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Appendix F Speaker Biographies David Berry, M.D., Ph.D., is a Partner at Flagship Ventures, having joined Flag- ship in 2005 while completing his M.D. from Harvard Medical School. David was previously awarded a Ph.D. through the Massachusetts Institute of Technol - ogy (MIT) Biological Engineering Division, where he studied the biological ef - fects of complex sugars with advisors Professor Ram Sasisekharan and Professor Robert Langer. David also did his undergraduate work at MIT, graduating in 2000 Phi Beta Kappa and Sigma Xi, with a degree in brain and cognitive sciences. He was named as a member of the MIT Corporation—its Board of Trustees—in 2006, and to the MIT Enterprise Forum Global Board in 2010. David’s work has led to 12 peer-reviewed publications, over 40 patents and applications, as well as over 30 awards and honors including the prestigious Lemelson-MIT Student Prize in 2005 for invention and innovation. David was also named the Innovator of the Year under the age of 35 by Technology Review in 2007. At Flagship, David focuses on investing in and founding early stage life science and cleantech ventures. He was a board member of Flagship portfolio company CGI Pharmaceuticals (acquired by Gilead in 2010). In 2005, as part of Flagship’s VentureLabs unit he co-founded and helped launch LS9, and more recently co-founded Joule Unlimited where he previously served as the founding CEO. In addition, David serves on the Board of Directors of Eleven Biothera - peutics and works closely with several other portfolio companies. He is currently co-founder and CEO of Theracrine, a company developing novel drugs to treat metastases. George Church, Ph.D., is professor of genetics at Harvard Medical School and Director of the Center for Computational Genetics. With degrees from Duke 539

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540 SYNTHETIC AND SYSTEMS BIOLOGY University in chemistry and zoology, he co-authored research on 3D software and RNA structure with Sung-Hou Kim. His Ph.D. from Harvard in biochemistry and molecular biology with Wally Gilbert included the first direct genomic sequenc - ing method in 1984; initiating the Human Genome Project then as a research scientist at newly formed Biogen Inc. and a Monsanto Life Sciences Research Fellow at the University of California, San Francisco (UCSF), with Gail Martin. He invented the broadly applied concepts of molecular multiplexing and tags, homologous recombination methods, and array DNA synthesizers. Technology transfer of automated sequencing and software to Genome Therapeutics Corp. resulted in the first commercial genome sequence (the human pathogen, H. pylori, in 1994). This multiplex solid-phase sequencing evolved into polonies (1999), ABI-SOLiD (2005), and open-source Polonator.org (2007) and Personal Genomes.org. He has served in advisory roles for 12 journals (including Nature Molecular Systems Biology), 5 granting agencies, and 24 biotech companies (e.g., 23andme and recently founding Codon Devices, Knome, and LS9). Current research focuses on integrating biosystems modeling with personal genomics and synthetic biology. James J. Collins, Ph.D., is an investigator of the Howard Hughes Medical In- stitute, 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. His research group works in synthetic biology and systems biology, with a particular focus on network biology approaches to antibiotic ac - tion and bacterial defense mechanisms. Andrew Ellington, Ph.D., received his B.S. in biochemistry from Michigan State University in 1981, and his Ph.D. in biochemistry and molecular biology from Harvard in 1988. As a graduate student he worked with Dr. Steve Benner on the evolutionary optimization of dehydrogenase isozymes. His postdoctoral work was with Dr. Jack Szostak at Massachusetts General Hospital, where he developed methods for the in vitro selection of functional nucleic acids and coined the term “aptamer.” Dr. Ellington began his academic career as an assistant professor of chemistry at Indiana University in 1992 and continued to develop selection meth- ods. He has received the Office of Naval Research Young Investigator, Cottrell, and Pew Scholar awards. In 1998 he moved to the University of Texas at Austin and is now the Fraser Professor of Biochemistry. Dr. Ellington’s lab works on the development of functional nucleic acids for practical applications, including aptamer biosensors, allosteric ribozyme logic gates (aptazymes), and internal - izing nucleic acids that can deliver siRNAs to cells. The next leap forward will hopefully be to develop synthetic genetic circuits that can perform amorphous

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541 APPENDIX F computations. Dr. Ellington was a member of the Defense Science Study Group, and is active in the DIA advisory group Biochem2020. Paul Freemont, Professor, FSB, holds the Chair of Protein Crystallography at Imperial College London and is currently the Head of the Division of Molecular Biosciences and Co-director of the new EPSRC Centre for Synthetic Biology and Innovation. Previous to this he was Head of the Imperial College Centre for Structural Biology having joined from Cancer Research UK London Research Institute where he was a principal scientist. His research interests over the last 20 years have focused on understanding the molecular basis and mechanisms of a number of human diseases including pathogenic infection, and he is the author of over 130 peer-reviewed scientific publications. He is currently co-leading an initiative at Imperial in the new field of synthetic biology based on engineer- ing design principles aimed at manufacturing biologically based systems and devices. He is co-founder of a spinout company Equinox Pharma Ltd and has held a number of external positions including membership of Royal Academy of Engineering enquiry into Synthetic Biology (2006–2008); current member of the Cancer Research UK Biological Sciences funding panel (since 2006); member of the Wellcome Trust Genes Molecules and Cells funding panel (2002–2005); member of the Wellcome Trust fellowships panel (2002–2005); and chair of the London Structural Biology Consortium (since 2004). Chris French, Ph.D., following a degree in biotechnology and bioprocess en- gineering, worked at the New Zealand Dairy Research Institute, developing processes for purification of high-value milk proteins, then undertook a Ph.D. at the Institute of Biotechnology, University of Cambridge, United Kingdom, during which he purified and cloned enzymes involved in biotransformations of mor- phine alkaloids and generated recombinant microorganisms for the bioconversion of morphine to higher-value opiate drugs. During his postdoctoral research at the University of Cambridge, he studied enzymes involved in degradation of explo - sives and used these to generate biosensors for explosives and transgenic plants able to break down explosive residues in soil. Dr. French was then appointed a lecturer in the Institute of Cell and Molecular Biology, University of Edinburgh, where he developed transgenic plants able to degrade chlorinated solvents, as well as biosensors for arsenic and other heavy metals. In 2006 he became inter- ested in synthetic biology and began supervising the University of Edinburgh entries in the International Genetically Engineered Machine competition (iGEM). His current research is focused on use of synthetic biology for novel whole-cell biosensors and for conversion of renewable cellulosic biomass to useful products, and collaborating on development of new technologies for synthetic biology. George Georgiou, Ph.D., is the Cockrell Endowed Professor at the University of Texas, Austin, where he has joint appointments in the Department of Chemical

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542 SYNTHETIC AND SYSTEMS BIOLOGY Engineering, Section of Molecular Genetics and Microbiology and Biomedical Engineering. He is also a member of the Institute for Cell and Molecular Biology at the University of Texas, Austin. He received his B.Sc. degree from the Univer- sity of Manchester, United Kingdom, and his Ph.D. from Cornell in 1987. He is a member of the U.S. National Academy of Engineering and a Fellow of American Society for Microbiology, the American Association for the Advancement of Sci - ences, and the American Institute of Medical and Biological Engineers. He has received numerous awards including the AIChE Professional Progress Award for outstanding contributions to chemical engineering by an individual under 45 (2003) and was named as “One of the Top 100 Eminent Chemical Engineers of the Modern Era” by AIChE (2008). His research is focused on the discovery and pharmacological optimization of protein therapeutics and also on the mecha - nisms of redox homeostasis and protein secretion in bacteria. Dr. Georgiou and his collaborators have developed one anti-infective antibody drug (Anthem™, currently in late-stage clinical development), an array of therapeutic enzymes in preclinical development, and finally, antibodies for cancer chemotherapy. Dr. Georgiou has published more than 170 research articles and is co-inventor of 38 U.S. patent applications of which 26 have been licensed to pharmaceutical and biotechnology companies. E. Peter Greenberg, Ph.D., received his bachelor’s degree from Western Wash- ington University, a master’s from the University of Iowa, and his Ph.D. from the University of Massachusetts. After a postdoctoral at Harvard, he joined the faculty at Cornell University, eventually moved back to the University of Iowa, and finally returned to the Pacific Northwest as a member of the University of Washington Medicine Microbiology faculty. He is an elected Fellow of the National Academy of Sciences, the American Academy of Arts and Sciences, the American Association for the Advancement of Science, and the American Academy of Microbiology. Dr. Greenberg has spent his scientific career uncov - ering the world of microbial social behavior. Due in part to his efforts we now understand that bacteria possess a chemical language for communication and we understand mechanisms of bacterial communication. Bacterial communica - tion controls virulence in a variety of pathogenic bacteria and has thus become a target for development of new therapeutic strategies. Bacteria have also become models for studies of selection for and evolution of cooperative behavior. Jim Heath, Ph.D., received his B.Sc. in chemistry from Baylor University in 1984 and his M.Sc. and Ph.D. in chemical physics in 1988 from Rice University. He was a Miller Research Postdoctoral Fellow at the University of California (UC), Berkeley, then joined the IBM Watson Labs as a research staff member in 1991. He was appointed assistant professor at the University of California, Los Angeles (UCLA), in 1994, and was promoted to professor in 1997. Heath founded the California NanoSystems Institute in 2000 and served as its director

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543 APPENDIX F until moving to Caltech. Heath has worked in a number of areas, including nano - materials, molecular electronics, and quantum phase transitions. More recently he has turned his efforts to addressing translational and fundamental research problems in oncology. Heath has been a recipient of several awards, including the Spiers Medal from the Royal Society, a Public Service Commendation from California Governor Gray Davis, the Sackler Prize in the Physical Sciences, and the Irvin Weinstein Prize and Lectureship from the American Association of Cancer Researchers. He has founded or co-founded several companies, includ - ing NanoSys, Momentum Biosciences, and Integrated Diagnostics. He serves as director of the National Cancer Institute–funded NSB Cancer Center. Clyde A. Hutchison III, Ph.D., is a distinguished professor in the synthetic biol- ogy group headed by Dr. Hamilton Smith at the J. Craig Venter Institute (JCVI) in San Diego, California. He graduated from Yale University (B.S., 1960), and Caltech (Ph.D., 1968), where he studied with Robert L. Sinsheimer. He joined the faculty at the University of North Carolina (UNC), Chapel Hill (1968–2005), where he collaborated with Marchall Edgell on early applications of restric - tion enzymes. While on sabbatical in Fred Sanger’s laboratory (1975–1976), he participated in determining the first complete sequence of a DNA molecule (phiX174). He developed site-directed mutagenesis with Michael Smith (1978). He also cloned and sequenced the beta-globin gene cluster in the mouse with Edgell. There they discovered L1, the major retrotransposon in the mammalian genome. In 1990, he began work with Mycoplasma genitalium, a model for the minimal cellular genome. This led to his collaboration with Smith and Venter and to his current work on synthetic genomics. In May of 2010 the Synthetic Biol- ogy Group at JCVI reported construction of the first synthetic cell. He is Kenan Professor Emeritas at UNC Chapel Hill, a member of the National Academy of Sciences, and a fellow of the American Academy of Arts and Sciences. Stephen Albert Johnston, Ph.D., is currently director of the Center for Inno- vations in Medicine in the Biodesign Institute at Arizona State University. His center focuses on formulating and implementing disruptive technologies for basic problems in health care. The center has three divisions: Genomes to Vac - cines, Cancer Eradication, and DocInBox. Genomes to Vaccines has developed high-throughput systems to screen for vaccine candidates and is applying them to predict and produce chemical vaccines. The Cancer Eradication group is working on formulating a universal prophylactic vaccine for cancer. DocInBox is devel - oping technologies to facilitate presymptomatic diagnosis. Dr. Johnston founded the Center for Biomedical Inventions (also known as the Center for Translation Research) at the University of Texas, Southwestern, the first center of its kind in the medical arena. He and his colleagues have developed numerous inventions and innovations, including the gene gun, genetic immunization, the tobacco etch virus protease system, organelle transformation, digital optical chemistry

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544 SYNTHETIC AND SYSTEMS BIOLOGY arrays, expression library immunization, linear expression elements, synbodies, immunosignaturing diagnosis, and others. He also was involved in transcription research for years, first cloning Gal4 and later discovering functional domains in transcription factors and the connection of the proteasome to transcription. He has been professor at the University of Texas Southwestern Medical Center at Dallas and associate and assistant professor at Duke University. He has been involved in several capacities as an adviser on biosecurity since 1996 and is a founding member of BioChem 20/20. Gerald F. Joyce, M.D., Ph.D., is a professor in the Departments of Chemistry and Molecular Biology, and an Investigator of the Skaggs Institute for Chemical Biology at The Scripps Research Institute in La Jolla, California. He received his B.A. from the University of Chicago in 1978 and both an M.D. and a Ph.D. from the University of California, San Diego (UCSD), in 1984. He carried out postgraduate medical training at Mercy Hospital in San Diego and postdoctoral research training at The Salk Institute before joining the faculty of The Scripps Research Institute in 1989. Dr. Joyce’s research involves the test-tube evolution of nucleic acids and the application of these methods to the development of novel RNA and DNA enzymes. He also has a longstanding interest in the origins of life and the role of RNA in the early history of life on Earth. He has published over 130 scientific papers and is the inventor of 11 issued patents. He was elected to the U.S. National Academy of Sciences in 2001. In 2005, he received the H.C. Urey Award, presented every 6 years by the International Society for the Study of the Origin of Life, and in 2010 he received the U.S. National Academy of Sciences Miller Medal. Jay Keasling, Ph.D., received his B.S. in chemistry and biology from the Uni- versity of Nebraska in 1986, received his Ph.D. in chemical engineering from the University of Michigan in 1991, and did postdoctoral work in biochemistry at Stanford University from 1991 to 1992. Keasling joined the Department of Chemical Engineering at the University of California, Berkeley, as an assistant professor in 1992, where he is currently the Hubbard Howe Distinguished Profes- sor of Biochemical Engineering. Keasling is also a professor in the Department of Bioengineering at Berkeley, a Senior Faculty Scientist and Associate Laboratory Director of the Lawrence Berkeley National Laboratory, and Chief Executive Officer of the Joint BioEnergy Institute. Dr. Keasling’s research focuses on en - gineering microorganisms for environmentally friendly synthesis of small mol - ecules or degradation of environmental contaminants. Keasling’s laboratory has engineered bacteria and yeast to produce polymers, a precursor to the antimalarial drug artemisinin, and advanced biofuels and soil microorganisms to accumulate uranium and to degrade nerve agents.

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545 APPENDIX F Kim Lewis, Ph.D., is professor of biology and Director, Antimicrobial Discovery Center at Northeastern University in Boston. He obtained his Ph.D. in biochem - istry from Moscow University in 1980 and was on the faculty of MIT, University of Maryland, and Tufts University prior to coming to Northeastern. Dr. Lewis has authored over 100 papers and is an inventor on several patents. These include the discovery of synergistically acting antimicrobials in medicinal plants; a general method to grow previously “unculturable” bacteria; the invention of sterile sur- face materials; the development of high-throughput screening for antimicrobials in a live infected animal; and the discovery of the culprit of recalcitrant biofilm infections, drug-tolerant persister cells. Dr. Lewis has presented over 70 invited lectures, including the 2005 Division A (Antimicrobial Chemotherapy) Lecture at the American Society for Microbiology General Meeting and the Harvard University Microbial Science Initiative lecture. Dr. Lewis has been a permanent member of the Drug Discovery and Drug Resistance NIH Study Section, and chair of two NIH Study Sections on Drug Discovery. Dr. Lewis is a member of Faculty 1000, a recipient of the MIT C.E. Reed Faculty Initiative Award for an innovative research project, and is a recipient of the NIH Director’s Transforma - tive RO1 Grant. Timothy Lu, M.D., Ph.D., is an assistant professor leading the Synthetic Biol- ogy Group in the Department of Electrical Engineering and Computer Science at MIT. He is also an associate member at the Broad Institute, a member of the MIT Computational and Systems Biology Initiative and the MIT Microbial Science and Engineering Program, and a cofounder of Novophage Therapeutics. Tim’s research focuses on engineering fundamental technologies to enable scalable biological systems and on applying synthetic biology to solve important medical and industrial problems, such as antimicrobial resistance and biofilms. Tim is a recipient of the Lemelson-MIT Student Prize, Grand Prize in the National Hall of Fame’s Collegiate Inventors Competition, and the Leon Reznick Memorial Prize from Harvard Medical School. He was elected to Technology Review’s TR35 for “Top Young Innovators Under 35” in 2010, named a Kavli Fellow of the National Academy of Sciences, and received the Bronze Medal (second place) and Best Paper in the Biomedical Technologies Session in the 27th Army Science Conference. Bernhard Palsson, Ph.D., is the Galetti Professor of Bioengineering and the Principal Investigator of the Systems Biology Research Group in the Department of Bioengineering at UCSD. Dr. Palsson has co-authored more than 300 peer- reviewed research articles and has authored or co-authored two textbooks, with one more in press. His research includes the development of methods to analyze metabolic dynamics (flux-balance analysis, and modal analysis), and the formula- tion of complete models of selected cells (the red blood cell, E. coli, hybridoma, and several human pathogens). He sits on the editorial board of several leading

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546 SYNTHETIC AND SYSTEMS BIOLOGY peer-reviewed microbiology, bioengineering, and biotechnology journals. He previously held a faculty position at the University of Michigan for 11 years and was named the G.G. Brown Associate Professor at Michigan in 1989, a Fulbright fellow in 1995, and an Ib Henriksen Fellow in 1996. He is the author of 38 U.S. patents, and is the co-founder of several biotechnology companies. He holds a Ph.D. in chemical engineering from the University of Wisconsin, Madison. Dr. Palsson is a member of the National Academy of Engineering and was recently voted in as a Fellow of both the AAAS and the AAM. Bali Pulendran, Ph.D., is a Charles Howard Candler Professor of Pathology and Laboratory Medicine, and Director of the Innate Immunity Program at the Emory Vaccine Center, Emory University in Atlanta. He received his under- graduate degree from Cambridge University and his Ph.D from the Walter & Eliza Hall Institute in Melbourne, Australia, under the supervision of Sir Gustav Nossal. He did his postdoctoral work at Immunex Corporation in Seattle, with Eugene Maraskovsky and Charlie Maliszweski. Dr. Pulendran’s work focuses on understanding the mechanisms by which the innate immune system regulates adaptive immunity and harnessing such mechanisms in the design of novel vac - cines against global pandemics. More recently, he has begun to apply systems biological approaches to predicting the efficacy of vaccines and deciphering new correlates of protection against infectious diseases. Dr. Pulendran’s research is published in front line journals such as Nature, Science, Cell, Nature Immunology, and the Journal of Experimental Medicine. Dr. Pulendran is the recipient of numerous grants from the NIH and from the Bill & Melinda Gates Foundation. He serves on the editorial boards of the Jour- nal of Clinical Investigation and the Journal of Immunology, the AIDS Vaccine Research Subcommittee, and is frequently invited to speak in the plenary sessions of many national and international conferences. Herbert Sauro, Ph.D., is currently an associate professor in the Department of Bioengineering at the University of Washington in Seattle. His work at present is focused on a number of areas that include development of exchange standards in synthetic biology, exploring the potential role of computer-aided design software in synthetic biology, applying engineering principles to biological networks, and understanding the factors that contribute to the demise of engineered biological networks over evolutionary time. He was one of the founding developers of the Systems Biology Markup Language, the Systems Biology Workbench, and one of the early proponents and developers of Metabolic Control Analysis. In 2008 he started the synthetic biology standards consortium (http://www.sbolstandard. org/), which has now grown to seven institutions and represents a community effort to develop exchange standards for synthetic biology design. In the past he has owned two small companies, a software consultancy business for large financial companies such as the Financial Times and GE Capital, and a company

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547 APPENDIX F that specialized in developing interactive educational software for K–12 and college-level students. He also is a proponent of open-source and affordable textbooks and online educational materials. His websites are at www.sys-bio.org, www.sysbiobooks.com, www.sbolstandards, synbio.washington.edu, and www. futureskill.com. Gregory Stephanopoulos, Ph.D., received his degrees in chemical engineering (B.S., NTU Athens; M.S., University of Florida; and Ph.D., University of Min - nesota, 1978). He taught at Caltech (1978–1985), after which he was appointed professor of chemical engineering at MIT. He served as Associate Director of the Biotechnology Process Engineering Center (1990–1997) and is also the Taplin Professor of HST (2001–present), Instructor of Bioengineering at Harvard Medi - cal School (1997–present), and the W. H. Dow Professor of Chemical Engineer- ing and Biotechnology. Professor Stephanopoulos’ current research focuses on metabolic engineer- ing, the engineering of microbes for the production of fuels and chemicals. He has co-authored or co-edited 5 books, more than 320 papers, and 35 patents and supervised more than 110 graduate and postdoctoral students. He is presently the Editor-in-Chief of Metabolic Engineering and Current Opinion in Biotechnology and serves on the editorial boards of seven scientific journals and the advisory boards of five chemical engineering departments. He has been recognized with numerous awards (Dreyfus, Excellence in Teaching-Caltech, AIChE Technical Achievement Award, PYI, AIChE-FPBE Division Award, M.J. Johnson Award of the American Chemical Society (ACS), Merck Award in Metabolic Engineering, the R.H. Wilhelm Award in Chemical Reaction Engineering of AIChE, and the Amgen Award in Biochemical Engineering). In 2002 he was elected to the AIChE Board of Directors, in 2003 to the National Academy of Engineering, and in 2005 was awarded an honorary doctorate degree (doctor technices honoris causa) by the Technical University of Denmark. In 2007 he won the C. Thom Award from SIM and the Founders Award from AIChE and in 2010 the ACS E. V. Murphree Award in Industrial and Engineering Chemistry and the George Washington Carver Award of BIO. Professor Stephanopoulos has taught undergraduate and graduate courses of the core of chemical engineering and biotechnology at Caltech and MIT and co- authored the first textbook on metabolic engineering. He is presently directing a research group of approximately 25 researchers. Christopher Voigt, Ph.D., is a synthetic biologist and an associate professor at UCSF. He holds a joint appointment as a Chemist Scientist at Lawrence Berke - ley National Labs. He is an adjunct professor at the Korea Advanced Institute of Science and Technology and an Honorary Fellow at Imperial College. He has been honored as a Sloan Fellow, Pew Scholar, Packard Fellow, MIT TR35, NSF CAREER Award, and Vaughan Lecturer. He received his B.S.E. in chemical

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548 SYNTHETIC AND SYSTEMS BIOLOGY engineering from the University of Michigan (1998) and Ph.D. in biochemistry/ biophysics at the California Institute of Technology (2002). Dr. Voigt reprograms cells to do new things by changing their DNA. Part of his work is foundational, involving the construction of new genetic sensors, circuits, and actuators and the tools required to combine these parts to create more complex programs. To push the engineering, his lab has constructed “toy systems,” including strains of bacteria that can take a photograph, perform an edge detection algorithm, swim to different targets in response to an external signal, and perform complex calcula - tions through intercellular communication. The new techniques developed using the toy systems are then applied to problems in biotechnology, including human therapeutics, green materials, and bioenergy. Hans V. Westerhoff, Ph.D., received his Ph.D. cum laude from the University of Amsterdam on the topic mosaic nonequilibrium thermodynamics and (the control of) biological free-energy transduction (1983). After a brief postdoc at the University of Padua he became Visiting Scientist at the NIH (USA) to work on DNA supercoiling, regulation and control, and antimicrobial peptides. After 6 years at the Netherlands Cancer Institute he became full professor of microbial physiology at the VU University Amsterdam, and professor of mathematical biochemistry at the University of Amsterdam. From 2005 he also holds the AstraZeneca Chair for Systems Biology at the University of Manchester, where he is director of the Manchester Centre for Integrative Systems Biology and the Doctoral Training Centre Integrative Systems Biology. Also as Director of the biennial FEBS advanced lecture course Systems Biology he actively promotes systems biology. His research interests include integrated experimental and com - putational systems biology of microorganisms, systems biology of cancer, carbon and energy metabolism, regulation of cell function, the silicon human, systems biology, and multifactorial disease. His more than 500 publications, cited more than 10,000 times, include a monograph and multiple success stories in synthetic and systems biology.