Postdoctoral Fellow |
Natalie is developing microfluidic devices to implement complex signal stimulation protocols in a NSF-sponsored collaboration with Todd Thorsen and Saman Amarasinghe at MIT. last updated on 23 October 2007 |
UG research student |
Kyle has worked on modelling calcium oscillations for Biochemical Sciences 91R and is now studying cell-to-cell variation in EGF signalling for his Senior Honours Thesis. last updated on 18 January 2008 |
Postdoctoral Fellow |
My dissertation work was in mathematics, studying the impact of positive and negative feedback on the behavior of dynamical systems in an abstract context. I have applied this work to models of biochemical reactions and reaction diffusion systems, and I have done some modeling of retinal interneurons. In Jeremy's lab, I am developing generic modules for biochemical reactions in little b and will use them to study signal transduction pathways associated with EGF receptors. My website is here. last updated on 23 October 2007 |
Director, Virtual Cell Program |
I used to be a very pure mathematician, an algebraic topologist, but fell from grace some years ago (to borrow Marc Kac's gracious way of putting it) when I volunteered to teach computer science while an L.E. Dickson Instructor in the Mathematics Department at the University of Chicago. That started my fascination with complexity, which eventually led to a long stint in industrial research at HP (Hewlett-Packard) Labs, where I ran part of the company's "blue skies" research programme. Post-genome systems biology brings complexity to centre stage and brought me to Harvard. Our focus in the Virtual Cell Program is on signal transduction in mammalian cells, particularly growth factor signalling. What are the information processing tasks which a signalling pathway has evolved to perform? How are these tasks carried out by the molecular mechanisms within cells? What systematic methodologies are needed for attacking such problems and how do we develop them? We approach these questions through a combination of experiment, theory and computation. last updated on 24 February 2006 |
Senior Research Scientist |
Prior to joining the Systems Biology Department, I spent several years at Millennium Pharmaceuticals during the heyday of genomics developing technology and leading efforts to integrate and share structured scientific knowledge. During that time, I had the opportunity to spend a year at the Harvard Center for Genomics Research to understand how systems theory could be applied to problems in drug discovery. One outstanding problem was how to simplify the process of building reliable models. I imagined a tool that would enable a modeler to "mix together" predefined, trusted components. These would automatically wire themselves together - in analogy to how a biochemist reconstitutes a system by mixing proteins in a test tube. I proposed a computational framework based on this idea, and this evolved into little b, a LISP-based programming language designed for building modular, shareable models. My formal training has been in cell biology and biochemistry, though I've had a long interest in computing. I got my start in science with Dan Jay, then a professor at the Harvard BioLabs. We created microCALI, a microscope-based version of the chromophore-assisted laser inactivation technology which he pioneered, and used it to investigate the role of molecules in nerve cell growth. I did my Ph.D. at UCSF with Tim Mitchison, developing photoactivation and photobleaching technologies to visualize cytoskeletal dynamics involved in: neuronal tip movement, mitosis, and cell division orientation. last updated on 24 February 2006 |
UG research student |
Raj has worked on steady-state invariants for multisite phosphorylation for Physics 90R and the results are being written up in a new paper. He is currently working with German Enciso on EGF receptor dimerisation. last updated on 30 October 2007 |
Postdoctoral Fellow |
I am one of the theoretically minded biologists to join the Virtual Cell Program. I worked on the problem of protein folding for my Masters thesis from Jawaharlal Nehru University (New Delhi, India). Thereafter I became interested in neuroscience and schizophrenia and joined Dr. Sabine Bahn's group for my PhD at Cambridge University. My PhD project developed into a systems based functional approach to understand schizophrenia using multiple "-omic" platforms (Prabakaran et al, 2004, Swatton et al 2004). During my PhD I realized that investigating "-omic" snapshots of gene, protein, lipid and other cellular component expression changes is not sufficient to understand such complex biological phenomena. I believe one has to investigate the dynamics of the interactions of these components to arrive at an hypothesis, for which one needs mathematical and computational modelling as well. Thus my interest shifted to the dynamics and mechanisms of interactions and self-organization in complex biological systems. I joined Dr. Gunawardena's lab in 2006 to develop methods to quantify phosphorylation patterns in multisite phosphorylation and understand its role in signal transduction and information processing in mammalian cells. I also want to develop models of Drosophila eye development and patterning with the modular programming language little b, in order to better understand multicellular interactions and organization. last updated on 19 May 2006 |
Postdoctoral Fellow |
My undergraduate training was in hydraulic engineering. In fact, some of my former classmates are building the San Xia (3 Gorges) Dam on the Yangtze river, one of the largest hydraulic constructions in the world. As the odd one out among my classmates, I developed an interest in the flow inside a heart, rather than that inside a turbine. I therefore did a Masters in bio-fluid mechanics and grasped some basic knowledge of physiology. In 1997, I came to the USA and pursued a Ph.D in biomedical engineering at Emory University and Georgia Tech with Professor Gang Bao. My work focused on the development and modeling of novel filtration based microarray techniques (PubMed) and FRET-based molecular beacons (PubMed). However, it has always been my interest to apply novel technology and computer modeling to biologically significant problems. After many exciting conversations with Jeremy Gunawardena, we found common interests in many things, particularly the potential application of fluorescence correlation spectroscopy. In March 2004, I joined his group in the Department of Systems Biology and started building a FCS system, with help from Antoine van Oijen and Marc Kirschner. One of our initial projects is to look at the function of scaffold proteins in the MAP kinase pathway. We are also carrying out other experiments on the dynamics of the MAP kinase pathway in collaboration with Tim Mitchison. Looking back, the scale of my research shrank from kilometers to nanometers within 10 years, but with a dramatic increase of complexity in the system. I find it truly fascinating. last updated on 21 June 2005 |
Summer student |
Felix wrote a generic module for receptor endocytosis, recycling and degradation in little b last updated on 19 May 2006 |
UG research student |
Mark did a Senior Honours Thesis on "Differential and graphical approaches to multistability in chemical reaction networks"; available at arxiv.org/abs/0709.0125. It was awarded a Department of Mathematics Friends' Prize and a Harvard University Thomas T Hoopes Prize. last updated on 18 January 2008 |
Research Assistant |
Matt is currently a graduate student in the Harvard Biophysics programme. He worked on several experimental, computational and theoretical projects, was co-author of one paper on little b and another on multistability in multisite phosphorylation. last updated on 23 October 2007 |
Summer student |
Ben has worked on various aspects of the little b system. He is studying computer science at Columbia. last updated on 24 February 2006 |
