Virtual Cell Program

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brunch, 21 July 2013, at Jeremy & Mary's

   

5 August 2012

Alexander Barabanschikov

Alexander Barabanschikov

Research associate
abarabanschikov at yahoo.com

My background is in theoretical physics, in particular, string theory. Having completed my Ph.D. at Northeastern University in 2004, I decided to move to biology and try to apply theoretical and computational methods to investigate some of the fascinating mechanisms of the functioning of the cell. At the molecular level I had experience in modeling and spectroscopic studies of active sites of (mostly heme) proteins. Numerous studies of theoretical models and chemical model compounds help to identify the reactive motions in the molecule that drive processes like ligand binding or dissociation. At the systems level one is immediately faced with the complexity of reaction networks and the extremely large number of difficult to measure parameters. Currently, I am investigating a certain class of reaction networks arising in post-translational modification with the purpose of finding biologically-important characteristics of these networks that are largely independent of the parameters (such as rate constants). I teach at the Moscow Institute of Physics and Technology and visit Boston regularly.

last updated on 10 October 2012

David Croll

David Croll

Sabbatical visitor
david.croll at regiscollege.edu

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

Tathagata Dasgupta

Tathagata Dasgupta

Postdoctoral Fellow
tathagata_dasgupta at hms.harvard.edu

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

Joseph Dexter

Joseph Dexter

UG research student
jdexter at princeton.edu

I am an undergraduate at Princeton in the Department of Chemistry and the Lewis-Sigler Institute for Integrative Genomics. My research with the Gunawardena group is focused on developing biochemically realistic mathematical models of important metabolic and signaling networks. I am particularly interested in understanding how robust behavior is implemented in biological systems through specific molecular features such as enzymatic multifunctionality and oligomerization. My models strive to capture essential biochemical details and make heavy use of algebraic geometric techniques developed by the Gunawardena group to enable analysis. At Princeton I also work on the application of microfluidics to a variety of problems in systems biology and biophysics. I am an active alumnus of the Research Science Institute and have taught at the program the past two summers. Outside of science, I am a student of the classics, where my research is mostly centered on ancient theatre and how classical literature has influenced modern literary and cultural concerns.

last updated on 8 August 2012

Javier Estrada

Javier Estrada

Graduate Research Intern
javier.estrada at uam.es

I am a PhD student at the Universidad Autónoma de Madrid, Spain. Trained as a physicist, I have been using simulations and analytical approaches to study the amplitude and frequency detection capabilities of different network motifs, taking into account both the response and the noise filtering properties of each network. In the Gunawardena Lab, I am working with different mathematical models describing calcium oscillations, focused mainly in the parameter problem. I am co-first author of the recently submitted paper on "celluar interrogation".

last updated on 11 August 2013

Daniel Gibson

Daniel Gibson

Research Assistant
daniel_gibson at hms.harvard.edu

I come from the Colorado School of Mines, in my native state, where I did research in non-linear acoustics relating to land mine detection as an undergraduate and research assistant. My degree is in Engineering Physics, with minors in Bioengineering & Life Science in addition to Music Technology. I am continuing the microfluidic side of the calcium signalling project started by Natalie Andrew and Fred Change. I am also collaborating with Kat Hadjantonakis' lab at Sloan Kettering to use microfluidic devices to assist in mouse embryo imaging.

last updated on 24 May 2011

Jeremy Gunawardena

Jeremy Gunawardena

Director, Virtual Cell Program
(617) 432 4839
jeremyat hms.harvard.edu

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 a 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 group is on information processing in mammalian cells. In what sense can cellular processes be considered to "process" information? What kind of information is it and how do we measure it? How are information processing tasks implemented 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 8 August 2012

Benjamin Gyori

Benjamin Gyori

Visiting PhD student
website

I am a computer scientist, and currently a PhD student at the National University of Singapore. My research interest centers around computational methods for modeling the dynamics of signaling pathways using probabilistic approaches. Probabilistic models allow us to handle uncertainty in biological systems arising from factors such as the stochasticity of biochemical processes, variability among individual cells, unmodeled components and measurement noise. My goal is to provide efficient solutions for the challenges involved in building and using such models. Currently, I am developing a scalable, general method for learning dynamic Bayesian networks, and applying this method for modeling signaling pathways involved in liver cancer progression.

last updated on 26 August 2013

Mohan Malleshaiah

Mohan Malleshaiah

Postdoctoral Fellow
mohan.malleshaiah at gmail.com

Biological functions arise as a result of the 'flow of information' through networks of interacting components. Elucidating and understanding the dynamics of key components thus enables control of information flow and response outputs including higher order phenomena such as cell-fate decisions and resulting cell structure transitions (Hartwell, Nature 1999; Nurse P., Nature, 2008). To explore the dynamics of such decision-determining component interactions in Saccharomyces cerevisiae, during my graduate studies at Prof. Michnick's lab, at the University of Montreal, we developed Protein fragment Complementation Assays (PCA) based on fluorescence and luminescence assays (Malleshaiah M. et al., PLoS ONE 2008; Michnick S. et al., Methods Enzymol. 2010). These assays allowed us to measure the in-vivo dynamics of protein-protein interactions. As a result, we could describe a central mechanism for the 'switch-like' yeast mating response (Malleshaiah M. et al., Nature 2010) and its sensitivity to availability of carbon-source nutrients (Stefan E., Malleshaiah M., et al., Nature Communications 2011).

I continue my quest for cell-fate decision mechanisms, but this time with Embryonic Stem Cells model, as a joint post-doc between Prof. Jeremy Gunawardena (Department of Systems Biology, Harvard University), Prof. Alfonso Martinez-Arias (Department of Genetics, Cambridge University) and Prof. Anna-Katerina Hadjantonakis (Memorial Sloan-Kettering Cancer Center, New York). I am interested in both experimental and computational approaches to elucidate the underlying molecular mechanisms of cellular decisions.

I also like art and theme oriented photography. You can have a glimpse of my pictures at mohanm.wix.com/auras-vision.

last updated on 23 August 2012

Prabakaran Sudhakaran

Prabhakaran Sudhakaran

Postdoctoral Fellow
(617) 432 4842
Sudhakaran_Prabakaran
at hms.harvard.edu

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.

Personal website.

last updated on 28 May 2012

Ved Topkar

Ved Topkar

UG research student
vedtopkar at college.harvard.edu

I am an undergraduate at Harvard College concentrating in Chemical & Physical Biology with a secondary in Computer Science. Supported by PRISE during the summer of 2013, I started computationally analyzing the colossal ENCODE datasets at promoter regions, with most of my attention being devoted to transcription factor binding analysis. I approach this big-data topic with the following question in mind: how do we quantitatively reduce such diverse biological complexity to something more easily understandable? You can see my PRISE presentation here. I hope to continue pursuing this work into the fall and eventually tie it back into a genome-scale application of our lab's linear framework.

You can view my website at vedtopkar.com.

last updated on 11 August 2013

Felix Wong

Felix Wong

UG research student
fwong at college.harvard.edu

I am a senior mathematics concentrator who is pursuing a joint SM degree in applied mathematics at Harvard University. I am interested in computational biophysics, biomedical engineering, and geometric analysis, and have done research in areas ranging from mathematical physics to computer vision. In the Gunawardena group, I focus on computational models of eukaryotic gene expression and in particular on a project to expand the "linear framework". My personal website is here.

last updated on 24 October 2013

Yangqing Xu

Yangqing Xu

Postdoctoral Fellow
(617) 432 5733
yangqing_xu at hms.harvard.edu

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

 

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