School Seminars, Events and Open Lectures
DSSP: Tools for Understanding and Programming Biological Computation
Tools for Understanding and Programming Biological Computation
Living cells assimilate various physical and chemical signals in order to make decisions. This information processing can be viewed as computation implemented using biochemical machinery. Understanding the biological computation performed by natural living systems could provide insights into cellular decision-making and reveal how diseases occur when computations go wrong. Beyond studying natural systems, the programming of biological computation, enabled by current techniques for reading, writing and editing DNA, can offer novel treatment strategies and allow the construction of engineered biochemical systems with potential transformative applications in the pharma, agriculture and energy sectors. So far, however, the complexity of biological systems has made it challenging to fully realize this promise.
Towards addressing these challenges, the Biological Computation Group at Microsoft Research is developing a variety of methods and tools for understanding and programming computation in biological systems. In this talk, I will describe approaches for expressing and analysing complex computational models using high-level domain-specific programming languages and applying formal synthesis techniques to automatically identify designs and models of biological systems capable of performing certain computations. I will illustrate how these tools are helping us understand and program biological computation, allowing us to uncover an essential biological program that governs stem cell pluripotency and design nucleic acid circuits for biochemical feedback control.
About the speaker
To prepare for interdisciplinary research at the intersection of biology and computing, Dr. Boyan Yordanov pursued a BA with a double major in biochemistry and computer science at Clark University, where he engaged in computational research of protein biochemistry and dynamics. In 2005, he joined the postgraduate program of Boston University’s Biomedical Engineering Department. As part of his PhD studies there, Dr. Boyan Yordanov developed a theoretical framework and computational tools enabling the analysis and design of synthetic gene networks through hybrid system modelling and formal verification techniques. After completing his PhD in January 2011, he worked as a post-doctoral researcher within the Mechanical Engineering Department at Boston University, focusing on the integration of these methods into bio-design automation frameworks for synthetic biology. In September 2011, Dr. Boyan Yordanov joined the Biological Computation Group at Microsoft Research as a post-doctoral scientist, working on methods allowing the characterization of components used for the construction of biological circuits. Dr. Boyan Yordanov also developed SMT-based analysis strategies for reasoning about biological systems, enabling novel approaches to the design and verification of DNA circuits and advancing the study of developmental systems and stem cell decision making. Dr. Boyan Yordanov became a permanent member of the Computational Science Laboratory at Microsoft Research in June, 2014.