Research+Profiles

toc //**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.)

Seth Blumberg
I study the transmission dynamics of emerging zoonotic disease (ex. Monkeypox in the Democratic Republic of the Congo). My current focus is to use branching process theory to infer epidemiological parameters (i.e. effective reproduction number and transmission heterogeneity) in the setting of imperfect case detection. In the near future I would like to couple epidemiological inference with concurrent sequencing data in order to ascertain transmission history. I am a physician, but have a physics research background. I am an NIH RAPIDD postdoctoral fellow and am based in Jamie Lloyd-Smith's lab at UCLA.

[|Lauren Childs]
I am currently a postdoc at Georgia Tech working with Joshua Weitz on various interactions of phage and host. In particular, I am interested in a bacterial defense system against invading viruses, known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). Unlike other bacterial defense systems, CRISPRs are virus-specific and heritable, producing a form of adaptive immune memory. Previously, I graduated from Cornell Applied Mathematics in 2011, where I used dynamical systems approaches to study biological applications including fish schooling and immune cell activation.

Fernando Fontanari
I work in the Physics Department of the University of São Paulo at São Carlos, Brazil. My research has focused on the applications of concepts and analytical tools from Physics (Statistical Mechanics, mainly) to problems in theoretical Biology (e.g., population genetics and prebiotic evolution), Computer Science (e.g., optimization problems and neural networks) and Cognitive Science (emotions and decision making). I'm currently interested on the mathematical modeling of cultural and language evolution. I served as a member of the editorial board of //Network: Computation in Neural Systems// in the beginning of the 1990s and I currently serve in the board of //Physics of Life Reviews// and //Theory in Biosciences,// and as review editor of //Frontiers in Neurobotics//.

[|Julia Gog]
I am a faculty member of the Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge, and also a Royal Society URF. My research is in modelling infectious disease dynamics. I have a particular interest in influenza, where we have developed models to explore the interaction of cocirculating strains and antigenic drift (see for example [|this paper], and [|that paper]). I have also explored a little bit some of the bioinformatics of influenza virion [|packaging]. In general, I'm interested in many aspects of the [|phylodynamics] of infectious disease.

Jeff Gore
I started as an Assistant Professor in the Physics Department at MIT a year ago. My laboratory uses microbes as experimental model systems to explore theories in evolutionary dynamics and quantitative ecology. A substantial portion of the lab studies the evolution of cooperative behaviors within and between species. We are also interested in rugged fitness landscapes that are the result of interactions between different mutations. Finally, we are also exploring the dynamics of populations before a "tipping point" causes population collapse.

Sid Goyal
I am currently a postdoc at KITP working on problems in population genetics. I graduated from Princeton Physics in 2009, where I worked on bacterial gene regulation and metabolic networks. My current interests are (1) population genetics of systems with multilevel selection, such as organelle genomes and (2) balance between deleterious and beneficial mutations in large asexual populations.

Chris Illingworth
I graduated from St John's College, Cambridge in mathematics before completing a PhD at the University of Essex, which focused on the issue of physical and electronic flexibility in protein-ligand binding sites, including work on the incorporation of polarization into the classical part of quantum-classical molecular models. Following this I worked in Oxford on the analysis of molecular dynamics simulations of ion channels and other proteins, and lectured briefly back at Essex on physical chemistry and bioinformatics. I am currently a postdoc working with Ville Mustonen at the Wellcome Trust Sanger Institute in Hinxton, UK, developing mathematical models of viral evolution.

Eugene Koonin
Eugene Koonin graduated from Moscow State University, Moscow, Russia (then USSR) in 1978 and received his PhD in Molecular Biology from the same University in 1983. He has been working in the fields of Computational Biology and Evolutionary Genomics since 1984. Dr. Koonin moved to the US in 1991, first, as a Visiting Scientist, and then, since 1996, as a Senior Investigator at the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD. Dr. Koonin’s group performs research in many areas of evolutionary genomics, with a special emphasis on whole-genome approaches to the study of major transitions in life’s evolution, such as the origin of eukaryotes, the evolution of eukaryotic gene structure, and the origin and evolution of different classes of viruses, as well as evolutionary systems biology. In 2005, Dr. Koonin founded the journal Biology Direct, with Drs. Landweber and Lipman, in an effort to explore a novel system of open peer review.

**Sergey Kryazhimskiy**
I am a postdoc with Michael Desai at Harvard University. I am interested in characterizing the microbial fitness landscapes and understanding the dynamics of adaptation on them. I am approaching these problems with mathematical modeling (see this paper, for example) and, more recently, with evolution experiments in yeast.

Richard Neher
I graduated from Munich University (Biophysics) in 2007 and thereafter spend 3 years at KITP working with Boris Shraiman on problems in population genetics. Since October 2010, I am at the Max-Planck Institute for Developmental Biology in Tuebingen, where I am currently building up a small research group. My research interest are the population genetics of rapidly evolving and strongly selected organisms. On one hand, I am studying the interplay of recombination, selection and genetic interactions using theoretical models, on the other hand, we are analyzing time series sequence data of HIV. The latter allows us to observe evolution as it is happening.

[|Sergei Maslov]
I am a permanent scientific staff member at Brookhaven National Laboratory on Long island, NY I am interested in a broad range of questions in systems and computational including: - How biological networks minimize the undesirable crosstalk and limit the effects of non-specific interactions ([|MSB 2008], [|PNAS 2007], [|NJP 2007],[|Science 2002])? - How they achieve robustness against noise and perturbations ([|PNAS 2007], [|PRL 2008], [|Science 2002])? - How topological properties of these networks affect their functioning inside living cells ([|Nucleic Acids Research 2005], [|Phys. Biol. 2007], [|BMC Bioinformatics 2006], [|PRL 2004,] [|Science 2002])? - How bio-molecular networks and underlying genomes change in the course of evolution ([|PNAS 2009], [|JMB 2009], [|BMC Evol. Biol. 2004], [|Nucleic Acids Research 2005], [|Biol. Direct 2007])? Right now I mostly think about the "Home Depot" model of bacterial evolution ( [|PNAS 2009], [|arxiv2010]) and how it can be extended to other complex systems composed of multiple functional units.

[|Namiko Mitarai]
I joined the Niels Bohr Institute in Denmark as an associate professor in 2009. I have broad interest in biological dynamics, including (1) translation process as a ribosome traffic problem and effect of choice of codons, (2) Small RNA regulation, (3) Transcriptional burst and regulation, (4) Role of space in ecosystems.

[|Ilya Nemenman]
My group is applying methods of theoretical physics and information theory to understand how biological systems, from molecular circuits to entire populations, learn from their surrounding environment and respond to it.

**Luca Peliti**
I am Professor of Statistical Mechanics at the University "Federico II" in Naples. I am interested in several aspects of the organization of living systems, from the physical level (membranes, biopolymers, motor proteins) to the evolutionary level. I have been working for quite some time on the statistical physics approach to evolutionary dynamics.

[|Alan Perelson]
I am a senior fellow at Los Alamos National Laboratory. I work on modeling the immune response and the within host dynamics of viral infections - particularly HIV, HCV and influenza. I am also interested in the within host evolution of HIV and HCV. I have published extensively on all of these issues.

Lilia Perfeito
I am currently a post-doc in the group of [|Michael Laessig] at the University of Cologne. I am interested in using models of experimental evolution to measure parameters and test predictions from population genetics. Recently I have been using the //lac// operon of //E. coli// as a model to study the evolution of regulatory sequences. In order to understand how these elements evolve, it is important to analyze the impact of changes in protein expression on fitness. In other words, knowing the intermediate phenotypes which are affected by mutations at the genome level, will help us understand the impact of particular mutations on fitness.

** [|Ganna Rozhnova] **
I am an FCT postdoctoral fellow working in the Physics of Biological Systems Research Group (with Prof. Ana Nunes, the University of Lisbon) and in the Theoretical Physics Group (with Prof. Alan McKane, the University of Manchester). I have been interested in the spatio-temporal modeling of the dynamics of infectious diseases and of predator-prey systems. My approach is based on the use of stochastic simulations together with analytical methods of dynamical systems, statistical physics and stochastic processes.

**Josep Sardanyes**
I am doing my first postdoc in the Institute of Molecular and Cellular Plant Biology (IBMCP) in Valencia, Spain. I am a biologist working in nonlinear dynamics, complex systems, and systems biology. My fields of research are the hypercycle (i.e., catalytic networks), quasispecies theory (origin of life and RNA viruses) and theoretical ecology. I am working as a theoretician in the lab of Prof. Santiago F. Elena. We are working on plant virus evolution and dynamics. I mainly work with differential equations and simulation models (Montecarlo simulations, digital genomes models, ...). I am also interested in bifurcation theory and chaos in biology. If you want more detailed information about my work and publications you can visit my website [|here].

Joshua Weitz
I am an Assistant Professor of Biology and Physics at Georgia Tech. My research group works in many areas of quantitative biology and theoretical ecology. Particularly relevant to this workshop are a number of projects we are actively pursuing in trying to understand viral dynamics and evolution including (i) the role of viral gene dosage in the phage lambda decision switch; (ii) quantifying the molecular basis of viral life history trait tradeoffs; and (iii) biophysics of enzymatic lysis of cells by viruses. We also have interests in developing methods for quantifying and predicting what viruses are doing to their bacterial hosts in the environment.