Ph.D. Weizmann Institute of Science, 2003

Researcher at Microsoft Research Cambridge

Affiliated Lecturer in the Cambridge Systems Biology Centre & Department of Biochemistry at University of Cambridge & the Computing Lab at University of Oxford 

Executable Biology

Our research focuses on the design and analysis of executable computer algorithms that mimic 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 enhance our comprehension of cell processing information (e.g., programmed cell death, cell cycle), developmental processes (e.g., C. elegans vulval development, segmentation process in Drosophila), and biological networks operating in disease (e.g., EGFR/Notch/Wnt crosstalk in cancer, metabolic disturbances in diabetes and obesity).

(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., Qualitative Networks, BioCharts).

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

• 'Computer - programmed' cell death

• Abstractions and large-scale modelling of biological signalling networks

• Multi-scale modelling of animal development

• Formal modelling languages designed specifically for biological systems

Publications

• Journals
• Book chapters
• Refereed Conference Papers

Post-docs & Students

• Avital Sadot (Post-doc, joint with David Harel)
• Garth Ilsley (Ph.D. student, EBI, Cambridge)
• Antje Beyer (Ph.D. student, Cambridge University)
• Marina Shudler (Ph.D. student, Weizmann Institute, joint with David Harel)
• Ariel Feiglin (Ph.D. student, Bar-Ilan University, joint with Yanay Ofran)
• Elzbieta Krepska (Ph.D student, MSRC internship, joint with Byron Cook)
• Nicola Bonzanni (Ph.D student, MSRC internship)

Former 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)

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)
• Poulin Gino (Manchester University, UK)
• Alex Hajnal (University of Zurich, Switzerland)
• David Harel (Weizmann Institute of Science, Israel)
• Michael Hengartner (University of Zurich, Switzerland)
• Tom Henzinger (EPFL, Switzerland)
• Ritsert Jansen (University of Groningen, The Netherlands)
• Jan Kammenga (Wageningen University, The Netherlands)
• Adi Kimchi (Weizmann Institute of Science, Israel)
• Gos Micklem (Cambridge University, UK)
• Yanay Ofran (Bar-Ilan University, Israel)
• Nir Piterman (Imperial College London, UK)
• Freddy Radtke (ISREC, Switzerland)
• James Scott (Imperial College London, UK)
• Roy Varshavsky (Microsoft R&D, Israel)

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