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2020. Lecture video on Thermodynamic limits in cellular information processing, at the programme on Statistical Biological Physics: From Single Molecule to Cell, held at ICTS, TIFR, Bengaluru, India.

2020. Lecture video on Hopfield barriers: the interplay of mathematics and physics in molecular biology, at the SIAM Conference on the Life Sciences 2020 (LS20), 11 June - 2 July, 2020.

2019. Lecture video on Beyond Big Data and Big Models: the role of abstraction in biology at the Workshop on Data, Knowledge and Genomic Causality, Ben-Gurion University, Dec 2019.

2019. Interview about our paper on avoidance behaviours in Stentor roeseli; and some comments on its implications.

2019. Lecture video on Some mathematical aspects of gene regulation at the SIAM Conference on Applied Algebraic Geometry, Bern, July 2019.

2019. Lecture ideo on Following the energy: the Hopfield barrier as an organising principle at the MBI Summit on the Rules of Life, Ohio, June 2019.

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

2017. 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.

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

group photographs


pandemic brunch, 5 June 2021, Magazine Beach, Cambridge, organised by Dan Lu
photo by Jeremy Owen

   

photo by Dan Lu

   
previous years

Krishna Amin

Krishna Amin

UG researcher

I am a third year undergraduate, in my final year reading Natural Sciences at St Catharine’s College, Cambridge, specialising in Biochemistry. I have previously worked on the impact of uncharacterised open reading frames and species-specific gene regulation on schizophrenia and bipolar disorder. Outside the lab and classroom, I am a keen tennis player. I also play the piano and viola, and I occasionally take pictures.

As an undergraduate researcher in the summer of 2021, I will be working with Jeremy Owen on the mathematical modelling of epigenetic mechanisms.

last updated on 10 June 2021

Neha Anand

Neha Anand

UG researcher

I am a Chemical Engineering undergraduate in my pre-final year at the Indian Institute of Technology, Madras, Chennai, India. My interests are predominantly in biostatistics, operations research, data science, and mathematics. Outside of academics, I enjoy sketching and writing, some of which can be found here. In the summer of 2021, I am working with Joseph Nasser on analysing the enhancer-promoter transcription dynamics and the stochasticity of gene expression.

last updated on 3 June 2021

Carlos Aude

Carlos Aude

UG researcher
c.aude at columbia.edu

I am a rising junior at Columbia University with interests in applied statistics and computational biology. Previously, I have investigated the transfection efficiency of hybrid HIV-1 infectious molecular clones and the use of split methyl halide transferase for in-situ gas conjugation bioreporting; I have also been a research assistant in a variety of clinical trials. Outside of academics, I enjoy tennis, soccer, volunteering, and getting to drive an ambulance through Manhattan as an EMT!

As a 2020 Systems Biology USRI summer intern, I am working with Chris Nam and Nazim Bouatta to apply deep learning as a new tool to study gene regulation. Specifically, we hope to uncover mechanistic information about gene regulation from the hidden layers of convolutional neural networks.

last updated on 18 June 2020

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

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

Varsha Chari

Varsha Chari

UG researcher
vchari2 at illinois.edu

I am a junior from the University of Illinois at Urbana-Champaign studying Chemistry with minors in Statistics and Mathematics. My research work currently lies in computational biology. I have previously worked on projects in which I develop computational pipelines in different programming languages to process data from spatial transcriptomics technology. As a 2021 summer intern, I will be working with Rosa Martinez-Corral in exploring multi-input gene regulation functions from a theoretical standpoint. I hope to pursue an MD/PhD and am particularly interested in applying mathematical modeling techniques towards answering large scale biological questions and improving medical diagnostics.

last updated on 7 June 2021

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

Marjan Faizi

Marjan Faizi

Postdoctoral Fellow
marjan_faizi at hms.harvard.edu

I am a computational biologist interested in developing tools and mathematical models to make sense out of experimental data. I have completed my bachelor’s and master’s degree in bioinformatics and expanded my training in computational systems biology during my PhD.

Currently, I am working with mass spectrometry data of the tumour suppressor protein p53. I am interested in the protein’s post-translational modifications (PTM) and the global patterns that can arise by different combinations of various PTM types. I am developing computational methods for analysing mass spectrometry data with the focus on global PTM patterns, or modforms, in order to gain insights into cellular information processing and cell fate decisions, using the example of p53.

last updated on 7 June 2021

Jeremy Gunawardena

Jeremy Gunawardena

Associate Professor of Systems Biology
(617) 432 4839
jeremy at 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

Olivia Lease

Olivia Lease

UG researcher
olivia dot lease at columbia.edu

I am a rising junior at Columbia University studying applied mathematics and history with interest in quantitative biology. In the past, I have used math and data analytics to amplify social justice platforms and nonprofits on social media. In my freetime, I love teaching kids, playing music, and playing pick-up basketball. This summer as a Systems Biology intern, I will be working with Ugur Cetiner on developing linear framework models to better understand kinetic proofreading and its constraints.

last updated on 9 June 2021

Sabina Haque

Sabina Haque

PhD student
sabina_haque at fas.harvard.edu

I am a second year PhD student in the Systems Biology program at Harvard University. I graduated from Middlebury College in 2018 with B.A. in Mathematics and Biochemistry. My research interests are broadly focused on elucidating the fundamental math and physics that govern biological processes, and my work in the Gunawardena lab is centered on understanding the implications of kinetic (or non-steady state) behavior in Markov dynamics and non-equilibrium biophysics.

last updated on 5 June 2019

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

Rosa Martinez-Corral

Rosa Martinez-Corral

Postdoctoral Fellow
Rosa_MartinezCorral at hms.harvard.edu

I am broadly interested in the phenomenon of "life". In particular, I would like to understand the molecular mechanisms for the proper functioning and development of living organisms, which I approach from a theoretical and computational perspective. As a postdoc between the Gunawardena and the DePace labs, I am studying eukaryotic gene regulation. Using the Drosophila embryo as a model system, I aim to develop a unified framework that allows to conceptualise, interrogate and understand the biophysical basis for combinatorial transcriptional control.

My formal training was at Universitat Pompeu Fabra in Barcelona (Spain), where I obtained a BSc in Human Biology, an MSc in Bioinformatics and a PhD in Biomedicine under the supervision of Prof. Jordi Garcia-Ojalvo, with whom I studied the role of spatial and dynamical cues on cell regulation.

last updated on 21 July 2019

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

Joseph Nasser

Joseph Nasser

Research associate

I started my academic career in mathematics and have since transitioned to think more about biological systems. I'm fascinated that organisms are able to function as they do even in the face of numerous obstacles such as external perturbations and the inherent stochasticity of molecular environments.

I was previously a staff scientist at the Broad Institute where I worked on studying the role of enhancers in gene regulation with applications to human genetics. I am looking to continue more theoretical exploration of enhancers in the lab. I'm also broadly interested in the role of modelling and theory in biology and will look to apply such approaches to other biological systems.

last updated on 20 April 2021

Giorgio Ravenelli

Giorgio Ravenelli

UG researcher

I graduated in Biotechnology from the University of Milano-Bicocca. Currently, I am attending a master’s degree program in Quantitative Biology. I am joining the Gunawardena lab to work on my master thesis project related to the role of energy dissipation in gene expression dynamics.

I have always seen myself as a prospective experimental molecular biologist. Although my formation is mainly centred around experimental molecular biology, since I fell in love with System Biology, I started considering the math side of biology. Even though I am well trained in fearing mathematics, one of my most important future goals is to learn to approach a biological problem with a real quantitative method based on mathematical formalism and physics. This will bring me to be part of a highly interdisciplinary group.

last updated on 3 June 2021

Isabel Thomas

Isabel Thomas

UG researcher
ithomas8 at jhu.edu

I am studying Applied Mathematics and Statistics at Johns Hopkins University, where I focus on characterizing the structures of fold-switching proteins to better understand protein folding thermodynamics. As a 2020 Systems Biology summer intern, I am working with Felix Wong, Ugur Cetiner, and John Biddle to analyze the impact of energy expenditure on the degree of sharpness of the response function when conformations are not at equilibrium.

last updated on 8 April 2020

Felix Wong

Felix Wong

Postdoctoral 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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