Predictive Toxicity In Silico

We have a very exciting talk this Wednesday (note the unusual day).

Title: Predictive Toxicity In Silico

Speaker: Dr. Kalyanasundaram Subramanian, popularly known as 'Kas,' is Chief Scientific Officer at Strand life sciences. Kas leads Strand's scientific and technical programs and coordinates the cross-divisional efforts in R&D. Kas's interests lie in the field of ADMET modeling and molecule design using machine learning and systems biology techniques. He has over a decade of experience in modeling biological systems.

An IIT - Bombay alumnus, Kas went on to complete his M.S. in Chemical Engineering from the State University of New York College at Buffalo. Equipped with a Ph.D. in Biomedical Engineering from Johns Hopkins University, Kas took up the position of Senior Scientist at Genetic Therapy Inc (Novartis) between 1997-2000, where he helped set-up a group to perform research in synthetic and hybrid vectors for gene delivery. Prior to Strand, Kas headed the Collaborative R&D group for immunology products at Entelos.

Abstract: Various in silico methods are employed to predict toxicity in pharmaceutical R&D. The methods can range from simple structural alerts all the way to detailed mechanistic modeling of biological systems. In my talk I will briefly go over some of these methods with a focus on structure-activity relationships, network-chemical similarity approaches and dynamic systems modeling. The talk will cover issues around how these models are built, their applicability and their impact on the pharmaceutical pipeline.I will discuss how the quality of predictions made influences decision-making.

Place: A 212, STCS seminar room

Time: Wednesday, April 13th, 2:30 pm

Catalysis in Reaction Networks

Venue: A 212 (STCS seminar room)

Date and Time: Thursday, February 24, 2:00 pm

Abstract: If networks of chemical reactions are the circuits of biology then catalysts are the switches. But which species should be called catalysts? Chemistry textbooks answer this question when there is a single reaction. For an entire network of reactions , the concept becomes more nuanced, and has been worked out in a recent paper (arXiv:1006.3627). I will discuss this notion of catalysis for reaction networks, and illustrate it with an example from the "seesaw gate" of Qian and Winfree, which is a motif for engineering large reaction networks out of DNA molecules.

Prerequisites: You should know what a graph is, what a monomial is, what the greatest common divisor of two monomials is, and what DNA is.

Chemical Reaction Networks

Date & Time: Thursday, 10th February 2011, 2:00 pm to 3:00 pm, followed by discussions.

Venue: A-212 (STCS Seminar Room) 

Abstract: An elaborate symphony is orchestrated in every living cell. The score is written in DNA, and is played out by RNA and protein enzymes, but where is the conductor of this symphony? Research in molecular biology over the past half century suggests that it is the intricate biochemical circuits (gene regulatory networks, cell signalling pathways, etc.) that play this role. It may be of value to learn to read and design the logic of biochemical circuits. I will give a tutorial-style introduction to the mathematics of chemical reaction networks, with a special emphasis on mass action kinetics.