedagogical State University of Nizhny Novgorod, Russia. After teaching geometry and mathematics for finance and business in London, she obtained an MRes in modeling biological complexity (CoMPLEX) and a PhD in statistical genomics under the supervision of Prof Ziheng Yang (Biology department), both at the University College London. During her PhD Maria worked on methods for detecting adaptive evolution on the protein-coding genes. Postdoctoral work included large-scale data analyses of viral and bacterial genomes with Prof Yang and statistical tests for clade supports with Prof Olivier Gascuel (LIRMM) at the Universit Montpellier II, France. Maria's current research interests involve applications of stochastic modeling of molecular evolution and computational genomics to spheres of medicine, pharmacology, biotechnology and agriculture.

Aglaia (Cilia) Antoniou
Ιnstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece

Aglaia Antoniou is a postdoctoral researcher at the Institute of Marine Biology and Genetics (HCMR; http://www.hcmr.gr/listview3.php?id=35). She is a biologist with a long-time interest in Evolutionary Biology, especially in the field of Population and Landscape Genetics, Phylogenetics, and Phylogeography. In 2008, she received a PhD in population and landscape genetics from the Biology Department of the University of Crete, Greece. Her current research focuses on the landscape genetics of marine animals by merging population genetics and phylogenetic approaches in space and time.

Aidan Budd
European Molecular Biology Laboratory (EMBL), 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.

Martin Embley
Institute for Cell and Molecular Bioscience, Medical School, Newcastle University, UK

Martin Embley is Professor of Molecular Evolution at Newcastle University. His current and long-term research interests are on the early evolution of eukaryotes and the evolution and functions of their organelles, particularly of mitosomes and hydrogenosomes. These are peculiar forms of mitochondria found in anaerobic and obligate intracellular parasitic protists. His lab also participated in the analysis of lateral gene transfer as it affects the genomes of major protozoan parasites.

Prof. Embley is an Associate Editor of Genome Biology and Evolution, a Fellow of the American Academy of Microbiology, a Royal Society Wolfson Research Merit award holder and a Member of the European Molecular Biology Organisation.

Olivier Gascuel
The Montpellier Laboratory of Computer Science, Robotics, and Microelectronics, 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 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-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, (HIV, malaria, leishmania...), especially in Africa and endemic countries.

Nick Goldman
EMBL - European Bioinformatics Institute, UK

Nick Goldman is a Research Group Leader at the EMBLEuropean 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, evolutionary multiple sequence alignment and various large-scale comparative genomics projects. Further information is available at www.ebi.ac.uk/goldman.

Tracy Heath

University of California Berkeley and University of Kansas, USA

Tracy Heath is currently a postdoctoral researcher in the Department of Integrative Biology at UC Berkeley and in the Department of Ecology and Evolutionary Biology at the University of Kansas, working with John Huelsenbeck and Mark Holder. She received her PhD in evolutionary biology at the University of Texas at Austin. Tracy's primary research interests are in macroevolution, Bayesian phylogenetic inference, and molecular evolution. Her current work focuses on developing, testing, and applying Bayesian inference methods for fully integrating genomic data and information from the fossil record to reconstruct phylogenetic relationships and estimate the timing of lineage

divergence events. For more information see http://phylo.bio.ku.edu/content/tracy-heath.

John Huelsenbeck
UC 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.

Paschalia Kapli

Biology Department University of Crete, Greece

Paschalia Kapli is a PhD candidate at the Natural History Museum of Crete. She is working on molecular phylogeny and phylogeography mainly of reptile taxa. She has studied Biology and obtained her M.Sc. in Environmental Biology at the University of Crete.

Adam Leaché
Department of Biology & Burke Museum, University of Washington, USA

Adam Leaché is an Assistant Professor in the Department of Biology at the University of Washington, and the Curator of Genetic Resources and Herpetology at the Burke Museum of Natural History and Culture. Research in his lab is focused on the evolutionary biology and systematics of amphibians and reptiles. Topics of interest include species tree inference, statistical phylogeography, Bayesian species delimitation, and comparative biology.

Adam received his PhD from the University of California, Berkeley in 2008, where he worked in the Museum of Vertebrate Zoology studying speciation, phylogeography, and hybridization in North American lizards. He received an NSF Bioinformatics Postdoctoral Research Fellowship and worked with Bruce Rannala on statistical aspects of species tree inference and species delimitation. Further information is available at faculty.washington.edu/leache/wordpress.

Brian Moore
UC Davis, USA

My primary research interests focus on developing quantitative methods for phylogeny estimation and for making phylogenybased inferences related to various evolutionary processes (particularly inference problems associated with differential rates of lineage diversification and historical biogeography), exploring the statistical behavior of these methods via simulation, and applying them to empirical data to explore fundamental evolutionary problems in flowering plant evolution.

Laura Emery

European Bioinformatics Institute, Hinxton, UK

Laura is a Scientific Training Officer at EMBL-EBI. She completed her undergraduate degree in Genetics at the University of Nottingham. After dabbling in experimental work on a summer placement at the Wellcome Trust Sanger Institute, she found joy in using computer-based analyses to explore biological questions. Laura completed her PhD in Evolutionary Genetics at the University of Edinburgh’s Institute of Evolutionary Biology. There she used a bioinformatics approach to investigate patterns of codon usage in Archaea while under the supervision of Prof Paul Sharp FRS. She also worked as a postdoc at the University of Manchester, where she explored molecular co-evolution among interacting proteins with Dr Simon Whelan. Having obtained qualified teacher status (QTS), Laura joined EMBL-EBI in 2012 and is responsible for the development and delivery of training courses.

Sarah Parks
European Bioinformatics Institute, Hinxton, UK

Sarah Parks is a PhD student in Nick Goldman's group at the EBI. She obtained an undergraduate degree in Mathematics from the University of Cambridge and then completed a Masters in Computational Biology. Her research focuses on theoretical phylogenetics.

Pavlos Pavlidis
Institute of Molecular Biology and Biotechnology Heraklion, Greece

Pavlos Pavlidis received his PhD from University of Munich (Ludwig Maximilians University) in the lab of Prof. Wolfgang Stephan. During his PhD he worked on population genomics of natural populations of Drosophila melanogaster. Specifically, he was interested in disentangling adaptation by positive selection of beneficial mutations from stochastic non-adaptive processes such as random genetic drift. Following graduation, he worked as a postdoctoral fellow in the lab of Prof. Alexandros Stamatakis at HITS gGmbH in Heidelberg, where he optimized algorithms related to detecting positive selection in whole-genome datasets. His current research interests are related to population genomics and bioinformatics. Specifically, he is interested in understanding the evolution of gene regulatory networks by means of random genetic drift and positive selection. Furthermore, he is conducting research on the analysis of microarray data focusing on understanding the effects of certain genes on the expression levels of other genes.

Bruce Rannala
Genome Center and Department of Evolution and Ecology, University of California, USA

Bruce Rannala is currently a Professor in the Genome Center and Department of Evolution and Ecology at UC Davis. He previously held positions on the faculty of SUNY Stony Brook and the University of Alberta and is currently a guest professor at the Chinese Academy of Sciences, Beijing and at Chiang Mai University, Thailand. In 2001, he was the Canadian Institutes of Health Research Peter Lougheed Scholar and in 2009 he was appointed as a Miller Professor at UC Berkeley.
Bruce Rannala's principal research interests include statistical aspects of population genetics and phylogenetic inference. He made early contributions to the development of Bayesian methods for phylogenetic inference, population genetic inference of fine-scale recombination rates and ages of mutations, and individual-based assignment methods and migration rate inference. Bruce Rannala received a B.Sc. in Zoology from the University of British Columbia in 1989 and a Ph.D. in Biology from Yale University in 1995. He was an NSERC postdoctoral fellow at UC Berkeley.

Benjamin Redelings
National Evolutionary Synthesis Center, North Carolina, USA

Benjamin Redelings is a postdoc at the National Evolutionary Synthesis Center (NESCent) in in Durham, NC. Ben is interested in mathematical models of protein sequence evolution, and hopes to make them more biologically realistic while remaining computationally tractable for estimating evolutionary trees. He has focused on Bayesian methods for estimating multiple sequence alignments and phylogenetic trees via MCMC. He received his Ph.D. in 2006 from the Biomathematics Department at UCLA. www.duke.edu/~br51

Antonis Rokas
Department of Biological Sciences, Vanderbilt University, USA

Antonis Rokas in an Assistant Professor 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 as.vanderbilt.edu/rokaslab

Stephen A. Smith

University of Michigan, USA

Stephen A. Smith is an evolutionary biologist at the University of Michigan, Ann Arbor in the Department of Ecology and Evolutionary Biology and affiliated with the Department of Computational Medicine and Bioinformatics. He received his doctorate from Yale University while working on methods for reconstructing biogeographic scenarios on phylogenies and developing methods for large scale data set construction. Through that work, he became interested in addressing broad evolutionary questions, especially in plants. He currently works on methods for incorporating next generation sequencing data into phylogenetic analyses. Specifically, he works on ways to better analyze transcriptomes from diverse non model species in a phylogenetic context. Also, starting with work that began during his graduate work, he continues to examine shifts in the rate of molecular evolution and detecting areas on the phylogeny where that has occurred. Finally, he is currently working on the Open Tree of Life project and developing ways to construct a draft and facilitate the construction of the whole tree of life.  

Tanja Stadler

ETH Zürich, Switzerland

Tanja Stadler is a group leader at ETH Zürich (Switzerland) since 2011. Tanja obtained a PhD in Mathematics from TU München (Germany) in 2008, and then was a postdoc in the Institute of Integrative Biology at ETH Zürich. Her work aims at understanding past evolutionary and epidemiological processes by looking at genetic sequencing data. This understanding is obtained through developing novel phylogenetic methodology, which becomes available as independent R packages and within the software package Beast. In particular, Tanja developed methodology to reliably estimate major shifts in past speciation and extinction rates, as well as to quantify the severity of spread of an emerging viral disease.

Alexandros Stamatakis
Heidelberg Institute for Theoretical Studies, Germany

"Alexandros (Alexis) Stamatakis studied computer science at TU Munich and ENS Lyon (with internships in Athens, Paris, and Madrid). In 2001 he received his diploma in computer science from TU Munich. In 2004 he received his PhD (also at TU Munich) for work on algorithms and parallel computing for phylogenetic inference (reconstruction of evolutionary trees using DNA data).

He continued working in the area of evolutionary Bioinformatics and parallel computing as a PostDoc at the Institute for Computer Science in Heraklion Greece (2005-2006) and at the Swiss Federal Institute of Technology at Lausanne (2006-2008).

In early 2008 he returned to Munich to start his own independent junior research group (DFG Emmy-Noether grant), initially at LMU and then at TU Munich.

In fall 2010 he moved to the Heidelberg Institute for Theoretical Studies (HITS) to start his new job as permanent research group leader of the scientific computing group that also entails the management of the entire IT & HPC infrastructure at HITS.

In 2012 he was appointed as adjunct professor at the Dept. of Ecology and Evolutionary Biology at the University of Arizona at Tucson and as full professor at the faculty of computer science of the Karlsruhe Institute of Technology. Both appointments are in conjunction with his position at HITS.

His main research interests are algorithms, parallel computing, parallel architectures and evolutionary Bioinformatics.

Jeff Thorne
Genetics and Statistics Departments, North Carolina State University, USA

Jeff Thorne is a professor in the Genetics and Statistics Departments of North Carolina State University. He was born in 1963 and 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. - Address: 311 Ricks Hall, Bioinformatics Research Center, North Carolina State University, Box 7566, Raleigh, NC 27695-7566, USA. E-mail: thorne@statgen.ncsu.edu

Ziheng Yang
Department of Genetics, Evolution and Environment, University College London, UK

Ziheng Yang is RA Fisher Professor of Statistical Genetics in University College London. After finishing his Ph. D. in Beijing Agricultural University, he worked as a postdoctoral researcher in Cambridge, London, and the USA, before taking up a faculty position in UCL in 1997. He was elected a fellow of the Royal Society in 2006. He develops statistical models and write computer programs for comparative analysis of DNA and protein sequence data in molecular evolution, molecular systematics, and population genetics. His contributions includes models of variable rates among sites, likelihood method of ancestral reconstruction, codon models, Bayesian methods of phylogeny reconstruction and divergence time estimation, partition and mixed models for analysing multi-gene datasets, and Bayesian computational analysis of phylogeographic data under the coalescent model. He maintains a computer program package called PAML. He published >100 papers and a book titled Computational Molecular Evolution (Oxford, 2006). Further information about his research is available at abacus.gene.ucl.ac.uk.