NMR assignment of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis H37Rv.
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Amino Acids↗
Biomedical subjects
Himanshu Agrawal
Publications and source records attributed to Himanshu Agrawal.
Potts ferromagnets on coexpressed gene networks: identifying maximally stable partitions.
Clustering gene expression data by exploiting phase transitions in granular ferromagnets requires transforming the data to a granular substrate. We present a method using the recently introduced homogeneity order parameter Lambda [H. Agrawal, Phys. Rev. Lett. 89, 268702 (2002)]] for optimizing the parameter controlling the "granularity" and thus the stability of partitions. The model substrates obtained for gene expression data have a highly granular structure. We explore properties of phase transition in high q ferromagnetic Potts models on these substrates and show that the maximum of the width of superparamagnetic domain, corresponding to maximally stable partitions, coincides with the minimum of Lambda.
Colonic Neoplasms↗
Extreme self-organization in networks constructed from gene expression data.
We study networks constructed from gene expression data obtained from many types of cancers. The networks are constructed by connecting vertices that belong to each others' list of K nearest neighbors, with K being an a priori selected non-negative integer. We introduce an order parameter for characterizing the homogeneity of the networks. On minimizing the order parameter with respect to K, degree distribution of the networks shows power-law behavior in the tails with an exponent of unity. Analysis of the eigenvalue spectrum of the networks confirms the presence of the power-law and small-world behavior. We discuss the significance of these findings in the context of evolutionary biological processes.
Adenocarcinoma↗
Probability distribution of the sizes of the largest erased loops in loop-erased random walks.
We have studied the probability distribution of the perimeter and the area of the kth largest erased loop in loop-erased random walks in two dimensions for k=1 to 3. For a random walk of N steps, for large N, the average value of the kth largest perimeter and area scales as N(5/8) and N, respectively. The behavior of the scaled distribution functions is determined for very large and very small arguments. We have used exact enumeration for N< or =20 to determine the probability that no loop of size greater than l is erased. We show that correlations between loops have to be taken into account to describe the average size of the kth largest erased loops. We propose a one-dimensional Levy walk model that takes care of these correlations. The simulations of this simpler model compare very well with the simulations of the original problem.
Journal Article↗