Marc W. Kirschner Ph.D.

    Marc W. Kirschner, Ph.D. is founding chair of the Department of Systems Biology. He and John Gerhart are co-authors of Cells, Embryos, and Evolution (Blackwell, 1997) and their newly published book, The Plausibility of Life: Resolving Darwin¹s Dilemma (Yale University Press, 2005). Dr. Kirschner was elected Foreign Member of the Royal Society of London and as a Foreign Member of the Academia Europaea in 1999.  In December 2003, Kirschner received the E.B. Wilson Medal, the American Society of Cell Biology¹s highest scientific honor.

Department Faculty

    Angela DePace Ph.D.

    Angela DePace received her B.S. in Molecular Biophysics and Biochemistry from Yale University, and her Ph.D. in Biochemistry from the University of California, San Francisco where she studied with Jonathan Weissman. She conducted her postdoctoral work at the University of California Berkeley with Michael Eisen.

    Walter Fontana Ph.D.

    I moved to Harvard Medical School in September 2004, attracted by a vision of systems biology that emphasized evolution and molecular physiology. A theoretician for 16 years, I was transformed by living for a while among molecular biologists and seeing the opportunities that quantitative thinking and technology bring to experimental biology. I started a group with a theoretical and an experimental component.

    Jeremy Gunawardena Ph.D.

    I am a pure mathematician by upbringing. I received my PhD in algebraic topology from Trinity College, Cambridge in 1981 and was subsequently L.E. Dickson Instructor at the University of Chicago and Research Fellow in Pure Mathematics at Trinity College, Cambridge. I joined Hewlett-Packard (HP) Research in 1987, becoming Director of Basic Research in Europe in 1994. I held visiting academic appointments at Stanford, MIT and Cambridge and was Professeur Invitée at the École Normal Supérieure in 2000.

    John Higgins M.D.

    John Higgins received an AB in Biology from Princeton University and then worked as a computer software engineer at MathWorks, Vermeer Technologies, and Microsoft. He received an MD from the Harvard-MIT Division of Health Sciences and Technology and an SM from MIT. He has done doctoral research with David Altshuler at the Whitehead/MIT Center for Genome Research and post-doctoral research with L. Mahadevan in Applied Mathematics at Harvard University.

    Allon Klein Ph.D.

    Dr. Klein is fascinated by the question of how stem cells choose between alternative fates in developing and adult tissues. Today, one can strip differentiated cells of their fate by inducing pluripotency, yet it remains exceedingly difficult to target differentiating stem cells to a specific fate. His work focuses on germ layer specification in the South African claw-toed frog, Xenopus Laevis, which is a powerful system for studying cell fate choice and differentiation in a "native" biological context (rather than in cell culture).

    Roy Kishony Ph.D.

    The Kishony lab is interested in understanding the system-level architecture of genetic networks and the interplay between their design and the evolutionary process. They combine theoretical and experimental approaches to study epistasis networks – networks that describe how perturbations (mutations or drugs) in a given biological system combine to aggravate or alleviate each other’s effect on a phenotype.

    Galit Lahav Ph.D.

    The Lahav lab studies the temporal dynamics of biological signals by combining quantitative live imaging of single human cells with mathematical modeling. They primarily study the signaling pathway of the tumor suppressor p53, with the goal of understanding how the dynamic behavior of p53 is controlled, and how dynamics affects cell fate decisions.

    Eric S. Lander Ph.D.

    Eric S. Lander received his B.A. in mathematics from Princeton University in 1978 and his Ph.D. in mathematics from Oxford in 1981, as a Rhodes Scholar. Heserved as assistant and associate professor of managerial economics at the Harvard Business School from 1981 to 1990.  In 1986, he joined the Whitehead Institute for Biomedical Research and founded the Whitehead/MIT Center for Genome Research in 1990.  Lander became the founding director of the newly created Broad Institute of Harvard and MIT in 2003. He is also professor of biology at MIT and member of Whitehead.

    Timothy J. Mitchison Ph.D.

    My lab is interested in the structure, dynamics, and function of the cytoskeleton. We use imaging-based assays in living cells and in vitro extracts, in conjunction with molecular biology and biochemical fractionation approaches, as well as theory and modeling. Most of of the lab works on cell division in some way. One major focus is on the mechanism of mitotic spindle assembly in Xenopus egg extracts.

    Vamsi Mootha M.D.

    Vamsi Mootha received a B.S. in Mathematical and Computational Sciences from Stanford University and an M.D. from the Harvard-MIT Division of Health Sciences and Technology.  After completing his Internship and Residency in Internal Medicine at Brigham and Women’s Hospital, he conducted postdoctoral research at the Whitehead Institute at MIT. He received a MacArthur Fellowship in 2004 for his contributions to mitochondrial biology.

    Johan Paulsson Ph.D.

    The Paulsson laboratory is interested in the sources and consequences of biological noise. They derive mathematical methods to interpret and analyze noise, develop experimental methods to count molecules in single cells, and combine theory and experiment to study the behavior of the simplest natural and engineered networks.

    Jagesh V. Shah Ph.D.

    The Shah lab is interested in understanding how molecular events drive the behavior of cell-scale structures. They use molecular techniques and modern biophysical tools to develop quantitative models of endogenous and synthetic cellular networks.

    Pamela A. Silver Ph.D.

    The Silver Lab works at the interface between systems and synthetic biology to design and build biological systems in both mammalian and prokaryotic cells. Some current projects include analysis of cells that remember past events, cell-based computation and therapeutics, and metabolic engineering for bio-energy and sustainability.

    Peter Sorger Ph.D.

    Peter Sorger, Ph.D is a Professor of Systems Biology at Harvard Medical School and holds a joint appointment in MIT’s Dept. of Biological Engineering and Center for Cancer Research. He received his A.B. from Harvard College, Ph.D. from Trinity College Cambridge, U.K. and trained as a postdoctoral fellow with Harold Varmus and Andrew Murray at the University of California, San Francisco.

    Ralph Weissleder M.D., Ph.D.

    Dr. Weissleder is a Professor at Harvard Medical School, Director of the Center for Systems Biology at Massachusetts General Hospital (MGH), and Attending Clinician (Interventional Radiology) at MGH. Dr. Weissleder is also a member of the Dana Farber Harvard Cancer Center, an Associate Member of the Broad Institute (Chemical Biology Program) and a member of the Harvard Stem Cell Institute (HSCI) leading its Imaging Program. Dr. Weissleder is a graduate of the University of Heidelberg, obtained his residency training at MGH and has been on staff at HMS since 1991.

    Peng Yin Ph.D.

    The Yin lab is interested in engineering programmable molecular systems inspired by biology. At present their main focus is information directed self-assembly of nucleic acid (DNA/RNA) structures and devices, and on exploiting such systems to do useful molecular work

Lecturers & Instructors

    Gavin MacBeath Ph.D.

    The MacBeath lab is interested in  identifying, characterizing, and perturbing large collections of proteins or protein domains as a first step in understanding how the cell exploits molecular recognition to regulate complex processes such as protein trafficking, intercellular communication, growth factor signaling, and apoptosis.

    Laura Maliszewski Ph.D.

    Laura Maliszewski, PhD joined HMS in September 2012 to manage the development of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science. She served previously as an Officer in the Science and Innovation Network of the UK Foreign and Commonwealth Office, developing a broad portfolio of research collaborations in regenerative medicine, health economics and stratified medicine.

    Debora Marks, Ph.D.

    I am a computational biologist interested in how to read the genome and interpret its variation.  Recently, we have used evolutionary couplings determined from genomic sequencing to accurately protein 3D structure from sequences alone, including the experimentally challenging transmembrane proteins. Continuing from this my lab aims to predict alternative conformations and plasticity of proteins, and the consequences of protein genetic variation on pharmacological intervention.

    Mario Niepel Ph.D.

    I earned my Diplom in Molecular Biology from the RWTH Aachen in Germany and an M.S. in Biochemistry at UC Riverside in 1998. I received my Ph.D. in 2005 from the Rockefeller University in New York working in the Laboratory of Cellular and Structural Biology with Dr. Mike Rout. In 2006 I joined Dr. Peter Sorger’s laboratory as a postdoctoral fellow. I was promoted to Instructor in the Systems Biology Department at Harvard Medical School in 2009.

    Caroline Shamu Ph.D.

    Dr. Shamu is the Director of the ICCB-Longwood Screening Facility. The ICCB-Longwood Investigator Initiated Screening Program assists academic researchers in carrying out high-throughput screens of chemical and RNAi libraries to identify new tools for biological research. In addition to her expertise in implementing new high throughput assay technologies, Dr.Shamu is active in the development of data standards and repositories for large-scale datasets from high-throughput assays.

    Tiao Xie Ph.D.

    Dr. Xie's research has been mainly focused on developing customized image analysis solutions for quantitative imaging projects carried out across HMS. In biology and medical research, imaging has always been the most direct and informative readout. With the heavy investment in imaging platforms at HMS in recent years, the data being collected has quickly exceeded the capability for manual quantification. In addition to the fact that very limited number of existing solutions is available for common image analysis problem, the fact that every imaging project is designed to extract unique information making the development of customized solutions almost always a necessity.Dr. Xie has been working with the researchers at HMS and affiliated hospital to help extract data from their fluorescence images, time-lapse videos, EM images, etc. Education on image analysis to distribute his expertise has also been a main focus of his work here.

Affiliated Faculty

    James Collins Ph.D.

    James J. Collins is an Investigator of the Howard Hughes Medical Institute, and a William F. Warren Distinguished Professor, University Professor, Professor of Biomedical Engineering, Professor of Medicine and Co-Director of the Center for BioDynamics at Boston University. He is also a core founding faculty member of the Wyss Institute for Biologically Inspired Engineering at Harvard University.

    L. Mahadevan Ph.D.

    The Mahadevan group is interested in understanding the organization of matter in space and time, particularly at the scale observable by our unaided senses. We use a combination of techniques to pursue this, ranging from simple observations of phenomena to quantitative experiments and theory.

Department Fellows

    Mohammed AlQuraishi PhD.

    Dr. AlQuraishi's research interests lie at the intersection of systems and structural biology. He aims to obtain a systems-level understanding of biological processes through a molecular-level understanding of biological structures and their interactions. Towards that end he is developing computational methods for predicting the binding partners and quantitative binding affinities of biological molecules from their atomic structure. His work combines recent advances in machine learning and artificial intelligence with concepts from statistical mechanics and biophysics.

    Martin Loose Ph.D.

    Dr. Loose's  research goal is to investigate the mechanisms of biochemical self-organization. He is particularly interested in how minimal protein systems are able to organize intracellular space and how these biochemical modules are conserved or change during evolution. For this he mainly uses biochemical approaches and microscopic techniques.


    Justin Meyer, Ph.D.

    Evolution is notoriously hard to predict primarily because a key population genetic term remains undefined: the fitness landscape. While often depicted in two dimensions, with hills and valleys, true fitness landscapes are many-dimensional with complicated interactions that cannot be described by the simple slopes of a hill. Until recently, the technology did not exist to permit direct experimental determination of landscapes. And even now, the technology is slow and much too laborious to capture the enormous size and dimensionality of landscapes.

    Jeanne Salje Ph.D.

    One of the fundamental problems in biology is how the individual components of a cell act together to form the dynamic and responsive structure that is a living cell. E. coli is an excellent model system for studying basic questions of cellular self organisation due to the topological simplicity that results from a lack of membrane-bound subcellular organelles, the extensive knowledge of components that comes from decades of dedicated research, as well as the fact that as a single celled organism it is not subjected to organism-level complexity.