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. In contrast to previous devices, these are two-layer PDMS chips with integrated valves and pumps, so that all fluid mixing is undertaken on-chip. One of her devices is described in a conference paper. last updated on 21 December 2008 |
Research assistant |
Fred graduated from UC Berkeley with a BS in Electrical Engineering and Computer Science in 2008. Currently, Fred is working with Natalie Andrew to understand cell to cell variability in the context of calcium oscillations, based on the data acquired from Natalie's microfluidic devices. last updated on 21 December 2008 |
Sabbatical visitor |
My involvement as a visitor to the Gunawardena group stems from my interest in biochemical reaction networks, especially metabolic pathways. I am building metabolic models in little b, with the goal of understanding the dynamic complexity of metabolism. I am also interested in the development of little b to provide a feature-rich language that will allow biological modelers to express biophysical and regulatory features of enzymes in a natural and convenient fashion. In graduate school at Purdue University I studied theoretical chemical physics and biophysical chemistry, doing my Ph.D. dissertation research in the group of John Markley, where I used multi-nuclear/multi-dimensional NMR techniques to study the physical chemistry of the ovomucoids, a family of protein-proteinase inhibitors. This was followed by a postdoc at the Biophysics Institute at the Boston University School of Medicine, where I used NMR spectroscopy and computation to study lipoprotein dynamics and biophysical properties. As a faculty member at Regis College, I have supervised model-oriented undergraduate research projects in biochemistry. I have also been involved in metabolically oriented research projects at Tufts University, including the modeling and measurement of whole body cholesterol metabolism. last updated on 21 December 2008 |
Postdoctoral Fellow |
Tathagata Dasgupta is a former string theorist now studying the regulation of glycolysis and the Warburg effect in a joint project with Lew Cantley and the Cell Decision Process Center. last updated on 21 December 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 |
Postdoctoral Fellow |
I studied bioinformatics at the Ludwig Maximilians University (LMU) and at the Technische Universitaet (TUM) in Munich. In parallel, I also studied Economics at the LMU. My Master's thesis was about the Microarray Data Analysis of Sex Biased Genes in Drosophila melanogaster, for which I created the Sex Bias Database. Based on large scale genome analysis and database management of sex biased genes, we found that male biased fly genes are less conserved than female biased genes. The fact that one can derive such patterns on the basis of As,Ts, Cs and Gs was very fascinating to me. The focus of my PhD study at the Max Planck Institute for Biochemistry was on the large-scale analysis and the database management of identified phosphorylation sites. Protein phosphorylation is a fundamental regulatory mechanism that controls many cell signaling processes. In this context, I created the phosphorylation site database PHOSIDA. I also worked on various proteomic studies and created the proteome database MAPU 2.0. I then worked at the European Bioinformatics Institute (EBI) in Cambridge UK on the annotation of the genome using mass spectrometry data. After completing my PhD, I started to work in Jeremy Gunawardena's group at the Harvard Medical School. We are studying the conservation of multisite phosphorylation. The idea to model the living cell along with its complex processes is also very fascinating and I plan to develop software infrastructure to support this. last updated on 4 May 2009 |
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 |
UG research student |
Raj worked on steady-state invariants for multisite phosphorylation for Physics 90R and is first author on the paper that emerged from that. He is currently working with German Enciso on EGF receptor dimerisation. last updated on 30 October 2007 |
UG research student |
I am a 4th year student from Anna University in Chennai, India doing my senior thesis in Bioengineering. Switching between the fundamentals of Mathematics, Biochemistry and Computers, I am studying the degree to which Flux Balance Analysis can correctly predict the internal fluxes in yeast. Also, I am trying to implement different biomass equations and additional constraints to improve the reliability and prediction capability of existing networks available in the literature. I will be pursuing my graduate studies at the University of California, Irvine. My website is here last updated on 4 May 2009 |
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 |
I have broad interdisciplinary backgrounds in both biological science and engineering. With an undergraduate degree in hydraulic engineering, some of my former classmates built the Three 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 interests in the flow inside a heart, rather than that inside a turbine. I therefore first did a Masters in bio-fluid mechanics. After focusing on biotechnology development during my PhD (in Biomedical Engineering), I joined the current laboratory and began my career in systems biology. My current research focuses on the study of complex dynamics of biological networks using a combination of quantitative imaging, cell biology and mathematical modeling. The measured dynamics leads to mathematical models for the structure and the regulation of the network, which can be iteratively tested by experiments. I apply this interdisciplinary systems biology approach to investigate information processing and decision making in growth factor signaling and autophagy cell death in mammalian cells. I always picture a cell as a country with various factories and heavy traffic on the connecting roads, and it has been a joyful trip in such a lively world watching the constructions, transportations and battles in it. As a systems biologist, I am repeatedly amazed how a cell coordinates so many activities and functions as an integrated and self-organized kingdom, yet without a king. Looking back over the last decade, the scale of my research shrank from kilometers to nanometers, but with a dramatic increase of complexity in the system. I find it truly fascinating. last updated on 21 December 2008 |