
Ph.D. Weizmann Institute of Science, 2003
Researcher at Microsoft Research Cambridge in the Programming Principles and Tools group
Affiliated Lecturer in the Cambridge Systems Biology Centre & Department of Biochemistry at University of Cambridge
Executable Biology
Our research focuses on the design and analysis of executable computer algorithms describing biological phenomena. We call this approach Executable Biology. These kinds of models hold great promise for new discoveries in a wide variety of biological systems. Once an executable model has been built of a particular system, it can be used to get a global dynamic picture of how the system responds to various perturbations. In addition, preliminary studies can be quickly performed using executable models, saving valuable laboratory time and resources for only the most promising avenues.
Research Overview
Our work is focused on two main directions:
(1) The use of different formalisms to create executable models of biological phenomena, aiming to gain new insights into the molecular mechanisms underlying the fundamental question of cell fate determination (or in other words - how cells make the decision to develop into a particular cell type) during the course of normal development (e.g., our work on C. elegans vulval development, blood stem cells development, regulation of cell-cycle quiescence in C. cereviciae), and in disease (e.g., stem cell differentiation in mammalian epidermis, EGFR/Notch/Wnt crosstalk in cancer cells, regulation of leukaemic blood stem cells).
(2) The development of tools and design of algorithms that are specifically tailored for modelling biological systems (e.g., bounded-asynchrony). We put a lot of emphasis on constructing user-friendly tools (i.e., visual, flexible), in order to facilitate the integration of such computational tools as mainstream techniques in biological research (e.g., Bio Model Analyzer).
Research Projects
Publications
Current Students
- Antje Beyer (Ph.D. student, Cambridge University)
- Ariel Feiglin (Ph.D. student, Bar-Ilan University, joint with Yanay Ofran)
- Ryan Chuang (M.Sc. student, Cambridge University)
- Lucinda Moore (M.Sc. student, Cambridge University, joint with Bertie Gottgens)
Former Post-docs & Students
- Sari Bacall (summer internship, Weizmann Institute of Science, 2003)
- Naamah Swerdlin (M.Sc. rotation, Weizmann Institute of Science, 2004)
- Dvir Netanely (M.Sc. rotation, Weizmann Institute of Science, 2004)
- Susmit Jha (summer internship, EPFL, 2005)
- Marc Schaub (M.Sc. student, EPFL, 2005-2006)
- Luvish Satija (summer internship, EPFL, 2006)
- Vaibahav Rajan (semester project, EPFL, 2006)
- Andrei Popescu (summer internship, joint with Byron Cook, MSRC, 2008)
- Dennis Wang (M.Sc. student, Cambridge University, 2008)
- Christopher Doman (Part II project, Cambridge University, 2007-2008)
- Antje Beyer (M.Sc. student, Cambridge University, 2008)
- Maria Mateescu (Ph.D. student, EPFL, joint with Tom Henzinger, 2006-2009)
- Luke Church (Ph.D. student, Cambridge University, 2007-2009)
- Avital Sadot (Post-doc, joint with David Harel, 2007-2010)
- Garth Ilsley (Ph.D. student, EBI, Cambridge, 2007-2010)
- Elzbieta Krepska (Ph.D. student, MSRC internship 2010, joint with Byron Cook)
- Peter Ackermann (M.Sc. student, Cambridge University 2011, joint with Steve Oliver)
- Jishnu Das (Ph.D. student, Cornell University, MSRC internship 2011)
- Nicola Bonzanni (Ph.D. student, VU University Amsterdam)
- Qinsi Wang (Ph.D. student, Carnegie Mellon University, MSRC internship 2011)
Collaborations
- Luca Cardelli (Microsoft Research Cambridge, UK)
- Byron Cook (Microsoft Research Cambridge, UK)
- Angela DePace (Harvard Medical School, US)
- Walter Fontana (Harvard Medical School, US)
- Bertie Gottgens (MRC Cambridge, UK)
- Alex Hajnal (University of Zurich, Switzerland)
- David Harel (Weizmann Institute of Science, Israel)
- Michael Hengartner (University of Zurich, Switzerland)
- Tom Henzinger (IST, Austria)
- Ritsert Jansen (University of Groningen, The Netherlands)
- Phil Jones (MRC Cambridge, UK)
- Jan Kammenga (Wageningen University, The Netherlands)
- Gos Micklem (Cambridge University, UK)
- Yanay Ofran (Bar-Ilan University, Israel)
- Steve Oliver (Cambridge University, UK)
- Nir Piterman (University of Leicester, UK)
- Poulin Gino (Manchester University, UK)
- Freddy Radtke (EPFL, Switzerland)
- James Scott (Imperial College London, UK)
- Alex Taylor (Microsoft Research Cambridge, UK)
- Moshe Vardi (Rice University, US)
Funding
Events
Formal Methods in Systems Biology June 4-5, 2008 Cambridge, UK
In the press
- Executable Biology: Computer Science Sheds Light On Animal Development
ScienceDaily (May 18, 2007) - Boffins turn to 'executable biology': Biological processes mapped as computer programs
New Scientist (November 9, 2007) - Upgraded systems biology?
Scientific Computing (November 13, 2007) - Computationa Biology: Biological Logic
Nature (November 26, 2009) - Injecting new life into cell-based assays Genetic Engineering News (September 15, 2011)
Jobs
If you are seeking a postdoctoral, PhD or MSc position and have an interest in joining our lab, please send your CV including a statement of interests to jasmin.fisher ''at'' microsoft.com
Contact
Dr. Jasmin Fisher
Microsoft Research Cambridge
7 JJ Thomson Ave.
Roger Needham Building
Cambridge CB3 0FB, UK
Phone: +44-1223 479 947
Fax: +44-1223 479 999
Email: jasmin.fisher"at"microsoft.com



