Publications
62 results found
Betney R, de Silva E, Mertens C, et al., 2012, Regulation of release factor expression through a translational negative feedback loop: a systems analysis, RNA
Liu C, Krishnan J, Xu X-Y, 2012, An investigation of effects of drugs on solid tunmours within a systems-based mathematical modelling framework, Innovative simulation methods in healthcare
Krishnan J, Liu C, 2012, An investigation of signal transduction and irreversible decision making in monostable and bistable circuits, Systems and Synthetic Biology: A Systematic View, Editors: kulkarni, Stan, Raman
Liu C, Krishnan J, Xu XY, 2011, A systems-based mathematical modelling framework for investigating the effect of drugs on solid tumours, THEORETICAL BIOLOGY AND MEDICAL MODELLING, Vol: 8
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- Citations: 10
Krishnan J, 2011, Chemical Engineering at the Cellular Scale: Cellular Signal Processing, INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, Vol: 50, Pages: 13236-13243, ISSN: 0888-5885
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- Citations: 1
Liu C, Krishnan J, Stebbing J, et al., 2011, Use of mathematical models to understand anticancer drug delivery and its effect on solid tumors, PHARMACOGENOMICS, Vol: 12, Pages: 1337-1348, ISSN: 1462-2416
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- Citations: 12
Seaton DD, Krishnan J, 2011, The coupling of pathways and processes through shared components, BMC SYSTEMS BIOLOGY, Vol: 5, ISSN: 1752-0509
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- Citations: 8
Krishnan J, 2011, Effects of saturation and enzyme limitation in feedforward adaptive signal transduction, IET SYSTEMS BIOLOGY, Vol: 5, Pages: 208-219, ISSN: 1751-8849
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- Citations: 8
Krishnan J, Alam-Nazki A, 2011, An investigation of design principles underlying repulsive and attractive gradient sensing and their switching, JOURNAL OF THEORETICAL BIOLOGY, Vol: 273, Pages: 80-99, ISSN: 0022-5193
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- Citations: 1
Seaton D, Krishnan J, 2011, Modular systems approach to understanding the interaction of adaptive and monostable and bistable threshold processes, IET SYSTEMS BIOLOGY, Vol: 5, Pages: 81-U25, ISSN: 1751-8849
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- Citations: 11
Seaton D, Krishnan J, 2011, Modelling the influence of allostery on crosstalk in the phosphatodylinositol pathway, IASTED International Computational Bioscience Conference, Publisher: ACTA Press
Alam-Nazki A, Krishnan J, 2010, A mathematical modelling framework for understanding chemorepulsive signal transduction in <i>Dictyostelium</i>, JOURNAL OF THEORETICAL BIOLOGY, Vol: 266, Pages: 140-153, ISSN: 0022-5193
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- Citations: 2
de Silva E, Krishnan J, Betney R, et al., 2010, A mathematical modelling framework for elucidating the role of feedback control in translation termination, JOURNAL OF THEORETICAL BIOLOGY, Vol: 264, Pages: 808-821, ISSN: 0022-5193
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- Citations: 7
Krishnan J, Seaton D, 2010, The effect of feedback regulation in irreversible biological networks, Int. Rev. of Automatic Control, Pages: 38-44
Betney R, de Silva E, Krishnan J, et al., 2010, Autoregulatory systems controlling translation factor expression: Thermostat-like control of translational accuracy, RNA, Pages: ---
In both prokaryotes and eukaryotes, the expression of a large number of genes is controlled by negative feedback, in some cases operating at the level of translation of the mRNA transcript. Of particular interest are those cases where the proteins concerned have cell-wide function in recognizing a particular codon or RNA sequence. Examples include the bacterial translation termination release factor RF2, initiation factor IF3, and eukaryote poly(A) binding protein. The regulatory loops that control their synthesis establish a negative feedback control mechanism based upon that protein’s RNA sequence recognition function in translation (for example, stop codon recognition) without compromising the accurate recognition of that codon, or sequence during general, cell-wide translation. Here, the bacterial release factor RF2 and initiation factor IF3 negative feedback loops are reviewed and compared with similar negative feedback loops that regulate the levels of the eukaryote release factor, eRF1, established artificially by mutation. The control properties of such negative feedback loops are discussed as well as their evolution. The role of negative feedback to control translation factor expression is considered in the context of a growing body of evidence that both IF3 and RF2 can play a role in stimulating stalled ribosomes to abandon translation in response to amino acid starvation. Here, we make the case that negative feedback control serves primarily to limit the overexpression of these translation factors, preventing the loss of fitness resulting from an unregulated increase in the frequency of ribosome drop-off.
Krishnan J, 2009, Signal processing through a generalized module of adaptation and spatial sensing, JOURNAL OF THEORETICAL BIOLOGY, Vol: 259, Pages: 31-43, ISSN: 0022-5193
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- Citations: 10
Krishnan J, Iglesias PA, 2009, Systems Analysis of Regulatory Processes Underlying Eukaryotic Gradient Perception, IEEE T AUTOMAT CONTR, Pages: 126-138, ISSN: 0018-9286
This paper analyzes regulatory processes involved in the biological process of directed cell locomotion-known as chemotaxis. We focus on the nature of regulation involved in a subprocess of chemotaxis called gradient perception. We examine two different models from a dynamics/control perspective to gain insight into the working mechanisms of these models. One model is a minimal model which reconciles gradient perception to the property of adaptation. The second model is a biochemical model of a lipid network and its regulation by enzymes. In both cases, we focus on the extent of regulation of the modules/networks by inputs, and examine various limiting cases. Both the models and the resulting insights hake broader applicability than the context in which they were developed.
Krishnan J, Iglesias PA, 2008, Systems analysis of regulatory processes underlying eukaryotic gradient perception, IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS I-REGULAR PAPERS, Pages: 126-138, ISSN: 1549-8328
Krishnan J, Iglesias PA, 2007, Receptor-mediated and intrinsic polarization and their interaction in chemotaxing cells, BIOPHYSICAL JOURNAL, Vol: 92, Pages: 816-830, ISSN: 0006-3495
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- Citations: 18
Krishnan J, 2007, Modelling gradient perception and polarization in chemotaxing <i>Dictyostelium</i> cells, BMC SYSTEMS BIOLOGY, Vol: 1, ISSN: 1752-0509
J Krishnan, PA Iglesias, 2005, A modeling framework describing the enzyme regulation of membrane lipids underlying gradient perception in Dictyostelium cells II: input-output analysis, Journal of Theoretical Biology, Vol: 235, Pages: 504-520, ISSN: 0022-5193
Krishnan J, Iglesias PA, 2004, Uncovering directional sensing: where are we headed?, Systems Biology, Pages: 54-61, ISSN: 1741-2471
Paliwal S, Ma L, Krishnan J, et al., 2004, Responding to directional cues: a tale of two cells, Control Systems Magazine, Pages: 77-90, ISSN: 1066-033X
J Krishnan, PAIglesias, 2004, A modeling framework describing the enzyme regulation of membrane lipids underlying gradient perception in Dictyostelium cells, Journal of Theoretical Biology, Vol: 229, Pages: 85-99, ISSN: 0022-5193
Krishnan J, Runborg O, Kevrekidis IG, 2004, Bifurcation analysis of nonlinear reaction-diffusion problems using wavelet-based reduction techniques, Computers and Chemical Engineering, Vol: 28, Pages: 557-574, ISSN: 0098-1354
Krishnan J, Iglesias PA, 2003, Analysis of the signal transduction properties of a module of spatial sensing in eukaryotic chemotaxis, Bulletin of Mathematical Biology, Vol: 65, Pages: 95-128, ISSN: 0092-8240
Krishnan J, Iglesias PA, Ma L, 2001, Analysis of a reaction-diffusion model of spatial sensing, International Conference on Systems Biology, Pages: 147-159
Or-guil M, Krishnan J, Kevrekidis IG, et al., 2001, A computational study of pulse dynamics in ring-shaped domains, Physical review E, Vol: 64, Pages: 212-222
J Krishnan, K Engelborghs, M Bar, et al., 2001, A computer-assisted study of pulse dynamics in anisotropic media, Physica D, Vol: 154, Pages: 85-110, ISSN: 0167-2789
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