Genomic population structures of microbial pathogens

Zhemin Zhou graduated from Nankai University in China in 2010 and spent 2 years as a Research Fellow at University College Cork in Ireland before moving to the University of Warwick in 2013. His research interests focus on using bioinformatics to investigate the evolutionary history of bacterial pathogens, such as typhoidal salmonellae and Vibrio cholerae. Looking backward to the history of pathogens reveals not only the current genetic diversity of these microbes but also their historical relationships with human beings. In particular, together with Professor Mark Achtman, they developed EnteroBase, which is an extensive, publicly accessible bacterial genomic database. Fine-grained core genome multi-locus sequence typing (cgMLST) schemes have also been developed to extract information content from EnteroBase. These cgMLST schemes, as well as the catalogued population structures of the pathogen, have been used for epidemiological tracking and influenced the recent developments of public health system.

Tanja Stadler is an Assistant Professor at the Department of Biosystems Science and Engineering of the Swiss Federal Institute of Technology (ETH Zürich) in Basel since 2014. Tanja studied Applied Mathematics at the Technical University of Munich (Germany), the University of Cardiff (UK), and the University of Canterbury (New Zealand). She obtained a Master degree in 2006 and a PhD in 2008 from the Technical University of Munich (with Prof. Anusch Taraz and Prof. Mike Steel). Tanja then joined ETH Zürich as a postdoctoral researcher with Prof. Sebastian Bonhoeffer in the Department of Environmental Systems Sciences, and was promoted to Group Leader in 2011. Her work is at the interface of mathematics, computer science, evolution, ecology and infectious diseases. In particular, she develops phylogenetic tools to address epidemiological and medical questions, as well as questions in the fields of ecology, species evolution, cell differentiation and language evolution. Her honors include the TUM PhD award 2008, the John Maynard Smith prize 2012, the ETH Latsis prize 2013, and the Zonta prize 2013. In 2013, Tanja received an ERC starting grant.

Philippe Lemey completed his PhD in Medical Sciences (2005) at the KU Leuven, Belgium, focusing on the evolutionary and population genetic dynamics of retroviruses. As a Marie-Curie postdoctoral fellow, he joined the Evolutionary Biology group at the Department of Zoology, University of Oxford. In 2007, he returned to the Rega Institute, KU Leuven, where he took up a tenure-track faculty position in 2010. His research interests include the evolutionary processes that shape viral genetic diversity, spanning large-scale epidemic processes as well as small-scale transmission histories and within-host evolutionary processes. He is the senior editor of the second edition of the Phylogenetic Handbook and a two-time ERC grant awardee. His team is part of the ARTIC consortium (http://artic.network) and contributes to BEAST (http://beast.community) software. These developments include phylogenetic diffusion models, molecular clock models and Bayesian model testing procedures.

Julia Gog is the Professor of Mathematical Biology at the Department of Applied Mathematics and Theoretical Physics, University of Cambridge. She is also the David N Moore Fellow at Queens’ College, Cambridge. Julia’s research interests are mainly in the dynamics and evolution of influenza. Part of her work is at the mathematical theory end, particularly in developing tractable approaches to modelling multiple strains and pathogen evolution, and also bioinformatic methods for application to viruses. Recent projects have also included using data to understand the spatial patterns of influenza spread in the US. In 2018, Julia and her research team appeared in a BBC documentary in 2018, which explored pandemic modelling and engaged the UK public in a large project to collect data on human movement and interaction.

Tami Lieberman completed her PhD in Systems Biology from Harvard University. Working in Roy Kishony’s laboratory, she studied bacterial evolution during human infections at the whole-genome level and developed experimental tools for understanding the evolution of antibiotic resistance. As a postdoc in Eric Alm’s laboratory at MIT, she applied genomic tools developed during her PhD to commensal bacteria. Dr Lieberman started as an Assistant Professor at MIT in 2018. 

The Lieberman Lab is uncovering the determinants of bacterial colonization in human microbiomes. Microbial-based therapies hold great promise for improving human health. However, they remain difficult to design, as we cannot predict which strains will stably colonize an individual. Dr Lieberman’s group seeks to close this knowledge gap, developing a mechanistic understanding of how individual strains behave in human microbiomes – including selective pressures they face, their niche ranges and survival strategies, and the degree to which they adapt within individuals microbiomes.

Dr A Murat Eren (Meren) and his group (http://merenlab.org) study microbial life through the lens of environmental DNA and RNA molecules. From human guts to insect ovaries and surface oceans, Meren Lab uses computational and wet-lab strategies to shed light on ecological and evolutionary processes that lead to the emergence of complex traits that microbes need to keep up with their ever-changing environments. Meren is a Fellow of the Marine Biological Laboratory, Faculty of the Committee on Microbiology, and an Assistant Professor at the Department of Medicine, University of Chicago.

Tandy Warnow is the Founder Professor of Computer Science at the University of Illinois at Urbana-Champaign. Tandy received her PhD in Mathematics at UC Berkeley under the direction of Gene Lawler, and did postdoctoral training with Simon Tavaré and Michael Waterman at USC. Her research combines computer science, statistics, and discrete mathematics, focusing on developing improved models and algorithms for reconstructing complex and large-scale evolutionary histories in biology and historical linguistics. She has published more than 160 papers and one textbook, graduated 11 PhD students, and has 5 current PhD students. Her awards include the NSF Young Investigator Award (1994), the David and Lucile Packard Foundation Award (1996), a Radcliffe Institute Fellowship (2006), and the John Simon Guggenheim Foundation Fellowship (2011). She was elected a Fellow of the Association for Computing Machinery (ACM) in 2015 and of the International Society for Computational Biology (ISCB) in 2017.

Professor Jukka Corander is particularly interested in microbial evolution and transmission modeling, statistical machine learning, genomics and Bayesian inference algorithms. He received the ERC Starting grant 2009 – 2014 and is currently leading an ERC Advanced grant project SCARABEE (2017 – 2022) for evolutionary epidemiology. The statistical methods introduced by Corander’s group have led to numerous discoveries on the evolution, resistance, virulence and transmission of pathogenic bacteria and viruses. These methods include software packages for population structure and recombination inference, GWAS and genome-wide epistasis analysis.  

Eduardo Rocha did MScs in Chemical Engineering and Applied Maths, a PhD in Bioinformatics and an Habilitation in Biology. He is a senior researcher at CNRS and head of the Microbial Evolutionary Genomics unit at Pasteur Institute. He is a Specialist in comparative genomics, in particular in the use of bioinformatics and biostatistics techniques to study microbial evolution. His research aims at understanding how and why genomes are organized, and how such organizational features evolve in respect to genome dynamics. In the last decade, his work has focused on the role of mobile genetic elements in driving their host evolution through horizontal gene transfer and how that affects the genomes of both Bacteria and their mobile elements.

Caroline Colijn works at the interface of mathematics, evolution, infection and public health. She joined SFU's Mathematics Department in 2018 as a Canada 150 Research Chair in Mathematics for Infection, Evolution and Public Health. She did her PhD in applied mathematics at the University of Waterloo, where she studied the foundations of quantum mechanics. She changed tack in her postdoctoral years, working on mathematical modelling of blood disorders at McGill and on tuberculosis dynamics and evolution at the Harvard School of Public Health and the Broad Institute at MIT. She moved to the Department of Engineering Mathematics in Bristol, England in 2007 and joined Imperial College London's Department of Mathematics in 2011. She has broad interests in applications of mathematics to evolution and public health.

Xavier Didelot is Professor of Statistical Epidemiology and Genomics at the University of Warwick. He studied for his doctorate at the University of Oxford, and carried postdoctoral research work in Warwick and Oxford. He also previously worked for several years in the Department of Infectious Disease Epidemiology at Imperial College London. Xavier Didelot's research is concerned with understanding the way bacterial pathogens evolve, spread and cause disease. He has analysed both epidemiological and genomic data from a wide range of bacteria, especially those causing healthcare associated infections and gastrointestinal infections. A key aim is to develop new bioinformatics and statistical methods that can handle the very large amounts of data made available by novel high-throughput sequencing techniques. Xavier Didelot is the author of ClonalFrame which is a phylogenetic method that accounts for the effect of recombination and TransPhylo which is a method that reconstructs transmission events from genomic data.