Ph.D. Weizmann Institute of Science, 2003
Researcher at Microsoft Research Cambridge in the Programming Principles and Tools group
Principal Investigator at the Cambridge Systems Biology Centre in 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 Post-docs & Students
- Ben Hall (post-doc, MSRC)
- Anthony Gitter (post-doc, MSR-NE)
- Steven Woodhouse (Ph.D. student, Cambridge University, joint with Bertie Gottgens)
- Ariel Feiglin (Ph.D. student, Bar-Ilan University, joint with Yanay Ofran)
- Ali Sinan Koksal (intern, Ph.D. student, UC Berkeley)
- Garvit Juniwal (intern, Ph.D. student, UC Berkeley)
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)
- Lucinda Moore (M.Sc. student, Cambridge University 2012, joint with Bertie Gottgens)
- Ryan Chuang (M.Sc. student, Cambridge University 2012, joint with Bertie Gottgens)
- Antje Beyer (Ph.D. student, Cambridge University 2009-2012)
- Curtis Madsen (Ph.D. student, University of Utah, MSRC internship 2011)
Collaborations
- Rastislav Bodik (UC Berkeley, US)
- Byron Cook (Microsoft Research Cambridge, UK)
- Angela DePace (Harvard Medical School, US)
- Ernest Fraenkel (MIT, US)
- Bertie Gottgens (University of Cambridge, UK)
- Alex Hajnal (University of Zurich, Switzerland)
- Michael Hengartner (University of Zurich, Switzerland)
- Yanay Ofran (Bar-Ilan University, Israel)
- Steve Oliver (University of Cambridge, UK)
- Nir Piterman (University of Leicester, UK)
- Alex Taylor (Microsoft Research Cambridge, UK)
- Moshe Vardi (Rice University, US)
Funding
Events
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)
- Computing Cancer Nature (November 22, 2012)
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
21 Station Road
Cambridge CB1 2FB, UK
Phone: +44-1223 479 947
Fax: +44-1223 479 999
Email: jasmin.fisher"at"microsoft.com
