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Photographs from the School on "A Systems Approach to Biology" at the University of Buenos Aires in June 2018. Jeremy's lectures are here.

Harvard Medicine Magazine has an Autumn 2017 feature on computational tools for analysing natural languages, which highlights other work of Joseph Dexter and Ben Gyori.

Photographs from the Slow Science talk given by JG at Bioquant in Heidelberg on 27 May 2015.

group photographs


brunch, 22 July 2018 at Jeremy & Mary's, camera courtesy of Suyang, photo by Jeremy.

    previous years

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

John Biddle

John Biddle

Postdoctoral Fellow
biddlephys at gmail.com

I did my PhD research in theoretical physics at the University of Maryland, focusing on thermodynamics and statistical mechanics, and especially the study of phase transitions and metastable states. My dissertation was directed by Mikhail Anisimov on the topic of thermodynamic anomalies in supercooled water.

Gene expression in eukaryotes is known to take place away from thermodynamic equilibrium. However, the models that are used to describe eukaryotic gene regulation have so far been derived from our understanding of prokaryotes, where gene expression takes place at equilibrium. My research in the Gunawardena lab aims to improve our understanding eukaryotic gene regulation by taking into account non-equilibrium effects.

last updated on 1 September 2016

Ugur Cetiner

Ugur Cetiner

Postdoctoral Fellow
cetiner dot ugur at gmail.com

I am a biophysicist with a wide range of interests varying from osmotic fitness of bacteria to stochastic processes to non-equilibrium statistical physics. I graduated from Bogazici University with a B.A. in Physics and received my PhD degree in Biophysics from University of Maryland, College Park where I worked with Professor Sergei Sukharev on the nanoscale thermodynamics of mechanosensitive ion channels.

One of the most fundamental differences between bacterial and eukaryotic gene regulation is energy expenditure. While equilibrium thermodynamics successfully describes the events that take place during bacterial gene regulation, the existence of highly dissipative processes begs the question of whether the equilibrium formalism could describe the enormous molecular complexity in eukaryotic gene regulation. In the Gunawardena Lab, I will develop the theoretical framework and design experiments to check whether or not gene regulatory systems are operating away from equilibrium.

last updated on 19 September 2018

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

Shreepriya Das

Shreepriya Das

Postdoctoral fellow

I am a Postdoctoral Research Fellow in Gunawardena Lab in the Department of Systems Biology, Harvard Medical School. I obtained my PhD from the Department of Electrical and Computer Engineering at The University of Texas at Austin under the advisement of Dr Haris Vikalo. Prior to that, I completed my B.Tech in Electronics and Electrical Communication Engineering from the Indian Institute of Technology, Kharagpur. My research interests are broadly in systems biology, signal processing and machine learning. More information can be found on my personal website.

last updated on 6 September 2017

Joseph Dexter

Joseph Dexter

PhD 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

Jeremy Gunawardena

Jeremy Gunawardena

Associate Professor of Systems Biology
(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 was a Dickson Instructor in the Mathematics Department at the University of Chicago. I volunteered to teach computer science, which made me interested in 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 brought 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

Dan Lu

Dan Lu

Postdoctoral Fellow
dan_lu at hms.harvard.edu

I completed my PhD in Biochemistry in 2016 at the University of Cambridge working in Gerard Evan's lab. Cancer therapies rely on targeting vulnerabilities in tumour cells that are not present in normal physiological cells. Systemic inhibition of the MYC transcription factor was shown to specific kill tumour cells, but not normal proliferating tissues, establishing a clear therapeutic window. My PhD project was therefore to identify the causal mechanisms of tumour cell death focusing on perturbations of the metabolic and apoptotic pathways.

Currently in the Gunawardena group in collaboration with Galit Lahav's lab, my research project revolves around the transcription factor, p53. The aim is to functionally attribute the roles of post-translational alterations on the p53 protein following stress induction to the subsequent cell fate. The benefits in qualitatively and quantitatively decoding dynamic cell signals are invaluable both in enhancing existing cancer therapies as well as understanding evolutionary and developmental processes.

last updated on 1 September 2016

Chris Nam

Chris Nam

PhD student
kmnam at g.harvard.edu

I am a second-year Ph.D. student in Harvard's Systems Biology program, working on the application of the "linear framework" to an integrated model of gene regulation and expression. I am broadly interested in understanding how different transcriptional regulatory mechanisms can influence the levels of output mRNA and protein molecules.

I graduated from Swarthmore College in 2015 with a B.A. in Mathematics and Computer Science. I began working with Jeremy as a Systems Biology USRI in 2013, supported by NSF 0856285. I worked on applying methods from numerical algebraic geometry to characterize the "parameter geography" of bistability in multisite post-translational modification systems, focusing on the two-site case. I presented multiple posters and two talks with preliminary conclusions on these questions, and we are now finishing up a paper on the results.

last updated on 25 April 2017

Ajeet Sharma

Ajeet Sharma

Postdoctoral Fellow
azitks at gmail.com

I am a post-doctoral research fellow in Gunawardena lab. I completed my Ph.D. in 2014 from the Department of Physics at IIT Kanpur. During my Ph.D. and subsequent post-doctoral research work at Penn State, I have developed and applied theories to understand various non-equilibrium features of the process of protein synthesis and co-translational protein folding. In those projects, I have also analyzed the high-throughput sequencing data using the tools of non-equilibrium statistical mechanics.

In the Gunawardena lab, my research aims to understand the role of non-equilibrium kinetics in cellular signal processing, specifically in the context of gene regulation.

last updated on 20 September 2018

Felix Wong

Felix Wong

PhD student collaborator
fwong at college.harvard.edu

I graduated from Harvard College with an A.B. degree in mathematics and an S.M. degree in computer science in 2014. I am currently a fifth-year Ph.D. student in Harvard's applied physics program, advised by Ariel Amir and supported by the NSF Graduate Research Fellowship. I have been working with Jeremy's lab since I was an undergraduate and am interested in the "linear framework" and its applications to biological information processing and non-equilibrium statistical mechanics (PMIDs 25475875 and 27368104). My personal website is here.

last updated on 13 June 2018

 

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