Venkatesh Mysore

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MOTIVATION Thousands of proteins are known to bind to DNA; for most of them the mechanism of action and the residues that bind to DNA, i.e. the binding sites, are yet unknown. Experimental identification of binding sites requires expensive and laborious methods such as mutagenesis and binding essays. Hence, such studies are not applicable on a large scale.(More)
Giuseppe Narzisi University of Catania, Courant Institute, NYU, Venkatesh Mysore Courant Institute, NYU, Lewis Nelson NYU School of Medicine, Dianne Rekow NYU College of Dentistry, Marc Triola NYU School of Medicine, Liza Halcomb NYU School of(More)
We describe an efficient algorithm to construct genome wide haplotype restriction maps of an individual by aligning single molecule DNA fragments collected with Optical Mapping technology. Using this algorithm and small amount of genomic material, we can construct the parental haplotypes for each diploid chromosome for any individual. Since such haplotype(More)
In this paper, we suggest a possible confluence of the theory of hybrid automata and the techniques of algorithmic algebra to create a computational basis for systems biology. We describe a method to compute bounded reachability by combining Taylor polynomials and cylindric algebraic decomposition algorithms. We discuss the power and limitations of the(More)
Agent-based models (ABMs) / multi-agent systems (MASs) are today one of the most widely used modeling– simulation–analysis approaches for understanding the dynamical behavior of complex systems. These models are often characterized by several parameters with nonlinear interactions which together determine the global system dynamics, usually measured by(More)
Presently, there is no clear way to determine if the current body of biological facts is sufficient to explain phenomenology. In the biological community, it is not uncommon to assume certain biological problems to have achieved a cognitive finality without rigorous justification. In these particular cases, rigorous mathematical models with automated tools(More)
Motivated by applications to systems biology, and the emergence of semi-algebraic hybrid systems as a natural framework for modeling biochemical networks, we continue exploring the decidability problem for model-checking with TCTL (Timed Computation Tree Logic) over this broad class of semi-algebraic hybrid systems. Previously, we had introduced these(More)
Even though many attempts have been made to define the boundary between decidable and undecidable hybrid systems, the affair is far from being solved. More and more low dimensional systems are being shown to be undecidable with respect to reachability, and many open problems in between are being discovered. In this paper, we present various two dimensional(More)
The human epidermal growth factor receptor (HER) tyrosine kinases homo- and heterodimerize to activate downstream signaling pathways. HER3 is a catalytically impaired member of the HER family that contributes to the development of several human malignancies and is mutated in a subset of cancers. HER3 signaling depends on heterodimerization with a(More)