Virtual Cell Program

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adebayo | agarwal | amin | anand | andrew | athreya | aude | balbi | basques | bhola | biddle | bonowski | chang | chattopadhyay | cooper | das | dasgupta | dexter | de pretis | duan | dumitrascu | dushime | eckert | enciso | estrada | feier | flores | ghalayini | gibson | gnad | gupta | gyori | hilgert | karp | lease | li | lipson | malleshaiah | mallavarapu | manrai | martinez-corral | mirzaev | mohan | nam | nguyen | owen | padula | patel | paul | perry | peters | prabakaran | ravenelli | schleich | seitz-shewmon | sharma | stanley | sullivan | talla | thomas | thomson | topkar | tran | tyree | ullian | venkatramani | wang | wells | williams | wood | woodward | xiang | xu | xue | yordanov | zhao

Julius Adebayo

Julius Adebayo

UG research student
2011

I was an undergraduate studying mechanical engineering with minors in math, chemistry and computer science at Brigham Young University in Provo, Utah. I joined the Gunawardena group as a Systems Biology Undergraduate Summer Research Intern in the summer of 2011, supported by NSF 0856285. I worked with Tathagata Dasgupta on a comparison of different network reconstruction/reverse engineering techniques with a focus on Bayesian approaches and was a co-author on the paper that we submitted; see my poster on this. I am broadly interested in control theory, machine learning, signal transduction, mathematical modeling of biological systems and using engineering approaches to elucidate biological systems. Manchester United, my favorite soccer team, visited Boston while I was here. That alone makes Boston cool. I am currently a Research Assistant at NECSI in Boston.

last updated on 8 August 2012

Deepesh Agarwal

Deepesh Agarwal

Postdoctoral fellow
2015-17

I am a Data scientist and software developer who is interested in facilitating data-driven decision making through predictive data modeling methods. In the past, I have worked with pharma giants as a project-coordinator to build a pipeline for deep-learning based heterogeneous reconstruction from CryoEM data. I have also handled and managed projects to semantically integrate various biomedical databases and make actionable predictions for problems such as drug repurposing and target identification. I have a long standing interest in teaching and training which I plan to realize through self-developed courses in statistics and machine learning to begin with.

I pursued an engineering degree (dual degree program - Bachelors and Masters) in Biochemical engineering and Biotechnology at IIT Delhi, India where I also had hands-on experience in certain wetlab techniques. I was, however, interested in application of mathematics and computer science to get insights into the working of biological systems. I then pursued a one year masters in computational biology and biomedicine at Polytech Sophia Antipolis, France. It was followed by a PhD at INRIA, Sophia Antipolis with Frederic Cazals, in which I undertook algorithmic investigations of the structure of large protein assemblies using native top-down mass spectrometry (PMID 25850436).

During my post-doc in Jeremy's lab, I invesitigated information processing by post-translational modification (PTM) with a particular focus on p53 PTMs. This was a collaboration with Galit Lahav's lab at HMS and Neil Kelleher's lab at Northwestern University. I developed algorithms based on linear programming and uniform sampling to analyze top-down and bottom-up mass spectrometry data for p53 in different cellular states. This was realised as a python module for analysis and visualization of modforms (bioRxiv:10.1101/456640).

During my free time, in addition to spending time with family, I like to meditate on questions in my head through book chapters, youtube videos, articles etc. The questions could be related to any aspect of life from financial management to parenting to philosophical questions of Dharma and Existence.

last updated on 9 January 2023

Krishna Amin

Krishna Amin

UG researcher
2021

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
2021

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 worked with Joseph Nasser on analysing the enhancer-promoter transcription dynamics and the stochasticity of gene expression. Here is a poster about my findings.

last updated on 13 November 2021

Natalie Andrew

Natalie Andrew

Postdoctoral fellow
2006-11

Natalie developed microfluidic devices to implement complex signal stimulation protocols in a NSF-sponsored collaboration with Todd Thorsen and Saman Amarasinghe at MIT. One of her devices is described in a conference paper. She subsequently used these to develop the method of "cellular interrogation" and is co-first author on the recently submitted paper on this.

last updated on 11 August 2013

Advait Athreya

Advait Athreya

UG research student
2019

I am a senior at the University of Rochester, studying molecular genetics and applied mathematics. In Rochester, I work in an aging lab using wet lab techniques such as mammalian cell culture and biochemical assays to study LINE1 retrotransposons. Over the summer of 2019, between junior and senior year, I wanted to explore the mathematical side of biology research at the Gunawardena lab. I worked with Rosa Martinez-Corral, Pencho Yordanov, and Ugur Cetiner on studying the transient dynamics of gene regulation by using the linear framework previously developed in the lab; see my poster on this.

last updated on 14 September 2019

Carlos Aude

Carlos Aude

UG researcher
2020

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 Undergraduate Summer Research 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

Petra Balbi

Petra Balbi

UG research student
2020

I was working with Dan Lu, studying post-translational modification of p53, when I became interested in the new direction of cell learning. I began reviewing historical studies of conditioning in single cells and this eventually led to a perspective paper in eLife.

last updated on 7 July 2022

Kyle Basques

Kyle Basques

UG research student
2008

I graduated from Harvard with an A.B. in biochemical sciences in 2008. Afterwards, I attended medical school at Northwestern University, earning an M.D. in 2012. I am now pursuing residency training in the field of radiology at University Hospitals Case Medical Center in Cleveland, Ohio. In Jeremy's lab, I worked first on the mathematical modeling of intracellular calcium oscillations. Then, for my senior honors thesis, I studied cell-to-cell variation in the phosphorylation events in the MAPK cascade. My favorite parts of living in Boston had to have been the amazing arts scene, the Red Sox, and the New England accent. One day I certainly hope to return.

last updated on 8 August 2012

Ashwin Bhola

Ashwin Bhola

UG research student
2017

I am an undergraduate at IIT Delhi in the Department of Chemical Engineering. My research with the Gunawardena group in 2017 is focussed on assessing the feasibility of some gene regulation phenomena like assisted loading from a thermodynamical point of view. I am particularly interested in understanding how the transcription factors can remodel the chromatin so that two transcription factors which bind to the same site on the chromatin region actually help each other in attaching to promoter region rather than competing with each other. To see if this happens at or away from equilibrium, I am using the linear framework to mathematically model the system and then simulating this model within the realistic range of parameters to see the enhancements that each of the TFs can provide to each other without expending energy. So the fundamental questions that I am trying to look at are: How much assistance can we achieve at equilibrium? How do homotypic and heterotypic cooperativities affect this phenomenon? Does the change in conformation along with binding differences produce any significant difference in assistance?

last updated on 12 July 2017

John W. Biddle

John Biddle

Postdoctoral fellow
2016-20

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

Felix Bonowski

Felix Bonowski

UG research student
2006

Felix wrote a generic module for receptor endocytosis, recycling and degradation in little b

last updated on 19 May 2006

Frederick Chang

Frederick Chang

Research assistant
2008-10

I studied Electrical Engineering and Computer Science at UC Berkeley with a focus in robotics, since I particularly enjoyed the exercise of diverting free energy into computation and movement. My previous research experience included understanding the physics of rare events in computational chemistry with Jhih-Wei Chu and exploring calcium signaling in mammalian cells using microfluidics with Jeremy Gunawardena. I am now a second year EPB PhD candidate through the Molecular Cell Biology Department and a student of Nancy Kleckner's. The bulk of my imagination is currently consumed by the question of how chromosomes execute search in homologous recombination. My favorite thing about Boston is cycling to Walden Pond, then eating an overpriced hot dog by the stand in the parking lot.

last updated on 8 August 2012

Arhana Chattopadhyay

Arhana Chattopadhyay

UG research student
2009-11

I am currently a medical student at Stanford. I spent 3 years in the Gunawardena lab while an undergraduate at Harvard studying chemical and physical biology. I worked with Natalie Andrew and Fred Chang on using microfluidics to study fascinating questions in systems biology. I undertook a senior thesis in the lab using microfluidic devices to study how Dictyostelium discoideum, a slime mold that serves as a model for eukaryotic cell migration, responds to chemotactic and mechanical signals. My thesis, which is available here, was awarded a Harvard University Thomas T Hoopes Prize in 2011. I am broadly interested in micro-scale engineering, cellular mechanics, surgery, and science in developing countries.

last updated on 30 December 2013

Virginia Cooper

Virginia Cooper

UG research student
2012

I am a senior Chemistry/Biology double major at Howard University. My research background is in synthetic organic chemistry, synthesizing analogs of the anti-oxidant gallic acid to enhance its anti-inflammatory, anti-mutagenic and anti-carcinogenic properties. I was a Systems Biology Undergraduate Summer Research Intern in the Gunawardena lab in the summer of 2012 supported by NSF 0856285. I worked with Sudhakaran to study the autophosphorylation activities of partial phospho-forms of Erk; see my poster on this. My favourite parts of Boston were the variety of foods and the history and culture. I also recommend a trip to Cape Cod if possible.

last updated on 13 August 2012

Shreepriya Das

Shreepriya Das

Postdoctoral fellow
2017-19

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

Tathagata Dasgupta

Tathagata Dasgupta

Postdoctoral fellow
2007-16

I did my PhD in string theory at the University of Cambridge. In the Gunawardena lab, I have been involved in applying and developing mathematical, statistical and computational techniques to learn complexities of living systems. Example projects span from computational algebraic geometry approach in the context of regulation of mammalian glycolysis (PMID 24634222) to using machine learning heuristics in the emerging area of "computational pathology" (PMID 26553024). The latter direction involves working closely in collaboration with clinicians to build predictive models using microenvironmental immunology profile in various contexts of human reproduction and cancer.

last updated on 5 September 2016

Joseph Dexter

Joseph Dexter

UG research student
PhD student
2014-18

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

Stefano de Pretis

Stefano de Pretis

PhD student on internship
2011-12

I am a PhD student of Bioinformatics at the "Università degli studi di Milano-Bicocca" and the main topic of my research is about whether certain chemical reaction networks exhibit bistability. In particular, I am interested in CRNT (Chemical Reaction Network Theory) and in conditions that lead a network to admit bistability. In the Gunawardena lab, I am applying my theoretical studies to a "real" network: a core model for differentiation of embryonic stem cells. I am drafting a paper on this, in addition to finishing my PhD thesis. I am getting more experienced with integrating computational and theoretical work with experiments. It is a great opportunity for me to work with people with a mathematical background that are used to deal with real experiments and biological data. I hope I could directly collaborate also with real experimentalist because I think that the great goal of Systems Biology resides in the direct influence between theory and experiments, in order to build realistic models of what really happens in the cell. I am interested in music, sports and photography. My favorite sport is soccer (both played and watched) but here in Boston I am getting involved in all the sports that are popular here, particularly baseball. Boston is a very nice city, where you can find fusion between European and American culture. I appreciate very much Cambridge because of the vitality that the many students there bring to the city.

last updated on 13 August 2012

Lisa Duan

Lisa Duan

UG researcher
2022

I am a rising sophomore at Brown University studying Computational Biology. I am especially interested in the intersection of computing, applied mathematics, and neuroscience, and I hope to pursue an MD-PhD in a related field. In my free time, I enjoy working with children, playing tennis, and trying food from different cultures.

As a 2022 Systems Biology Intern, I am working with Ugur Cetiner to study the thermodynamics of learning and the predictive capabilities of biological systems through Markov chain simulations.

last updated on 9 June 2022

Bianca Dumitrascu

Bianca Dumitrascru

UG research student
2011

Since high school I decided that for me mathematics is the way to go. It is about connections, about structure, about creativity. I am currently a rising junior studying Applied Mathematics at MIT. I have been working for the last year in Prof Bonnie Berger's lab in metabolomics, RNA structure prediction and, most currently, protein interaction networks. My research interests are currently directed towards computational biology and systems biology, but I am also interested in different parts of theoretical computer science. I usually have problems answering the question "and... what do you do for fun?" since all the things that I do are terribly fun. However, I could say that I write for fun. I am interested in all forms of art and all forms of literature, and I have a particular liking for anything related to social anthropology and history of religion. My favorite thing about Boston: its European air which reminded me of home. I say "reminded" because I can easily call it home now. In the summer of 2011, I was a Systems Biology Undergraduate Summer Research Intern in the Gunawardena lab, supported by NSF 0856285. I worked with Bobby Karp on a model of Wnt signalling in mammalian cells; see my poster on this. I had a blast working with everyone. I like stories and during the summer I had the chance to meet amazing people and hear their amazing stories. The Sys Bio group is an unbelievable learning environment, and I look forward to continue the work that I started during the summer.

last updated on 8 August 2012

Rosine Dushime

Rosine Dushime

UG research student
2013

I am a rising senior at Spelman College studying Biochemistry with a minor in Mathematics. My research background is in biochemistry, molecular analysis of Dibenzoylmethane in androgen-refractory prostate cancer cells. I joined the Gunawardena group in summer 2013, as a Systems Biology Undergraduate Summer Research Intern supported by NSF 0856285. I am working with Tathagata Dasgupta on identification and characterization of bi-functionality in Escherichia coli using computational approaches; see my poster on this. I have had a great experience in Boston; it is quite similar to European cities with great culture and history.

last updated on 11 August 2013

Lina Eckert

Lina Eckert

Master's student
2022

I am a student in interdisciplinary science at ETH Zürich, joining the lab to work on my Master’s thesis. During my bachelor's degree I focused on biology and chemistry. But soon I realised that physics and mathematics are invaluable tools to investigate the fundamental mechanisms of life. My program in interdisciplinary science allows me to pursue these diverse interests and provides me with the perfect background for my current work in Systems Biology.

My project in the lab is about habituation — one of the simplest forms of learning. Supervised by Rosa Martinez-Corral, and building on previous work by Ziyuan Zhao, I am trying to develop a theoretical model based on biologically plausible mechanisms which can reproduce the main characteristics of habituation observed not only in higher organisms but notably in in single cells, too. Since I have always been curious about the interceptions of natural science with other scientific disciplines, I am very happy that this project makes me contemplate not only about the behaviour of mathematical models, but also about cognitive science and the phenomenon of learning itself.

Lina's Master Thesis can be found here.

last updated on 21 November 2022

German Enciso

German Enciso

Postdoctoral fellow
2007-9

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. I am currently an Assistant Professor at UC Irvine.

My website is here.

last updated on 28 October 2009

Javier Estrada

Javier Estrada

Postdoctoral fellow
2013-17

I was a joint postdoc between the Gunawardena and DePace labs from 2013 to 2017. During that period we proved how transcription in animals can only be explained assuming energy dissipation and/or complex interplay between transcription factors and their corregulators, a key step towards understanding such a central process in biology (PMID 27368104). Since 2017 I am an investigator at Novartis Institutes for Biomedical Research working on immuno-oncology. There, we try to answer key questions like: how does the immune system behave within the tumor micro environment? How is the interaction between tumor cells and lymphocytes? How does the evolutionary pressure shape tumors to make them resistant to drugs and the immune system? Can we use all this knowledge to develop better, more efficient drugs?

I trained as a physicist at the Universidad Autónoma de Madrid, Spain and previously worked with the Gunawardena lab on "cellular interrogation" (PMID 27367445).

last updated on 12 June 2018

Roxana Feier

Roxana Feier

UG research student
2011

I am a rising senior at Harvard majoring in mathematics with a minor in astrophysics. Although most of my undergraduate courses were in pure mathematics, I recently became more interested in its applied counterparts. This change of interests was what brought me to systems biology for the summer of 2011 as an Undergraduate Summer Research Intern, supported by the Harvard College PRISE. My project, working with Bobby Karp, attempts to model biological systems (particularly the Wnt pathway) through the use of polynomial dynamical systems over finite fields. This is done by building upon algorithms initially developed in the context of algebraic geometry, for Grobner basis computations. These models can be used to infer the network structure of the pathway, as well as to make predictions about the dynamics; see my PRISE poster on this. Academic interests aside, I am also an avid (although not very good yet) photographer. I have done both film and digital, and long walks around Harvard Square with my camera never fail to relax me when schoolwork gets stressful.

last updated on 19 August 2012

Andrés Flórez

Andrés Flórez

UG research student
2009-10

I am a graduate student at the German Cancer Research Center in Heidelberg. I am focused on understanding the restriction point control in the cell cycle of a specific children's tumor called Neuroblastoma. The strategy is to combine experiments and mathematical modeling to elucidate the molecular mechanisms involved in cell cycle progression of this disease. I worked as a research intern in the Gunawardena lab in 2009-10 basically from the experimental side and trying to combine mathematical modeling to understand calcium signaling in the context of parasite infection in collaboration with Dr. Barbara Burleigh from the Department of Immunology and Infectious diseases at the Harvard School of Public Health. I studied the patterns of agonist-induced oscillations in infected and non-infected primary fibroblasts and macrophages with the protozoan parasite, Trypanosoma cruzi. The initial results showed that T. cruzi alters the amplitude and time delay of the oscillations probably by a cytokine-mediated mechanism. My experience in the Gunawardena lab was really exciting as I could see working in action experiments and modeling together to ask meaningful questions to the cells. And Boston I have to say it is a lovely city, where you can breathe knowledge everywhere, helped by the inspiring landscapes. I enjoyed really much the salsa dancing activities in Boston where I had the chance to learn the New York style, which is very different from the Colombian style I was used to.

last updated on 8 August 2012

Layla Ghalayini

Layla Ghalalyini

UG researcher
2022

I am a third-year Chemical and Biomolecular Engineering student at the Georgia Institute of Technology, and I enjoy blending Engineering, Chemistry, Biology, and Technology. My current research interests include drug delivery, hematology, genomics, and gene regulation, and my past research experience has been in epidemiology and computational biology. In my free time, I enjoy volunteering, spending time with my friends and family, and origami.

As a Systems Biology intern, I am working with Joseph Nasser on exploring how variability in the concentration of a transcription factor affects variability in one of the transcription factor’s target genes.

last updated on 17 June 2022

Daniel Gibson

Daniel Gibson

Research assistant
2010-13

Daniel came to us from the Colorado School of Mines, in his native state, where he did research in non-linear acoustics relating to land mine detection as an undergraduate and research assistant. His degree was in Engineering Physics, with minors in Bioengineering & Life Science in addition to Music Technology. Daniel continued the microfluidic side of the calcium signalling project started by Natalie Andrew and Fred Chang, which led to a 2016 paper in PLoS Comput Biol. He also collaborated with Kat Hadjantonakis' lab at Sloan Kettering to use microfluidic devices to assist in mouse embryo imaging. Daniel is currently working as a data scientist in San Francisco.

last updated on 22 August 2016

Florian Gnad

Florian Gnad

Postdoctoral Fellow
2009-10

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 24 May 2009

Namita Gupta

Namita Gupta

UG research student
2010

I was a Systems Biology Undergraduate Summer Research Intern in the Gunawardena group in 2010. In my internship, I worked with Bobby Karp on a project that studies the steady state properties of molecular pathways for a wide range of parameters. I helped develop a program that analyzes the number and types of steady states in the framework of mass action kinetics, using high performance numerical techniques and algebraic geometry; see my poster on this. I used Python, C++, and Mathematica, learned homotopy continuation, and most importantly understood how biochemical pathways can be realistically modeled, and how these models are connected to the experiments that are underway in the lab. I received a B.S. in applied mathematics and a B.A. in biology from the University of Chicago. I am currently a Ph.D. candidate at Yale in Computational Biology and Bioinformatics. I am currently rotating in labs that develop computational methods for biologists. My favorite thing about Boston is how easy it is to get around the city on foot in the summertime. I also love how there is a great balance of greenery mixed in with the buildings - especially the Common!

last updated on 8 August 2012

Benjamin Gyori

Benjamin Gyori

Visiting PhD student
2013

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

Nicholas Hilgert

Nicholas Hilgert

UG research student
2019

I am a rising senior at Purdue University interning with the Harvard Systems Biology program for summer 2019. I study physics and mathematics, though I'm interested in their intersections with biology, which drew me to this lab. Borrowing ideas from statistical mechanics and Markov processes, I am working on an understanding of the conditions that imply ordered assembly of transcription factors during eukaryotic gene regulation; see my poster on this.

last updated on 9 September 2019

Bobby Karp

Robert Karp

Postdoctoral fellow
2009-2012

Bobby Karp joined the group in 2009 with a background in mathematics (PhD at Duke in algebraic geometry) and physics (PhD Eotvos University in quantum field theory). He worked on the parameter geography problem and was also co-first author of our paper on "complex-linear" invariants. He joined Goldman Sachs in New York in 2012.

last updated on 28 June 2013

Olivia Lease

Olivia Lease

UG research student
2021

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

Yen-Der Li

Yen-Der Li

UG research student
2012-13

I am a 4th year medical student with doublemajor in physics at National Taiwan University. In the Gunawardena group, I was working with Yangqing Xu to investigate how cell density affects ERK signaling heterogeneity. My research interest lies in biophysics and systems biology. Besides research, I am also interested in the consulting industry as well as biopharmaceutical entrepreneurship.

last updated on 16 August 2013

Mark Lipson

Mark Lipson

UG research student
2006-7

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

Mohan Malleshaiah

Mohan Malleshaiah

Postdoctoral fellow
2011-17

I am interested in understanding the nature of molecular networks and how they process signal information to "compute" cell fate decisions. To this end I utilize integrative approaches by combining quantitative measurements (at single-cell & population level) with computational analysis and modelling. I have explained new mechanisms for cell state transition in the budding yeast as well as in pluripotent stem cell model systems.

I did my PhD with Professor Stephen Michnick at University of Montreal where I analyzed the protein complex dynamics within living cells. I analyzed the MAPK signaling proteins to explain a unique zero-order ultrasensitivity mechanism for switch-like budding to mating decision in yeast cells (PMID 20400943). I also explained how yeast cells simultaneously integrate multiple signals and prioritize their response by tuning sensitivity to signals through cross-pathway interactions (PMID 22186894).

Inspired to explain cell fates in the highly complex mammalian system, I chose to analyze stem cells for my postdoctoral research. As a CIHR (Canadian Institutes of Health Research) Fellow at Professor Jeremy Gunawardena's lab, I developed an integrative approach to analyze embryonic stem cells (ESC). In collaboration with Professor Alfonso Martinez-Arias' lab at Cambridge University, I applied this approach to understand the dynamics of transcription factors (TFs) network of pluripotency during ESCs differentiation into the alternative cell fates. We discovered that a subset of pluripotency TFs is reconfigured to generate new networks that promote differentiation (PMID 26832399 and Cell Reports, 2016).

To better understand individual stem cell behavior and their population heterogeneity, I have further implemented single-cell proteomics, and computational methods to analyze the complex data. In collaboration with Professor George Daley's lab. I am analyzing distinct cell populations during reprogramming of pluripotent stem cells to a) totipotent cells and b) hematopoietic stem cell progenitors.

My publications on NCBI. After finishing my postdoctoral fellowship, I joined the Montreal Clinical Research Institute.

last updated on 20 September 2018

Aneil Mallavarapu

Aneil Mallavarapu

Senior scientist
2003-8

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. Please feel free to contact me if you have questions about little b.

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

Arjun (Raj) Manrai

Raj Manrai

UG research student
2006-8

Raj worked on steady-state invariants for multisite phosphorylation for Physics 90R and is first author on the paper that emerged from that. He also worked with German Enciso on EGF receptor dimerisation. He is currently a graduate student in the Harvard-MIT HST programme.

last updated on 28 October 2009

Rosa Martinez-Corral

Rosa Martinez-Corral

Postdoctoral fellow

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.

I am currently an Independent Fellow at the Barcelona Collaboratorium and the Centre for Genomic Regulation.

last updated on 16 July 2023

Inomzhon Mirzaev

Inom Mirzaev

UG research student
2011

As an undergraduate research student in Prof. Gunawardena's lab, I worked on dynamical aspects of the linear framework. Our findings were later published in this paper. I received my B.S. in mathematics from the Middle East Technical University in Ankara, Turkey and my PhD in applied math from the University of Colorado Boulder. During grad school, I used various mathematical techniques to study the reversible combination and separation of suspended particles in a fluid. I also followed up the earlier studies of the linear framework (PMID 25795319). After grad school, I had a joint postdoctoral position with the Mathematical Biosciences Institute at the Ohio State University and the Cleveland Clinic in Cleveland, Ohio. As a postdoc, I was interested in applications of machine learning in the automated segmentation of anatomical structures from MRIs. Summaries of some other projects that I have worked on can be found on my personal webpage. After finishing my postdoc, I joined Workday Inc as a machine learning scientist.

last updated on 26 November 2018

Nandukumar Mohan

Nandukumar Mohan

UG research student
2013

I grew up in Sharon, Massachusetts and graduated from Sharon High School. I am currently a student at the University of Massachusetts at Amherst. I am a neuroscience major working his way through pre-med and getting ready for medical school. Science has always been sort of a calling for me and I have always wished to pursue it. While my background is more with chemistry research and chemistry lab experience, as compared to biology, I pursued a position at Harvard to expand upon the biology knowledge that I already have in a more technical way. This internship has been eye opening for me. All summer I have been working with Sudhakaran Prabhakaran on studying the multi-site phosphorylation of the EGF pathway protein ERK (technically known as MAPK). I have been studying the multiple phospho-forms of ERK and quantifying phospho-form ratios in response to EGF stimulation. I have worked with many techniques such as growing bacterial and mammalian (HeLa) cells, plasmid transformation, immuno-precipitation, protein purification, running gels, mass spectrometry and much more. I hope to not only take the knowledge that I have acquired from this job and apply it everywhere I go from here on in my career but also I hope to come back here and continue working on the same project.

last updated on 24 August 2013

Kee-Myoung ("Chris") Nam

Chris Nam

UG research student
PhD student
2016-21

I have maintained a long association with the group, as both an undergraduate intern through the Harvard FAS Center for Systems Biology (during the summer of 2013), supported by NSF 0856285, and a graduate student in Harvard's Ph.D. program in Systems, Synthetic, and Quantitative Biology (from 2015 to 2021). Throughout this time, I have been broadly interested in the use and development of mathematical approaches for understanding various forms of biomolecular information processing. Namely, we combined the graph-theoretic linear framework for timescale separation with methods from numerical algebraic geometry to study the "parameter geography" of steady-state multiplicity in a general model of multisite post-translational modification (PMID 32365103); we extended the linear framework to cover biochemical processes operating within a transient regime via graph-theoretic formulations of its first-passage times, as well as processes involving synthesis and degradation, particularly within the context of stochastic gene expression; and we applied this extended framework to study the emergence of accuracy-speed tradeoffs in DNA recognition and cleavage by CRISPR–Cas9. (Papers arising from these projects are in preparation.) I continue to be interested in how molecular processes can give rise to complex phenomena on cellular, organismal, and ecological scales, how tradeoffs between system properties emerge from the details of these processes, and what mathematical and computational techniques can bring to bear on these questions.

last updated on 23 November 2022

Maximilian Nguyen

Maximilian Nguyen

UG research student
2017

In the spirit of Schrodinger's approach to the age-old question of "What is Life?", I am interested in uncovering the physical principles by which we may distill the complexity in biological systems. Some fields of modern biology lie at a junction where they may finally be susceptible to theoretical treatment. Excited by the potential for such discoveries, I came to the Gunawardena group to start my foray into quantitative biology.

An open problem in cellular information processing is a theoretical understanding of the physics by which transcription factors and other regulatory machinery can control gene expression. Together with Jeremy and John Biddle, we investigated the thermodynamics of coupled transcription factor binding (PMID 30762521). In doing so, we uncovered the concept of reciprocity, which hints at the possibility of discovering other functional quantities of nonequilibrium systems.

I received a BS and MS in Chemical Engineering from Georgia Tech and Cornell University, respectively, and am currently pursuing a PhD in biophysics at Princeton University.

last updated on 22 April 2019

Jeremy Owen

Jeremy Owen

UG research student
Visiting researcher
2013-22

I was at the Gunawardena group as a Systems Biology Undergraduate Summer Research Intern in the summer of 2012, and I worked on extending some mathematical results, established previously for a special case of the Goldbeter-Koshland loop (arrived at using the linear framework), to the general case, where the enzymes involved in the loop can be reversible; see my poster on this. I am co-author of a paper on this, in which we apply the theory to analyse the switching efficiency of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, which regulates glucose metabolism. I returned in the summer of 2013 to work on some other mathematical issues related to the linear framework–exploring, for example, what conditions might guarantee monostability in general post-translational modification systems.

I am an undergraduate studying Mathematics at King's College, Cambridge. I am passionate about mathematics both for its intrinsic beauty, and for its application to describe natural phenomena, especially in biology.

last updated on 11 August 2013

Samuel Padula

Samuel Padula

UG research student
2019

I was an undergraduate student studying mathematics at Wofford College. I spent the Summer of 2019 working with Chris Nam on calculating a Hopfield barrier for CRISPR-Cas9 specificity and efficiency; see my poster on this. I am currently finishing up a master’s degree in mathematics from Wake Forest University and I am in the middle of applying to math PhD and computer science masters programs.

last updated on 30 November 2021

Vishal Patel

Vishal Patel

UG research student
2009

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.

last updated on 4 May 2009

Debdas Paul

Debdas Paul

Visiting PhD student
2017

Currently, I am a third-year doctoral student (Dr.-Ing.) at the Institute for Systems Theory and Automatic Control, University of Stuttgart, Germany, working with Professor Nicole Radde. My thesis is to develop a theoretical framework to compare the design principle of nature and technical load-bearing structures in terms of robustness, optimality, and multi-functionality.

Previously, I have completed my bachelors and masters in computer science and engineering from the West Bengal University of Technology and from the Jadavpur University, India respectively. As a computer science engineer, I have worked on data-driven bioinformatics and application of spectral graph theory in large-scale networks.

Later, I also pursued a double-degree masters in computational systems biology from the Royal Institute of Technology (KTH), Sweden and the Aalto University, Finland where I worked on the machine learning based computational biology (specifically on kernel methods to predict protein-protein interactions) as well as on parameter estimation techniques for stochastic chemical kinetics based on the chemical master equation.

At Jeremy's lab as a visiting graduate student, I am developing a model for the polymerase-II dynamics (recruitment, pause, elongation and termination) in order to bring the gene expression and regulation under a common unified linear framework.

last updated on 6 September 2017

Daniela Perry

Daniela Perry

UG research student
2016

Dani was a Systems Biology Undergraduate Summer Research Intern in 2016, supported by NSF 1462629. She enjoyed working with Tathagata and Joseph and our collaborator, Dr Nicolas Orsi, at the University of Leeds Institute of Cancer and Pathology, on a machine learning project. She developed a support vector machine model to identify patients with polycystic ovary syndrome (PCOS) from cytokine profiles obtained from tissue and blood and she further explored the inflammatory landscape of the disease; see her poster on this project. Dani's favorite part of her brief time at HMS was learning about and getting to know all the wonderful people in the lab. When not working at Harvard, Dani studies statistics at Cornell University and loves to play golf and enjoy the outdoors with friends.

last updated on 15 August 2016

Gregory Peters

Gregory Peters

UG research student
2017

I am currently an undergraduate intern from Pacific Lutheran University in Tacoma, Washington where I am working towards degrees in Biochemistry and Computer Science. My interests revolve around protein dynamics and computational drug discovery.

Allostery is the indirect interactions between distinct binding sites, which allows for regulation of activity. Proteins exist in an ensemble of conformations, continually interconverting between the different conformations with varying energies. The distribution of the conformational ensemble can be viewed through the free-energy landscape of a protein. Allostery can be viewed as a redistribution, or "population shift", that takes place because of the relative stabilities of the conformational change. My work in the Gunawardena lab, which is supported by NSF 1462629, involves studying the conformational ensembles and free-energy landscapes of proteins as a means to understand allostery in order to apply the linear framework to describe allostery and allosteric regulation; see my poster.

last updated on 3 September 2017

Sudhakaran Prabakaran

Prabhakaran Sudhakaran

Postdoctoral fellow
2006-14

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 am currently a group leader in the Department of Genetics at Cambridge.

last updated on 13 Nov 2016

Giorgio Ravenelli

Giorgio Ravenelli

Master's student
2022

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

Kolja Schleich

Kolja Schleich

Master's student
2009

I studied Molecular Biotechnology (BSc, MSc) in Heidelberg, Germany. Currently I am a PhD student in the Division of Immunogenetics (Prof Dr Peter Krammer), in the group of Prof Dr Inna Lavrik, at the German Cancer Research Center in Heidelberg. I worked in Jeremy's lab as a summer intern in 2009 on the switching capabilities of multisite phosphorylation systems. Such systems show unlimited multistability and could therefore be used as memory storage modules capable of storing multiple bit of information. I analysed the possibility of switching between any steady states, which would be of interest for synthetic biologists in particular. In my PhD project I work on the CD95 signaling pathway. CD95 (also named Fas/APO-1) belongs to the tumor necrosis family of death receptors. Besides its well known functions in triggering cell death it can also lead to the activation of non-apoptotic pathways resulting in cell proliferation. It is, however, still unknown how the decision between these two outcomes is taken. Upon CD95 stimulation a multi-component death-inducing signaling complex (DISC) is formed. In order to get further insight into this decision process, I study the stoichiometry of the DISC using quantitative western blot, mass spectrometry, single-cell fluorescence microscopy and mathematical modeling. I especially like about Boston that its architecture is quite similar to European cities. I very much like the area around Boston Common, Beacon Hill and Quincy Market.

last updated on 19 August 2012

Sophia Seitz-Shewmon

Sophia Seitz-Shewmon

high-school student
2023

I am a junior at Commonwealth School in Boston. For most of my life, I was based in Los Angeles. I am bilingual with German and English, and I’m also fluent in Mandarin. In recent years my academic interests have increasingly been mathematics and natural sciences, in particular genetics. At the Gunawardena Lab, my interest is focused on deriving steady state probabilities from graphs using graph-theoretical methods.

last updated on 30 January 2023

Ajeet Sharma

Ajeet Sharma

Postdoctoral fellow
2018-19

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

Julian Stanley

Julian Stanley

UG research student
2018

I am an undergraduate at Northeastern University studying Computer Science and Biology and working as a summer 2018 intern with Shreepriya Das. I am generally interested in genetics and genomics in all of their manifestations, but especially when their insights are relevant to clinical medicine. During summer 2018 I am working to identify genomic delineators of type 1 and type 2 endometrial cancers from whole-genome data; see my poster on this.

last updated on 16 September 2018

Monica Sullivan

Monica Sullivan

UG research student
2010

Monica joined the lab in 2010 as a Systems Biology Undergraduate Summer Research Intern, supported by NSF 0856285. She was majoring in mathematics at Fort Valley State University in Georgia. She worked with Bobby Karp to develop a mathematical model of the Wnt pathway; see her poster on this.

last updated on 10 September 2012

Pranay Talla

Pranay Talla

High-school student
2019

I am a rising senior at Horace Greeley High School in NY. This summer, I am interning at the Gunawardena Lab to work on exciting research problems at the intersection of mathematics, biology and physics.

My investigation involves the steady-state properties of general covalent modification cycles and their function as biological switches. I am working under the mentorship of John Biddle to expand on previous mathematical results by determining the extent to which physical quantities such as the thermodynamic force affect the sensitivity and dynamic range of such systems; see my poster on this. This is now a preprint. My website is here.

Pranay went on to study Life Sciences at Columbia and was selected as a 2023 Goldwater Scholar.

last updated on 1 April 2023

Isabel Thomas

Isabel Thomas

UG research student
2020-2021

I studied mathematics and biology at Johns Hopkins University. As a Systems Biology Intern, I investigated ultrasensitivity in non-equilibrium systems under Felix Wong, Ugur Cetiner, and John Biddle in summer 2020. In summer 2021, I extended our project to explore how ultransensitivity is affected by the entropy production index under Ugur Cetiner. Outside of research, I enjoy learning languages, strength training, and baking.

last updated on 26 October 2021

Matt Thomson

Matt Thomson

Research assistant
Visiting researcher
2004-11

Matt is currently a Systems Biology Fellow at the UCSF Centre for Systems and Synthetic Biology. He first came to the lab as a research assistant and then became 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 first author on two others on multisite phosphorylation.

last updated on 28 June 2013

Ved Topkar

Ved Topkar

UG research student
2013

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

Sieu Tran

Sieu Tran

UG research student
2016

I was a Systems Biology Undergraduate Summer Research Intern in 2016, supported by NSF 1462629. I worked with Javier Estrada and others to understand how complicated the pattern of activation and repression could be for a gene regulated by a single transcription factor; see my poster describing this work. When not working at Harvard, I study mathematics, microbiology, and biological sciences at Virginia Tech University. The summer in the Gunawardena lab was an eye-opening opportunity for me as I was not even aware of the variety of systems biology research out there. I hope to continue extending on my work and develop my own model in the future.

last updated on 1 September 2016

Gary Tyree

Gary Tyree

UG research student
2017

I am an undergraduate intern from the University of Arizona. I've been studying Biomedical Engineering, Molecular & Cellular Biology, and Biochemistry in the hopes of pursuing research in Genetic Engineering and Synthetic Biology after graduation.

My research in the Gunawardena lab is focused on developing a model able to accurately represent the combinatorial and context-dependent nature that epigenetic modifications have on gene regulation; see my poster. It is currently not understood whether or not the complex regulatory effects that have been recorded in the literature have a substantial effect on gene regulation or have little impact on regulation as a whole. But as synthetic gene circuits for use in eukaryotic organisms become more complex, these epigenetic regulatory mechanisms will need to be characterized to ensure proper engineering of genomes. Thus, it's my hope that my work will be able to aid in better understanding epigenetic regulation as well as provide a new tool for synthetic biologists in the future.

last updated on 3 September 2017

Ben Ullian

Ben Ullian

UG research student
2006-7

Ben has worked on various aspects of the little b system. He is studying computer science at Columbia. Ben's work contributed to our paper PMID 18647734.

last updated on 24 February 2006

Aishwarya Venkatramani

Aishwarya Venkatramani

UG research student
2017

I am an undergraduate at UC San Diego majoring in physics and biochemistry. Currently as a summer intern at Gunawardena group, I am trying to find biological systems that show higher order cooperatively and use molecular dynamics to quantify copperativity. In the past I have done research in computational biology to identify potential drugs against malarial parasite Plasmodium falciparum at Andy McCammon's group in UCSD. I have also worked with experimental research groups to develop a program to quantify RNA in FISH experiments and a code to simulate waves of Cdk1 during S-phase synchronization in Drosophila embryos. Outside of research, I enjoy traveling, hiking, exploring new places and learning about different cultures.

last updated on 12 July 2017

Ning Wang

Ning Wang

UG research student
2012

I spent my summer of 2012 at the Gunawardena lab working with Tathagata Dasgupta and David Croll to model thymidylate synthase/tetrahydrofolate reductase. This wonderful research experience further ignited my passion in systems biology, and eventually lead me to study in Chao Tang's lab at Peking University during my gap year. Later, I obtained my PhD from UCLA bioinformatics program and trained in Alexander Hoffmann's lab, where I developed a computational platform to identify combinatorial gene regulatory strategy for key immune response genes.

Now, I am working as a bioinformatics scientist at Arcus Biosciences (a mid-size immune-oncology pharma) on immune-oncology drug development. I am spending my efforts to improve current best practice in immune-oncology drug development using systems approaches.

last updated on 1 November 2021

Danny Wells

Danny Wells

UG research student
2009

I spent the summer of 2009 in the Gunawardena lab as part of the Undergraduate Summer Research Intern program identifying novel phosphorylation cascade invariants. Expanding on previous work, I used techniques from commutative algebra and algebraic geometry to identify three new parameter-independent invariants which can be used to distinguish different cascade topologies experimentally. After graduating from Carleton College with a BA in math in 2010, I am now a third year graduate student in the Department of Engineering Sciences and Applied Mathematics at Northwestern University, where I hold an NSF Graduate Research Fellowship. My current work is in computational systems biology, specifically in developing theoretical methods to modulate the response to noise in genetic regulatory networks. I am broadly interested in computational methods for biological design and in integrating applied mathematical approaches deeper into modern biology.

last updated on 20 November 2012

Darnell (Adrian) Williams

Adrian Williams

UG research student
2018

My name is Darnell Keith Adrian Williams and I am passionate about research that has a direct affect on the health and wellbeing of people. I am currently involved in immunohistochemistry ALS research involving staining the motoneuron of mice to help examine the expression of ion channels on the cell membrane of motoneurons. In the Gunawardena lab, I am currently working on identifying regulatory differences in neuron type specification across the animal phylogeny (especially the C. elegans worm.) The poster describing my work is here. I was Elected Student Body Vice-President and will serve this upcoming school year, along with having been chosen to represent North America at the World Health Organization annual meeting in Switzerland at the United Nations building for a week to lobby for lower drug prices in third world countries. I am an avid golfer and love leadership, hanging with my friends, and listening to music.

last updated on 16 September 2018

Ezgi Wood (previously Ezgi Temamogullari)

Ezgi Temamogullari

UG research student
2010

I was a summer intern in 2010 in Jeremy's lab, where I worked with Jeremy, Tathagata and David. We had in mind the following question as the starting point: why in some processes do cells use bifunctional enzymes for two different reactions, rather than using two different enzymes? We studied several pathways containing bifunctional enzymes and then came up with a mathematical model of the EnvZ/OmpR signaling pathway which takes into account the dimerization of EnvZ in addition to its bifunctionality. This model might suggest that dimerization and bifunctionality together increase the system's robustmess to internal perturbations, such as fluctuations in EnvZ concentration.

I graduated from the Molecular Biology & Genetics and Mathematics Double Major Program at Bogazici University and did my PhD in the Mathematics Department at Duke University, working with Mike Reed. I modeled perifusion cell culture experiments and analyzed transport-reaction equations with moving source terms. As a postdoctoral researcher at UT Southwestern, I studied cellular decision making processes, analyzing mechanisms that predispose cells to their future fates before cell-fate-specific signaling starts. Currently, I am a senior research investigator in quantitative systems pharmacology at Bristol Myers Squibb, where I develop mechanistic mathematical models to support drug discovery.

last updated on 18 January 2023

Sophie Woodward

Sophie Woodward

UG research student
2019-20

I am an undergraduate student at Harvard College studying mathematics and statistics, and especially passionate about biology. I am finishing up my third year and hope to apply to graduate programs in biostatistics in the fall. From Fall 2019 to 2020, I worked with the Gunawardena lab under postdoctoral research fellow Rosa Martinez-Corral, studying energy expenditure during transcription factor binding. Specifically, I looked into the non-monotonicity of gene regulation functions; see this poster on my work. This summer I am researching with the Dominici lab at the Chan School, studying methods to correct ecological bias in a statistical analysis on COVID-19 and air pollution.

last updated on 4 May 2021

Mark Xiang

Mark Xiang

UG research studentr
2018

I am an undergraduate student at UMass Amherst double majoring in Biology and Mathematics. Currently as a summer intern at Gunawardena Lab, I am developing mathematical models of kinetic cooperativity in monomeric receptors; see my poster on this work. Outside of research, I like listening to music, camping and I want to learn skiing as well.

last updated on 16 September 2018

Yangqing Xu

Yangqing Xu

Postdoctoral fellow
2004-13

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

Katherine Xue

Katherine Xue

UG research student
2010-11

While in the Gunawardena lab in 2010-2011, Katherine worked with Tathagata Dasgupta on modeling the bifunctional enzyme thymidylate synthase-dihydrofolate reductase (TS-DHFR). She graduated from Harvard with a degree in Chemical and Physical Biology in May 2013 and plans to enter a PhD program in Genome Sciences at the University of Washington.

last updated on 28 June 2013

Pencho Yordanov

Pencho Yordanov

Postdoctoral fellow
2018-20

My research interests lie in the field of systems biology, and particularly center around the development of computational and mathematical approaches to uncover biochemical mechanisms of cellular information processing. I studied bioinformatics and computational biology at Jacobs University Bremen. I completed my PhD at ETH Zurich, where I worked in the group of Prof. Joerg Stelling and investigated differential cell signaling though the lens of algebraic graph theory.

My postdoctoral research in the Gunawardena group intends to expand the scope of the "linear framework" by relaxing its time-scale separation assumption. With the developed theory I plan to study concurrent processes acting on transcription factors such as non-specific binding and post-translational modifications away from DNA. My work is supported by the Swiss National Science Foundation.

last updated on 29 November 2018

Ziyuan Zhao

Ziyuan Zhao

UG research student
2020-21

I am currently a rising sophomore at Harvard College intending to study chemical and physical biology. I joined the lab in Spring 2020 and will work with Rosa Martinez-Corral during the summer under the support of Harvard's Program for Research in Science and Engineering (PRISE). My project will focus on the theoretical aspects of single-cell learning. My long-term academic goal is to be able to understand biological systems quantitatively with models and experiments, and I hope that journey could begin in earnest this summer.

last updated on 27 April 2020

 

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