vikas bansal

Molecular iodine has been used an efficient catalyst for an improved and rapid one-pot synthesis of 3,3′-arylmethylenebis-(4-hydroxycoumarin) and 2,2′-arylmethylenebis(3-hydroxyl-5,5-dimethyl -2-cyclohexen-1-one) in excellent yields using water as a reaction medium. This aqua ...

Elemental iodine is used as an efficient catalyst for the synthesis of 2,4,5-triarylimidazoles in excellent yields via condensation of benzoin, ammonium acetate, and aromatic aldehydes. This is a simple, one-pot, high yielding technique using cheap, non-toxic iodine in catalytic amounts.

Recombination is an important evolutionary mechanism responsible for creating the patterns of haplotype variation observable in human populations. Recently, there has been extensive research on understanding the fine-scale variation in recombination across the human genome using DNA polymorphism data. Historical recombination events leave signature patterns in haplotype data. A nonparametric approach for estimating the number of historical recombination events is to compute the minimum number of recombination events in the history of a set of haplotypes. In this paper, we provide new and improved methods for computing lower bounds on the minimum number of recombination events. These methods are shown to detect a higher number of recombination events for a haplotype dataset from a region in the lipoprotein lipase gene than previous lower bounds. We apply our methods to two datasets for which recombination hotspots have been experimentally determined and demonstrate a high density of detectable recombination events in the regions annotated as recombination hotspots. The programs implementing the methods in this paper are available at www.cs.ucsd.edu/users/vibansal/RecBounds/.

Phylogenetic networks are models of evolution that go beyond trees, allowing biological operations that are not consistent with tree-like evolution. One of the most important of these biological operations is recombination between two sequences (homologous chromosomes). The algorithmic problem of reconstructing a history of recombinations, or determining the minimum number of recombinations needed, has been studied in a number of papers [10, 11, 12, 23, 24, 25, 16, 13, 14, 6, 9, 8, 18, 19, 15, 1]. In [9, 6, 10, 8, 1] we introduced and used “conflict graphs” and “incompatibility graphs” to compute lower bounds on the minimum number of recombinations needed, and to efficiently solve constrained cases of the minimization problem. In those results, the non-trivial connected components of the graphs were the key features that were used. In this paper we more fully develop the structural importance of non-trivial connected components of the incompatibility graph, to establish a fundamental decomposition theorem about phylogenetic networks. The result applies to phylogenetic networks where cycles reflect biological phenomena other than recombination, such as recurrent mutation and lateral gene transfer. The proof leads to an efficient O(nm 2) time algorithm to find the underlying maximal tree structure defined by the decomposition, for any set of n sequences of length m each. An implementation of that algorithm is available. We also report on progress towards resolving the major open problem in this area.

We consider the following problem: Given a set of binary sequences, determine lower bounds on the minimum number of recombinations required to explain the history of the sample, under the infinite-sites model of mutation. The problem has implications for finding recombination hotspots and for the Ancestral Recombination Graph reconstruction problem. Hudson and Kaplan gave a lower bound based on the four-gamete test. In practice, their bound Rm often greatly underestimates the minimum number of recombinations. The problem was recently revisited by Myers and Griffiths, who introduced two new lower bounds Rh and Rs which are provably better, and also yield good bounds in practice. However, the worst-case complexities of their procedures for computing Rh and Rs are exponential and super-exponential, respectively. In this paper, we show that the number of nontrivial connected components, Rc, in the conflict graph for a given set of sequences, computable in time O(nm2), is also a lower bound on the minimum number of recombination events. We show that in many cases, Rc is a better bound than Rh. The conflict graph was used by Gusfield et al. to obtain a polynomial time algorithm for the galled tree problem, which is a special case of the Ancestral Recombination Graph (ARG) reconstruction problem. Our results also offer some insight into the structural properties of this graph and are of interest for the general Ancestral Recombination Graph reconstruction problem.