Contents Detailed Methods 2 Supplementary Table 5 (2009)
Illés J Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N
basis of signal integration in the transcriptionalregulatory
3.1.2 Functional Motions of Proteins Are Cooperative (2008)
A. J. Rader, Chakra Chennubhotla, Lee-wei Yang, Ivet Bahar
Structure and Function.............................................. 43
Perceptual Distance Normalization for Appearance Detection (2008)
Chakra Chennubhotla, Allan Jepson
In this paper we develop a novel contrast-invariant appearance detection model. The goal is to classify object-specific images (e.g. face images) from generic background patches. The novel...
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations (2007)
Chakra Chennubhotla, Ivet Bahar
Elastic network (EN) models have been widely used in recent years for describing protein dynamics, based on the premise that the motions naturally accessible to native structures are relevant to...
Eyal, Eran, Chennubhotla, Chakra, Yang, Lee-Wei, Bahar, Ivet
Motivation: A common practice in X-ray crystallographic structure refinement has been to model atomic displacements or thermal fluctuations as isotropic motions. Recent high-resolution data reveal,...
1 Markov Methods for Protein Dynamics (2007)
Prof Ivet Bahar, Chakra Chennubhotla, Ivet Bahar
Elastic network models (ENMs), and in particular the Gaussian Network Model (GNM), have been widely used in recent years to gain insights into the machinery of proteins. The extension of ENMs to...
Farkas, Illes J., Wu, Chuang, Chennubhotla, Chakra, Bahar, Ivet, Oltvai, Zoltan N.
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response...
Farkas, Illés J, Wu, Chuang, Chennubhotla, Chakra, Bahar, Ivet, Oltvai, Zoltán N
Abstract Background Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in...
Markov methods for hierarchical coarse-graining (2006)
Chakra Chennubhotla, Ivet Bahar
Elastic network models (ENMs) and, in particular, the Gaussian Network Model (GNM) have been widely used in recent years to gain insights into the machinery of proteins. The extension of ENMs to...
Hierarchical eigensolver for transition matrices in spectral methods (2005)
Chakra Chennubhotla, Allan D. Jepson
We show how to build hierarchical, reduced-rank representation for large stochastic matrices and use this representation to design an efficient algorithm for computing the largest eigenvalues, and...
Spectral embedding and min-cut for image segmentation (2004)
Francisco Estrada, Allan Jepson, Chakra Chennubhotla
Recently it has been shown that min-cut algorithms can provide perceptually salient image segments when they are given appropriate proposals for source and sink regions. Here we explore the use of...
Half-lives of eigenflows for spectral clustering (2002)
Chakra Chennubhotla, Allan D. Jepson
Using a Markov chain perspective of spectral clustering we present an algorithm to automatically find the number of stable clusters in a dataset. The Markov chain’s behaviour is characterized by...
Sparse coding in practice (2001)
Chakra Chennubhotla, Allan Jepson
The goal in sparse coding is to seek a linear basis representation where each image is represented by a small number of active coefficients. The learning algorithm involves adapting a basis vector...
Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES
Chennubhotla, Chakra, Bahar, Ivet
We introduce a novel approach for elucidating the potential pathways of allosteric communication in biomolecular systems. The methodology, based on Markov propagation of ‘information' across the...
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
Chennubhotla, Chakra, Bahar, Ivet
Elastic network (EN) models have been widely used in recent years for describing protein dynamics, based on the premise that the motions naturally accessible to native structures are relevant to...