Virtual Cell Program

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adebayo | andrew | basques | bonowski | chang | chattopadhyay | cooper | de pretis | dumitrascu | dushime | enciso | feier | flores | gibson | gnad | gupta | gyori | karp | li | lipson | mallavarapu | manrai | mirzaev | mohan | nam | owen | patel | perry | prabakaran | schleich | sullivan | temamogullari | thomson | topkar | tran | ullian | wang | wells | xu | xue

Julius Adebayo

Julius Adebayo

UG research student

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 USRI 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

Natalie Andrew

Natalie Andrew

Postdoctoral Fellow

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

Kyle Basques

Kyle Basques

UG research student

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

Felix Bonowski

Felix Bonowski

UG research student
felix at Bonowski.de

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
frdchang at gmail.com

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

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

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 USRI 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

Stefano de Pretis

Stefano de Pretis

PhD student, on internship

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

Bianca Dumitrascu

Bianca Dumitrascru

UG research student

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 USRI 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

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 USRI 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

German Enciso

German Enciso

Postdoctoral Fellow

My dissertation work was in mathematics, studying the impact of positive and negative feedback on the behavior of dynamical systems in an abstract context. I have applied this work to models of biochemical reactions and reaction diffusion systems, and I have done some modeling of retinal interneurons. In Jeremy's lab, I am developing generic modules for biochemical reactions in little b and will use them to study signal transduction pathways associated with EGF receptors. I am currently an Assistant Professor at UC Irvine.

My website is here.

last updated on 28 October 2009

Roxana Feier

Roxana Feier

UG research student

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 USRI, 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

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

Daniel Gibson

Daniel Gibson

Research Assistant

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

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

I was a Systems Biology USRI 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
website

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

last updated on 26 August 2013

Bobby Karp

Robert Karp

Postdoctoral Fellow

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

Yen-Der Li

Yen-Der Li

UG research student
yenderlimedphy at gmail.com

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
mark.lipson at gmail.com

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

Aneil Mallavarapu

Aneil Mallavarapu

Senior Research Scientist
Head of the little b project
www.littleb.org

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
manrai at fas.harvard.edu

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

Inomzhon Mirzaev

Inom Mirzaev

UG research student

Inom is from Tajikistan and was reading mathematics at the Middle Eastern Technical University (METU) in Ankara, Turkey, when he came to the group in 2011 as a summer intern. He worked on dynamical aspects of the linear framework with Jeremy and is first author on a paper on this topic. He is currently a PhD student in the Department of Applied Mathematics at the University of Colorado in Boulder.

last updated on 11 August 2013

Nandukumar Mohan

Nandukumar Mohan

UG research student

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

Chris Nam

Chris Nam

UG research student

I am an undergraduate at Swarthmore College majoring in mathematics and computer science. I joined the Gunawardena group in the summer of 2013 as a Systems Biology USRI supported by NSF 0856285. I am working on using methods from numerical algebraic geometry to characterize the parameter geography of a two-site phosphorylation system. In particular, I use Bertini and Paramotopy — recently developed software that uses homotopy continuation to solve polynomial systems — to identify the subset of this system's parameter space that gives rise to multistability and quantitatively describing the geometry and topology of this multistable region. On August 15th, 2013, I presented a poster with preliminary conclusions on these questions; I am currently working on further corroborating these claims as well as deriving new ones

last updated on 16 August 2013

Jeremy Owen

Jeremy Owen

UG research student

I was at the Gunawardena group as a Systems Biology USRI 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

Vishal Patel

Vishal Patel

UG research student
write2vishal at gmail.com

I am a 4th year student from Anna University in Chennai, India doing my senior thesis in Bioengineering. Switching between the fundamentals of Mathematics, Biochemistry and Computers, I am studying the degree to which Flux Balance Analysis can correctly predict the internal fluxes in yeast. Also, I am trying to implement different biomass equations and additional constraints to improve the reliability and prediction capability of existing networks available in the literature. I will be pursuing my graduate studies at the University of California, Irvine. My website is here

last updated on 4 May 2009

Daniela Perry

Daniela Perry

UG research student
danielaperry2015 at gmail.com

Dani was a Systems Biology USRI summer 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

Sudhakaran Prabakaran

Prabhakaran Sudhakaran

Postdoctoral Fellow
(617) 432 4842
sp339 at cam.ac.uk

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.

Personal website.

last updated on 13 Nov 2016

Kolja Schleich

Kolja Schleich

MSc student, on internship

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

Monica Sullivan

Monica Sullivan

UG research student

Monica joined the lab in 2010 as a Systems Biology USRI, supported by NSF 0856285. She was majoring in mathematics at from 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

Ezgi Temamogullari

Ezgi Temamogullari

UG research student

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 now I am a PhD candidate in the Mathematics Department at Duke University, working with Mike Reed. I am especially interested in how cells acquire information about their environment despite being "confined" by their membranes and how they process this information.

last updated on 20 November 2012

Matt Thomson

Matt Thomson

Research Assistant

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
vedtopkar at college.harvard.edu

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

You can view my website at vedtopkar.com.

last updated on 11 August 2013

Sieu Tran

Sieu Tran

UG research student
tsieu95 at vt.edu

I was a Systems Biology USRI summer 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

Ben Ullian

Ben Ullian

UG research student
bnu2101 at columbia.edu

Ben has worked on various aspects of the little b system. He is studying computer science at Columbia.

last updated on 24 February 2006

Ning Wang

Ning Wang

UG research student

I am a third year undergraduate student at the University of Science and Technology of China (USTC), in the electric engineering department. In the Gunawardena group, I am working with Tathagata Dasgupta and David Croll to compare models of thymidylate synthase/tetrahydrofolate reductase in the bifunctional and monofunctional cases. As a former member of the USTC iGEM team, I am interested in synthetic biology and systems biology. I like research into the structure of both enzyme and gene regulation networks.

last updated on 13 August 2012

Danny Wells

Danny Wells

UG research student

I spent the summer of 2009 in the Gunawardena lab as part of the USRI 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

Yangqing Xu

Yangqing Xu

Postdoctoral Fellow
yangqing_xu at hms.harvard.edu

I have broad interdisciplinary backgrounds in both biological science and engineering. With an undergraduate degree in hydraulic engineering, some of my former classmates built the Three Gorges Dam on the Yangtze River, one of the largest hydraulic constructions in the world. As the odd one out among my classmates, I developed interests in the flow inside a heart, rather than that inside a turbine. I therefore first did a Masters in bio-fluid mechanics. After focusing on biotechnology development during my PhD (in Biomedical Engineering), I joined the current laboratory and began my career in systems biology. My current research focuses on the study of complex dynamics of biological networks using a combination of quantitative imaging, cell biology and mathematical modeling. The measured dynamics leads to mathematical models for the structure and the regulation of the network, which can be iteratively tested by experiments. I apply this interdisciplinary systems biology approach to investigate information processing and decision making in growth factor signaling and autophagy cell death in mammalian cells.

I always picture a cell as a country with various factories and heavy traffic on the connecting roads, and it has been a joyful trip in such a lively world watching the constructions, transportations and battles in it. As a systems biologist, I am repeatedly amazed how a cell coordinates so many activities and functions as an integrated and self-organized kingdom, yet without a king. Looking back over the last decade, the scale of my research shrank from kilometers to nanometers, but with a dramatic increase of complexity in the system. I find it truly fascinating.

last updated on 21 December 2008

Katherine Xue

Katherine Xue

UG research student

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

 

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