Members: Please place your sketch in alphabetical order by last name
(Use the Heading 3, not boldface, setting for the line with your name on it.)

Anne-Florence Bitbol

I am a Postdoctoral Research Fellow at the Lewis-Sigler Institute for Integrative Genomics at Princeton University (New Jersey, USA). I work in the Theoretical Biophysics Group, with Ned Wingreen and William Bialek.
I have broad research interests in biophysics. In the field of evolution, I have been studying quantitatively the effect of population subdivision on fitness valley crossing with David Schwab. I am also working on the self-assembly of protein complexes, and on fundamental constraints on biological signaling networks.
My background is in physics, and I worked on the theoretical physics of complex biological membranes for my PhD, which I completed at Universite Paris-Diderot (Paris, France) under the supervision of Jean-Baptiste Fournier.

Hanrong "Ron" Chen

I am a PhD student in Applied Physics at Harvard, and my advisor is Mehran Kardar at MIT. Right now, I am developing computational tools to study the evolutionary trajectories of viral sequences in a fitness landscape. The goal is to apply this to fitness landscapes inferred from patient-derived HIV sequence prevalence data, to predict the evolutionary trajectories of a HIV population in response to a drug, and to better inform treatment and vaccination strategies.

Tom Chou

I am a professor in the Depts. of Biomathematics and Mathematics with a background in statistical physics and applied mathematics. My current research interests include population modeling, stochastic processes, and cellular biophysics.

Arjan de Visser

I am associate professor at the laboratory of Genetics at Wageningen University (Netherlands). I am broadly interested in the causes and constraints of evolution, in particular the interplay between fitness landscape topography and population dynamics. We use experimental evolution with bacteria, yeast and multicellular fungi to address these issues, and closely collaborate with theoreticians to get the most out of experiments. A major theme presently is the evolution of antibiotic resistance, for which we use TEM beta-lactamase both in in vitro and in vivo evolution experiments.

J.J. Dong

I am an assistant professor at Bucknell University. My research lies at the interface of statistical physics and biological physics. I have worked on modeling transcription and translation, evolution of codon bias in bacteria and ventured a wet-lab experiment on the effects of ionizing radiation to embryos. I look forward to learning more about the emergence of drug resistance from both the evolution perspective and at the population level.

Maria D'Orsogna
I am an Associate Professor of Mathematics at the California State University at Northridge. I am trained as a theoretical physicist and work on modeling of biological and social systems using methods from statistical physics, stochastic processes, game theory and PDEs. I have worked on mechanistic models for viral dynamics and entry into cells, nucleation and clustering in biology, swarming and collective behavior of many particle systems, filament growth. I have also worked on models of crime, including the creation of criminal hotspots, recidivism and rehabilitation of repeat offenders, and the formation of crime networks.

Tim Downing

I am a lecturer at NUI Galway in Ireland in the Bioinformatics part of the School of Maths. My research interests focus on using genomics, population genetics and evolutionary modelling of DNA sequences to infer the origin, spread and phylogeography of infectious diseases. This includes the experimental evolution of drug resistance in Leishmania parasites and in S. aureus, and the population genomics of infected patients in Leishmania and in E. coli. I also dabble in pathogen genome assembly, plant/livestock population genomics and differential gene expression. I am here to learn about mathematical and computational modelling of molecular data and am in room 2323.

Marie-Cécilia Duvernoy

I am a PhD student sharing my time between two labs in France : the ABCD group at the Statistical Physics Laboratory of the Ecole Normale Supérieure in Paris and in the Complex Fluid Dynamics and Morphogenesis group (DyFCoM) at the LIPhy in Grenoble. I am currently studying the mechanics underlying the formation of a bacterial biofilm. To do so, I adapted an experimental method usually used for eucaryotic cells allowing us to measure directly the forces applied by a growing microcolony on its substrate. With it and other experiments, we are trying to find out how a confined microcolony of different strains (E. Coli and P. aeruginosa) take shape and what are the biological mechanisms implied in this process.

Chris Field

I am a postdoc in Erik van Nimwegen's Lab at the University of Basel. I studied Control Engineering at the University of Cambridge, but transitioned into Microbiology for my PhD there, working in plasmid biology. I'm now working on a project with a collection of naturalised E. coli strains dug out of lake watershed soil in Minnesota. We're interested in their phylogeny, diversity of gene content and phenotypes. The big question is: what might we be able to deduce about how they have been selected historically based on what we can observe about them now, and what constraints or trade-offs involved in that process. I'm here for the QBio school, and hoping to learn more about how to approach evolutionary questions like this one.

Matteo Figliuzzi

I am a Postdoc at Laboratory of Computational and Quantitative Biology of Université Pierre et Marie Curie in Paris and my background is in Statistical Physics and Quantitative Biology. My current research concerns the prediction of phenotypic fitness landscapes combining coevolutionary and structural information via statistical inference methods. In the specific, taking a beta-lactamase enzyme in E-coli as model system, I am studying the impact of mutations on bacterial antibiotic resistance.

Julia Kamenz

I am a PhD student in Silke Hauf's lab (we recently moved to Virginia Tech) and a biochemist by training. Our lab is interested in understanding the mechanisms ensuring faithful segregation of chromosomes to the newly arising daughter cells during every cell division. To this end we combine molecular biology and yeast genetics with quantitative microscopy and mathematical modeling. My current research addresses the question how a robust temporal coordination of the events during cell division is achieved in fission yeast (S. pombe). Beyond my immediate research, I am generally interested in the mechanisms and evolution of cellular networks, especially in the context of cellular decision making. I am particularly looking forward to gain some experience with microfluidics devices during the course.

Greg Huber

I am a biophysicist and a Deputy Director at the KITP. I like cheese and yeast (S. pombe).

Chris Graves

I am a PhD student in Dan Weinreich's Lab at Brown University and a participant in the qbio course here at KITP. My research is centered around adaptation to varying environments and involves a combination of quantitative modeling and experimental evolution. Current projects include applying theory of adaptation to varying environments to problems in infectious disease evolution and experimental evolution of bet-hedging in budding yeast.

Mehran Kardar

I am a statistical physicist at MIT. In the context of this program, I am interested in extracting fitness landscapes for HIV proteins from patient derived sequences, and using such data for inferring compensatory mutations related to drug resistance.

Johannes Knebel

I am a PhD student with Erwin Frey in Munich, Germany. My research focuses on the application of methods from evolutionary game theory to problems and phenomena in biology and condensed matter physics (work done together with Markus ). I am particularly interested in theoretical models for the evolution of microbial cooperation and phenotypic heterogeneity in bacteria. From a mathematical point of view, the interplay between nonlinear dynamics, stochasticity, and spatial degrees of freedom are appealing to me. It will be fun to try myself out with some experiments during the QBIO summer course.

Gwen Knight

I am a Research Fellow at the London School of Hygiene and Tropical Medicine, UK. My work involves building mathematical models of the spread of the bacterium Mycobacterium tuberculosis that have public health relevance. Currently, I am working on a project investigating how resistance to new drug regimens for tuberculosis (TB) might be prevented from arising and spreading. I am also interested in how drug resistance affects bacterial fitness and am trying to build simple models of fitness evolution over time, building on work from my PhD on antibiotic resistance within Staphylococcus aureus.

Katia Koelle

I am an Associate Professor in the Department of Biology at Duke University in Durham, North Carolina. My group studies the interplay between the population dynamics and the evolutionary dynamics of infectious diseases, most notably rapidly evolving viral pathogens such as influenza and dengue. Our research involves the development of mathematical dynamical systems models to understand patterns of viral evolution as well as the development of statistical approaches to quantitatively interface these models against time series data and viral sequence data.

Sasha Levy

I am and Assistant Professor at the Laufer Center for Physical and Quantitative Biology at Stony Brook University in New York. My group studies
how cell populations cope with and adapt to environmental change. A core focus of our lab is the continuing development of high-throughput technologies that track large numbers of cell lineages in competing populations to determine their relative fitnesses and evolutionary trajectories. In collaboration with theorists, we use these measurements to quantitatively describe the adaptive process of large populations. We are also using these technologies to study how environmental fluctuations shape evolutionary strategies, how genetic and protein-protein interaction networks change across environments, and how epistasis impacts the adaptive process.

Richard J. Maude

I am a senior clinical research fellow at the University of Oxford based in Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand and visiting scientist at Harvard School of Public Health. My research is on mathematical modelling and epidemiology of artemisinin-resistant P. falciparum malaria. I also run clinical and epidemiological studies on the pathogenesis and treatment of severe malaria.

Michael Mwangi
I am an Assistant Professor in the Department of Biochemistry and Molecular Biology and the Center for Infectious Disease Dynamics at Penn State University. I am interested in better understanding antibiotic resistance in a variety of bacterial pathogens including MRSA and ESBL-producers. Reflecting my background in physics, my lab is very quantitative and so tends to attract post-docs and students not only in traditional microbiology but also in physics, mathematics, and computer science. Our projects range from dissecting the molecular mechanisms of antibacterial resistance in a single cell to understanding the epidemiology of emerging pathogens across a country. A prominent feature of our work is next-generation-sequencing (e.g. Illumina and PacBio).

Richard Neher

Richard is a group leader at the Max Planck Institute for Developmental Biology in Tuebingen, Germany. Our lab studies virus evolution and works on population genetics theory. Most of us work on HIV evolution, but we have recently become interested in predicting influenza virus evolution (see here for recent preprint) and the evolution of antibiotic resistance in Pseudomonas. We are interested in collaborations with clinicians and public health organizations and hope to apply our experience with intra-patient evolution of HIV and deep sequencing of virus population to other organisms.

Erik van Nimwegen

I am Associate Professor for Computational Systems Biology at the Biozentrum of the University of Basel, Switzerland. Our lab studies the functioning and evolution of gene regulatory networks in organisms from E. coli to human. On the hand we develop computational tools for inferring gene regulatory networks from comparative genomic and other high-throughput biological data, see this work for a recent example. Another interest of our group is quantitative laws in microbial genome evolution. On the other hand, although I am a theorist by training, in the last 4 years I have also started a wet lab where we are focusing on single-cell gene regulation and genome evolution in E. coli (here is a preprint of a manuscript that we just finished on the relation between gene expression noise and the evolution of gene regulation). For an overview of all recent work from my group, visit my google scholar page.

Ulrich Nübel

I study the evolution of bacterial pathogens, especially those that cause healthcare-associated infections (e. g., Staphylococcus aureus, Clostridium difficile, multiresistant enteric bacteria). We and others only recently discovered that natural populations of bacteria may accumulate measurable genetic variation over epidemiological timescales, which we have exploited to track their spatial spread and resistance development. In June 2014, I started as head of a newly founded research group on microbial genomics at the Leibniz Institute DSMZ and as an associate professor at the Technical University in Braunschweig, Germany. I am particularly interested in the mechanisms and constraints of bacterial evolution, and during the workshop I hope to learn about theoretical and experimental approaches to this topic.

Shaul Pollak

I am a PhD student at the lab of Avigdor eldar in Tel-Aviv univerisity. Our lab is interested in understanding the design principles of cooperative behavior in bacteria. More specifically, we focus on how bacterial communication (also known as quorum sensing) is involved in the regulation of cooperation. Our aim is to elucidate the impact of social structure, spatial form and phenotypic hetrogeneity on the development of cooperation and its evolution. My project is concerned with understanding how horizontal gene transfer affects the evolutionary dynamics of social traits. More specifically, my current project is concerned with trying to elucidate the evolutionary mechanisms that underly the pervasive variably encountered when looking at bacterial Quorum sensing systems.

Orso Maria Romano

My background covers Physics and Biology. My past research projects span from DNA replication in yeast, to RNA transcription in bacteria, and to evolutionary game theory applied to the evolution of phenotypic switches. I am currently a 1st-year Ph.D. student, supervised by Silvia De Monte at the Eco-Evolutionary Mathematics Lab of the Institute of Biology of ENS Paris, and in collaboration with Paul Rainey. My doctorate thesis is focused on theoretical quantitative and predictive models applied to the evolution of social phenotypic switches in microbial population. The theoretical work is accompanied by experimental activity on Pseudomonas fluorescens, especially on the characterization of its switching behaviours and epigenetic inheritance mechanisms.

Xinxian Shao

Xinxian is a PhD student in Ilya Nemenman's group at Emory University, also collaborating with Bruce Levin's Lab EcLF. My current research interests include theoretical modelling of bacterial population and experimental studies of colonies grown in/on physically structured habitats. I built a minimal model for E.coli colony growth in 3D and obtained preliminary data from the experiments I designed. Our next goal is to investigate more about bacterial colonies at single cell level, such as phenotypic heterogeneity and physiological states of the cells in a colony.

Lloyd Ung

Lloyd is a PhD candidate working with David Weitz (weitzlab) at Harvard University. His work focuses on the development of high-throughput microfluidic screening methods and instrumentation with applications in the directed evolution of proteins and organisms. He has been involved in the development of a droplet microfluidic screening method for cellulases with high activity, using an enzymatic cascade; studies of prion induction in yeast, including interactions with wild-type bacteria (in collaboration with the Lindquist and Bisson Labs); and a method for screening antibody-secreting cells with droplet microfluidics.

JulieAnn Villa

I am a high school teacher in science research and chemistry. I teach in a public school just outside of Chicago. I am interested in engaging young students in primary STEM research and all forms of outreach from universities to schools. I also am interested science communication- those skills required by scientists as researchers and those involved in communicating science to the public.

Markus F. Weber

I am a PhD student with Erwin Frey at LMU München. My research started out studying critical phenomena in non-equilibrium systems but I was pulled away to collaborate with the microbiology group of Madeleine Opitz. I thus found myself studying Rock-paper-scissors games of Escherichia coli. Currently, I am working together with Hannes to link evolutionary game theory and Bose-Einstein condensation, fields that have remained apart for too long (under review, keep fingers crossed).

Martin Weigt

I am professor at the Université Pierre & Marie Curie in Paris, France. My group has a background in theoretical statistical physics, our research concentrates mainly on the statistical inference from / the statistical modeling of biological data. We study in particular the sequence variability in families of homologous proteins, with the aim to detect residue coevolution and to predict protein structure, function and interactions. In relation to the topic of this meeting, we recently started a project on inferring mutational landscapes of the beta-lactamase TEM-1 by combining coevolutionary sequence information, structural protein simulations and mutagenesis data.

Daniel Weinreich

Dan is a professor at Brown University in Providence, Rhode Island. My group uses both wet and dry methods, chiefly to dissect the mechanistic causes and evolutionary consequences of epistasis. Wet work is primarily in ß-lactamase, an enzyme that gives bacteria resistance to antibiotics related to penicillin. This has recently been complemented by a formal exploration of patterns of higher-order epistasis. Students are currently also using complementary theoretical and experimental approaches to study evolution in changing environment, the consequences of chromosomal instability mutators, and the evolution of robustness.

Scott Wylie

I am a postdoc with Dan Weinreich at Brown University, where I do experimental molecular evolution, protein biochemistry, and, of course, theoretical work. I did my Ph.D. with Herbie Levine at UCSD, applying non-equilibrium statistical mechanics to evolutionary dynamics. Ph.D. topics included the evolution of mutation rate and recombination in bacteria. Subsequently, I joined Eugene Shakhnovich's group at Harvard and worked on connections between fitness landscapes and protein thermodynamic stability. At Brown I'm learning the experimental molecular biology needed to test theoretical predictions-- past and future.

Fabio Zanini

I am a PhD student @ MPI for Developmental Biology in Tübingen, Germany, in Richard Neher's lab. My PhD work is on intrapatient HIV evolution,i.e. how genetic changes accumulate in the virus during a single infection.

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