Drawid, Amar, Gupta, Nupur, Nagaraj, Vijayalakshmi H, Gélinas, Céline, Sengupta, Anirvan M
Abstract Background DNA sequence binding motifs for several important transcription factors happen to be self-overlapping. Many of the current regulatory site identification methods do not explicitly...
Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks (2009)
Adel Dayarian, Madalena Chaves, Eduardo D. Sontag, Anirvan M. Sengupta
The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the...
Nagaraj, Vijayalakshmi H, O'Flanagan, Ruadhan A, Sengupta, Anirvan M
Abstract Background Characterizing transcription factor binding motifs is a common bioinformatics task. For transcription factors with variable binding sites, we need to get many suboptimal binding...
Shape, size and robustness: feasible regions in the parameter space of biochemical networks (2007)
Chave, Madalena, Sontag, Eduardo D., Sengupta, Anirvan M.
The concept of robustness of regulatory networks has been closely related to the nature of the interactions among genes, and the capability of pattern maintenance or reproducibility. Defining this...
Epigenetic Chromatin Silencing: Bistability and Front Propagation (2007)
Sedighi, Mohammad, Sengupta, Anirvan M.
The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in...
Quantitative modeling and data analysis of SELEX experiments (2005)
Djordjevic, Marko, Sengupta, Anirvan M.
SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is an experimental procedure that allows extracting, from an initially random pool of DNA, those oligomers with high affinity for a...
Nagaraj, Vijayalakshmi H, O'Flanagan, Ruadhan A, Bruning, Adrian R, Mathias, Jonathan R, Vershon, Andrew K, Sengupta, Anirvan M
Abstract Background The analysis of gene expression using DNA microarrays provides genome wide profiles of the genes controlled by the presence or absence of a specific transcription factor. However,...
Optimal Path to Epigenetic Switching (2004)
Roma, David Marin, O'Flanagan, Ruadhan A., Ruckenstein, Andrei E., Sengupta, Anirvan M., Mukhopadhyay, Ranjan
We use large deviation methods to calculate rates of noise-induced transitions between states in multistable genetic networks. We analyze a synthetic biochemical circuit, the toggle switch, and...
Repression of the yeast HO gene by the MAT{alpha}2 and MATa1 homeodomain proteins (2004)
Mathias, Jonathan R., Hanlon, Sean E., O'Flanagan, Ruadhan A., Sengupta, Anirvan M., Vershon, Andrew K.
The HO gene in Saccharomyces cerevisiae is regulated by a large and complex promoter that is similar to promoters in higher order eukaryotes. Within this promoter are 10 potential binding sites for...
A Biophysical Approach to Transcription Factor Binding Site Discovery (2003)
Djordjevic, Marko, Sengupta, Anirvan M., Shraiman, Boris I.
Identification of transcription factor binding sites within regulatory segments of genomic DNA is an important step toward understanding of the regulatory circuits that control expression of genes....
Communication through a Diffusive Medium: Coherence and Capacity (2000)
Moustakas, Aris L., Baranger, Harold U., Balents, Leon, Sengupta, Anirvan M., Simon, Steven H.
Coherent wave propagation in disordered media gives rise to many fascinating phenomena as diverse as universal conductance fluctuations in mesoscopic metals and speckle patterns in light scattering....
Hall effect in the perovskite manganites (1998)
Majumdar, Pinaki, Simon, Steven H., Sengupta, Anirvan M.
We compute the zero temperature phase diagram and the Hall response of the doped perovskite manganites within the model of double exchange and Jahn-Teller coupling, employing the large dimensionality...
Spin in a Fluctuating Field: The Bose (+Fermi) Kondo models (1997)
I consider models with an impurity spin coupled to a fluctuating gaussian field with or without additional Kondo coupling of the conventional sort. In the case of isotropic fluctuations, the...
Overscreened Single Channel Kondo Problem (1996)
Sengupta, Anirvan M., Kim, Yong Baek
We consider the single channel Kondo problem with the Kondo coupling between a spin $S$ impurity and conduction electrons with spin $j$. These problems arise as multicritical points in the parameter...
Non-equilibrium Dynamics Following a Quench to the Critical Point in a Semi-infinite System (1995)
Majumdar, Satya N., Sengupta, Anirvan M.
We study the non-equilibrium dynamics (purely dissipative and relaxational) in a semi-infinite system following a quench from the high temperature disordered phase to its critical temperature. We...
Non Fermi Liquid Behaviour near a $T=0$ spin-glass transition (1995)
Sengupta, Anirvan M., Georges, Antoine
In this paper we study the competition between the Kondo effect and RKKY interactions near the zero-temperature quantum critical point of an Ising-like metallic spin-glass. We consider the mean-field...
On the Emery-Kivelson Solution of the two channel Kondo problem (1993)
Sengupta, Anirvan M., Georges, Antoine
We consider the two channel Kondo model in the Emery-Kivelson approach, and calculate the total susceptibility enhancement due to the impurity $\chi_{imp}=\chi-\chi_{bulk}$. We find that $\chi_{imp}$...
Target Space Interpretation of New Moduli in 2D String Theory (1992)
Mahapatra, Swapna, Mukherji, Sudipta, Sengupta, Anirvan M.
We analyze the new states that have recently been discovered in 2D string theory by E. Witten and B. Zwiebach. Since the Liouville direction is uncompactified, we show that the deformations by the...
Instabilities in the gravitational background and string theory (1991)
We indicate the tentative source of instability in the two-dimensional black hole background. There are relevant operators among the tachyon and the higher level vertex operators in the conformal...
Specificity and robustness in transcription control networks
Sengupta, Anirvan M., Djordjevic, Marko, Shraiman, Boris I.
Recognition by transcription factors of the regulatory DNA elements upstream of genes is the fundamental step in controlling gene expression. How does the necessity to provide stability with respect...
A Biophysical Approach to Transcription Factor Binding Site Discovery
Djordjevic, Marko, Sengupta, Anirvan M., Shraiman, Boris I.
Identification of transcription factor binding sites within regulatory segments of genomic DNA is an important step toward understanding of the regulatory circuits that control expression of genes....
Combined analysis of expression data and transcription factor binding sites in the yeast genome
Nagaraj, Vijayalakshmi H, O'Flanagan, Ruadhan A, Bruning, Adrian R, Mathias, Jonathan R, Vershon, Andrew K, Sengupta, Anirvan M
Repression of the yeast HO gene by the MATα2 and MATa1 homeodomain proteins
Mathias, Jonathan R., Hanlon, Sean E., O'Flanagan, Ruadhan A., Sengupta, Anirvan M., Vershon, Andrew K.
The HO gene in Saccharomyces cerevisiae is regulated by a large and complex promoter that is similar to promoters in higher order eukaryotes. Within this promoter are 10 potential binding sites for...
Ramanathan, Sharad, Detwiler, Peter B., Sengupta, Anirvan M., Shraiman, Boris I.
G-protein-coupled enzyme cascades are used by eukaryotic cells to detect external signals and transduce them into intracellular messages that contain biological information relevant to the cell's...
Thermodynamic and kinetic modeling of transcriptional pausing
Tadigotla, Vasisht R., Maoiléidigh, Dáibhid Ó, Sengupta, Anirvan M., Epshtein, Vitaly, Ebright, Richard H., Nudler, Evgeny, ...
We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC)....
Specificity and robustness in transcription control networks
Sengupta, Anirvan M., Djordjevic, Marko, Shraiman, Boris I.
Recognition by transcription factors of the regulatory DNA elements upstream of genes is the fundamental step in controlling gene expression. How does the necessity to provide stability with respect...
A Biophysical Approach to Transcription Factor Binding Site Discovery
Djordjevic, Marko, Sengupta, Anirvan M., Shraiman, Boris I.
Identification of transcription factor binding sites within regulatory segments of genomic DNA is an important step toward understanding of the regulatory circuits that control expression of genes....
Combined analysis of expression data and transcription factor binding sites in the yeast genome
Nagaraj, Vijayalakshmi H, O'Flanagan, Ruadhan A, Bruning, Adrian R, Mathias, Jonathan R, Vershon, Andrew K, Sengupta, Anirvan M
Repression of the yeast HO gene by the MATα2 and MATa1 homeodomain proteins
Mathias, Jonathan R., Hanlon, Sean E., O'Flanagan, Ruadhan A., Sengupta, Anirvan M., Vershon, Andrew K.
The HO gene in Saccharomyces cerevisiae is regulated by a large and complex promoter that is similar to promoters in higher order eukaryotes. Within this promoter are 10 potential binding sites for...
Ramanathan, Sharad, Detwiler, Peter B., Sengupta, Anirvan M., Shraiman, Boris I.
G-protein-coupled enzyme cascades are used by eukaryotic cells to detect external signals and transduce them into intracellular messages that contain biological information relevant to the cell's...
Thermodynamic and kinetic modeling of transcriptional pausing
Tadigotla, Vasisht R., Maoiléidigh, Dáibhid Ó, Sengupta, Anirvan M., Epshtein, Vitaly, Ebright, Richard H., Nudler, Evgeny, ...
We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC)....
Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks
Dayarian, Adel, Chaves, Madalena, Sontag, Eduardo D., Sengupta, Anirvan M.
The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the...