Dr. Stefanie Widder is a computational biologist at the Department of Medicine 1, Medical University of Vienna. Her research focus lies on modeling microbial communities, their organization, function and dynamics. She aims to develop predictive understanding of complex, microbial community functions that find application in human health and related fields. In this context, a strong emphasis lies on identification and inference of microbial interactions from big data resources. Methods applied include network analysis (causal, correlational), process-oriented models (ODEs, individual-based), statistical modeling and bioinformatics. Stefanie aims to bridge between theory and the experimental world to further mechanistic understanding of complex, biological systems.
Katharine Coyte is a mathematical biologist based at Memorial Sloan Kettering Cancer Center in New York. Her research focuses on developing theoretical, computational, and occasionally experimental methods to study the ecology and evolution of microbial communities. In particular Katharine wants to understand how the ways in which members of host-associated microbial communities interact with one another and their host affects the initial assembly and subsequent stability of such microbiome communities.
Elisa Benincà is a theoretical ecologist specialized in complex dynamics of ecological communities. She obtained her PhD from Wageningen University in the Netherlands (2010). During her PhD she studied the dynamics of plankton populations using mathematical models and time series analysis. After that, she worked as postdoctoral fellow at the University of Amsterdam developing models to understand the dynamics of interacting species in benthic communities. Currently, she is working as mathematical modeler at the Centre for Infectious Disease Control at the Dutch National Institute for Public Health and the Environment.
Didier Gonze is a computer biologist from the Unit of Theoretical Chronobiology at Université Libre de Bruxelles. He is interested by non-linear dynamical systems, ranging from genetic networks to microbial population. He is developing and studying mathematical models for circadian clocks in mammals and plants, for the mammalian cell cycle, for cell fate determination during embryonic development in mouse, and for the dynamics of small and large microbial communities. A common goal of all these projects is to unravel links between network structure, dynamical properties (oscillations, multi-stability, etc), and their robustness towards noise and environmental factors. In the context of microbial ecosystems, a particular attention is given to the emergence of complex dynamics and of distinct community types.
Karoline Faust is a biologist turned bioinformatician who graduated at the Humboldt University in Berlin and earned her PhD at the Université Libre de Bruxelles under the supervision of Prof. van Helden. As an FWO-funded postdoctoral researcher in the group of Prof. Raes, she developed tools to infer the structure of microbial communities from sequencing data and contributed to the analysis of large-scale sequencing data sets collected by the Human Microbiome Consortium, the TARA Oceans Consortium and the Flemish Gut Flora Project. She is the main developer of CoNet, a popular Cytoscape plugin for the construction of microbial networks from sequencing data. Her research aims to improve our understanding of microbial community structure and dynamics.
Gipsi Lima-Mendez is a trained biochemist with a PhD in bioinformatics. Her interests are in applying/developing computational methods to gain insights into the mechanisms underlying the evolution and functioning of biological systems, ranging from cellular processes to entire ecosystems. She uses statistical analyses, networks and classification methods to integrate different layers of biological information: genotypes –(meta)genomes, gene expression –(meta)transcriptomes, environmental conditions, etc, and have applied these approaches to studies on the evolution and ecology of mobile genetic elements and to the prediction and discovery of ecological interactions in ocean plankton communities.
|Thomas Sebastian Schmidt
Sebastian Schmidt is a postdoctoral researcher at the European Molecular Biology Laboratory in Heidelberg, Germany. His research focuses on understanding the structure and function of microbial communities across different environments. Using high-resolution metagenomics and related types of meta-omics data, he investigates global patterns in microbial communities, recurring in diverse habitats such as the human body and the ocean. Current projects also include the mechanistic elucidation of clinically relevant microbe-host associations, the re-wiring of microbial interaction networks along biotic gradients and an interpretation of (microbial) diversity in an interaction network context.
I obtained an Engineering degree in biology option environmental technology from Ecole de Biologie Industrielle (EBI, Cergy-Pontoise, France) that I completed by a Master degree in sustainable technology from Université Technologique de Compiègne (UTC, France) in 2009. I moved then to Luxembourg to obtain my PhD in systems biology applied to microbial ecology at the Luxembourg Centre for Systems Biomedicine in 2013 (LCSB, Luxembourg University). My PhD thesis focus on the development of methodologies for integrated multi-omics analyses of complex microbial consortia into metabolic models. From 2013, I moved to the Center for Microbial Ecology and Technology (Cmet, Ghent University, Belgium) where I developed molecular biology methodologies and bioinformatics tools to characterize mixed microbial communities involved in various sustainables technologies using targeted and shotgun metagenomics analysis. I have been recently nominated as research engineer and operational manager of a high-throughput next generation sequencing platform dedicated to quantitative metagenomics for the characterization of the human gut microbiota at MetaGenoPolis Unit (www.mgps.eu) of the French National Institute for Agricultural Research (INRA).
Leo Lahti is an Adjunct Professor in applied mathematics University of Turku, Finland, focusing on ecological modeling of the human microbiome in large population cohorts. He obtained doctoral degree in bioinformatics in the Department of Computer Science, Aalto University, Finland in 2010, developing statistical machine learning methods for data integration in functional genomics. He is currently a visiting researcher in VIB/KU Leuven, Belgium.
Jing Tang is a Group leader at the Institute for Molecular Medicine Finland and Docent in biometry at University of Helsinki, Finland. He obtained his PhD in Statistics from University of Helsinki (2009) when he developed Bayesian model-based clustering methods for identifying population structures in bacteria. His recent research focuses on computational pharmacology modeling, aiming at a systems-level understanding of how cancer pathways can be inhibited by synergistic drug combinations through multi–target perturbations. He has developed a series of computational approaches for drug combination prediction, modeling and testing. He is particularly interested in personalized cancer medicine by integrating molecular biology and pharmacology data using mathematical modeling and machine learning. More information about his group: http://cosphar.utu.fi
Miguel A. Fortuna obtained a PhD in Biology by the University of Seville (Spain) in 2009, supervised by Prof. Jordi Bascompte. After that, he was awarded a postdoctoral Marie Curie Outgoing International Fellowship by the European Union (2009-2012) for working with Prof. Simon Levin at Princeton University (USA). Currently, he is as postdoc at the Department of Evolutionary Biology and Environmental Studies, at the Unversity of Zurich (Switzerland). He is interested in understanding how evolution shapes the architecture of species interaction networks.
Vasilis Dakos is a theoretical-quantitative ecologist broadly interested in ecosystem resilience and tipping points under environmental change. He has been using simple models to develop statistical tools for detecting tipping points in climate records, semi-arid ecosystems, plankton populations, or plant-pollinator networks. He obtained a PhD from Wageningen University in the Netherlands, and has worked in the Biological Station of Doñana in Spain, and in ETH in Switzerland. Currently, he is senior CNRS researcher in the Institute of Evolution in Montpellier, France.