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 

• Predictive modelling of C. elegans vulval development
• Computational analysis of segmentation in Drosophila embryogenesis
• Mechanistic insights into metabolic disturbance during Diabetes and Obesity
• Modelling of the Notch/Wnt crosstalk in keratinocytes
• Algorithms to characterize stabilization of biological systems
• Abstractions and large-scale modelling of biological signalling networks
• Multi-scale modelling of cell growth regulation in S. cerevisiae
• Formal modelling languages designed specifically for biological systems

Publications

• Journals
• Book chapters
• Refereed Conference Papers

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

• Swiss National Science Foundation
• PANACEA, FP7 European Consortium

Events

Formal Methods in Systems Biology June 4-5, 2008 Cambridge, UK

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