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Mutation-selection networks of cancer initiation: tumor suppressor genes and chromosomal instability.
Komarova NL, Sengupta A, Nowak MA. Komarova NL, et al. Among authors: sengupta a. J Theor Biol. 2003 Aug 21;223(4):433-50. doi: 10.1016/s0022-5193(03)00120-6. J Theor Biol. 2003. PMID: 12875822
A main assumption is that cancer is initiated in tissue compartments, where only a relatively small number of cells are at risk of mutating into cells that escape from homeostatic regulation. In this case, the evolutionary dynamics can be approximated by a lo
A main assumption is that cancer is initiated in tissue compartments, where only a relatively small number of cells are at ris
The role of chromosomal instability in tumor initiation.
Nowak MA, Komarova NL, Sengupta A, Jallepalli PV, Shih IeM, Vogelstein B, Lengauer C. Nowak MA, et al. Among authors: sengupta a. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16226-31. doi: 10.1073/pnas.202617399. Epub 2002 Nov 21. Proc Natl Acad Sci U S A. 2002. PMID: 12446840 Free PMC article.
Chromosomal instability (CIN) is a defining characteristic of most human cancers. Mutation of CIN genes increases the probability that whole chromosomes or large fractions of chromosomes are gained or lost during cell division. ...A major question of cancer genetics …
Chromosomal instability (CIN) is a defining characteristic of most human cancers. Mutation of CIN genes increases the probability tha …
Stochastic evolutionary dynamics on two levels.
Traulsen A, Sengupta AM, Nowak MA. Traulsen A, et al. Among authors: sengupta am. J Theor Biol. 2005 Aug 7;235(3):393-401. doi: 10.1016/j.jtbi.2005.01.019. J Theor Biol. 2005. PMID: 15882701
We consider a population that is subdivided into groups. Individuals reproduce proportional to their fitness. When a group reaches a certain size it has a probability to split into two groups while another group is eliminated. ...We show that the descr …
We consider a population that is subdivided into groups. Individuals reproduce proportional to their fitness. When a group rea …
Inheritance of epigenetic chromatin silencing.
David-Rus D, Mukhopadhyay S, Lebowitz JL, Sengupta AM. David-Rus D, et al. Among authors: sengupta am. J Theor Biol. 2009 May 7;258(1):112-20. doi: 10.1016/j.jtbi.2008.12.021. Epub 2008 Dec 31. J Theor Biol. 2009. PMID: 19174167 Free PMC article.
In addition, DNA duplication and the consequent dilution of marked histones act as a large perturbation for a stable state of histone modifications. ...
In addition, DNA duplication and the consequent dilution of marked histones act as a large perturbation for a stable state of …
Epigenetic chromatin silencing: bistability and front propagation.
Sedighi M, Sengupta AM. Sedighi M, et al. Among authors: sengupta am. Phys Biol. 2007 Nov 7;4(4):246-55. doi: 10.1088/1478-3975/4/4/002. Phys Biol. 2007. PMID: 17991991 Free PMC article.
Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. ...The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. …
Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms …
The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state.
Mukhopadhyay S, Sengupta AM. Mukhopadhyay S, et al. Among authors: sengupta am. PLoS Comput Biol. 2013;9(7):e1003121. doi: 10.1371/journal.pcbi.1003121. Epub 2013 Jul 18. PLoS Comput Biol. 2013. PMID: 23874171 Free PMC article.
We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. ...We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive r …
We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the …
Breaking an epigenetic chromatin switch: curious features of hysteresis in Saccharomyces cerevisiae telomeric silencing.
Nagaraj VH, Mukhopadhyay S, Dayarian A, Sengupta AM. Nagaraj VH, et al. Among authors: sengupta am. PLoS One. 2014 Dec 23;9(12):e113516. doi: 10.1371/journal.pone.0113516. eCollection 2014. PLoS One. 2014. PMID: 25536038 Free PMC article.
We study hysteresis in this system by perturbing it with a histone deacetylase inhibitor. We find that SIR silencing has many characteristics of a non-linear bistable system, as observed in conventional genetic switches, which are based on activities of a few …
We study hysteresis in this system by perturbing it with a histone deacetylase inhibitor. We find that SIR silencing has many charact …
Shape, size, and robustness: feasible regions in the parameter space of biochemical networks.
Dayarian A, Chaves M, Sontag ED, Sengupta AM. Dayarian A, et al. Among authors: sengupta am. PLoS Comput Biol. 2009 Jan;5(1):e1000256. doi: 10.1371/journal.pcbi.1000256. Epub 2009 Jan 2. PLoS Comput Biol. 2009. PMID: 19119410 Free PMC article.
In this paper, we show that, in addition to volume, the geometry of this region has important consequences for the robustness and the fragility of a network. ...Our method provides a more complete measure of robustness to parameter variation. As a general mod …
In this paper, we show that, in addition to volume, the geometry of this region has important consequences for the robustness and the fragil …
Thermodynamic and kinetic modeling of transcriptional pausing.
Tadigotla VR, O Maoiléidigh D, Sengupta AM, Epshtein V, Ebright RH, Nudler E, Ruckenstein AE. Tadigotla VR, et al. Among authors: sengupta am. Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4439-44. doi: 10.1073/pnas.0600508103. Epub 2006 Mar 13. Proc Natl Acad Sci U S A. 2006. PMID: 16537373 Free PMC article.
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). ...We also present a kinetic model for the rate of recovery of bac …
We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived fr …
Optimal path to epigenetic switching.
Roma DM, O'Flanagan RA, Ruckenstein AE, Sengupta AM, Mukhopadhyay R. Roma DM, et al. Among authors: sengupta am. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jan;71(1 Pt 1):011902. doi: 10.1103/PhysRevE.71.011902. Epub 2005 Jan 11. Phys Rev E Stat Nonlin Soft Matter Phys. 2005. PMID: 15697625
We analyze a synthetic biochemical circuit, the toggle switch, and compare the results to those obtained from a numerical solution of the master equation....
We analyze a synthetic biochemical circuit, the toggle switch, and compare the results to those obtained from a numerical solu …
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