Upinder S Bhalla

Summary

Affiliation: National Centre for Biological Sciences
Country: India

Publications

  1. ncbi request reprint Use of Kinetikit and GENESIS for modeling signaling pathways
    Upinder S Bhalla
    GKVK Campus, National Centre for Biological Sciences, Bangalore 560065, India
    Methods Enzymol 345:3-23. 2002
  2. ncbi request reprint Models of cell signaling pathways
    Upinder S Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra Campus, Bangalore 560065, India
    Curr Opin Genet Dev 14:375-81. 2004
  3. pmc Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways
    Upinder S Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
    Biophys J 87:733-44. 2004
  4. pmc Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties
    Upinder S Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
    Biophys J 87:745-53. 2004
  5. ncbi request reprint Temporal computation by synaptic signaling pathways
    Upinder S Bhalla
    National Centre for Biological Sciences, GKVK Campus, 560065 Bangalore, India
    J Chem Neuroanat 26:81-6. 2003
  6. pmc How to record a million synaptic weights in a hippocampal slice
    Upinder S Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
    PLoS Comput Biol 4:e1000098. 2008
  7. doi request reprint Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability
    Upinder S Bhalla
    National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore 560065, India
    Neural Netw 24:943-9. 2011
  8. ncbi request reprint Understanding complex signaling networks through models and metaphors
    Upinder S Bhalla
    National Centre for Biological Sciences, GKVK Campus, Bangalore 560065, India
    Prog Biophys Mol Biol 81:45-65. 2003
  9. pmc Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states
    Upinder Singh Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
    Biophys J 101:21-32. 2011
  10. ncbi request reprint MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network
    Upinder S Bhalla
    National Center for Biological Sciences, Bangalore 560065 India
    Science 297:1018-23. 2002

Collaborators

Detail Information

Publications31

  1. ncbi request reprint Use of Kinetikit and GENESIS for modeling signaling pathways
    Upinder S Bhalla
    GKVK Campus, National Centre for Biological Sciences, Bangalore 560065, India
    Methods Enzymol 345:3-23. 2002
  2. ncbi request reprint Models of cell signaling pathways
    Upinder S Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra Campus, Bangalore 560065, India
    Curr Opin Genet Dev 14:375-81. 2004
    ..Increasing numbers of models have been developed in close conjunction with experiments, and this interplay gives a deeper and more reliable insight into signaling function...
  3. pmc Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways
    Upinder S Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
    Biophys J 87:733-44. 2004
    ..These outcomes may include washout of the signal, reinforcement of signals, and conversion of steady responses to transients...
  4. pmc Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties
    Upinder S Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
    Biophys J 87:745-53. 2004
    ..These results imply that simple scaling of signaling conditions to femtoliter volumes is unlikely, and microenvironments, such as reaction complex formation, may be essential for reliable small-volume signaling...
  5. ncbi request reprint Temporal computation by synaptic signaling pathways
    Upinder S Bhalla
    National Centre for Biological Sciences, GKVK Campus, 560065 Bangalore, India
    J Chem Neuroanat 26:81-6. 2003
    ..Downstream pathways that exhibit temporal integration or amplitude thresholding select different input patterns and thus perform temporal computation...
  6. pmc How to record a million synaptic weights in a hippocampal slice
    Upinder S Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
    PLoS Comput Biol 4:e1000098. 2008
    ..I extrapolate from current high-speed optical stimulation and recording methods, and show that this approach may scale up to the order of a million synapses in a single two-hour slice-recording experiment...
  7. doi request reprint Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability
    Upinder S Bhalla
    National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore 560065, India
    Neural Netw 24:943-9. 2011
    ..Even in this very narrow slice of cellular events, interesting system properties arise at the interface between multiple scales of cellular function...
  8. ncbi request reprint Understanding complex signaling networks through models and metaphors
    Upinder S Bhalla
    National Centre for Biological Sciences, GKVK Campus, Bangalore 560065, India
    Prog Biophys Mol Biol 81:45-65. 2003
    ..Thus, a combination of computer modeling methods to capture the complexity and details, and useful abstractions revealed by these models, is necessary to achieve both rigorous description as well as human understanding...
  9. pmc Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states
    Upinder Singh Bhalla
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
    Biophys J 101:21-32. 2011
    ..This general framework shows how the interplay between molecular movement and local reactions can generate many system functions, and give distinct identities to different parts of the cell...
  10. ncbi request reprint MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network
    Upinder S Bhalla
    National Center for Biological Sciences, Bangalore 560065 India
    Science 297:1018-23. 2002
    ..Thus, the MAPK 1, 2/PKC controller network is flexibly designed, and MAPK phosphatase may be critical for this flexible response...
  11. ncbi request reprint Biochemical signaling networks decode temporal patterns of synaptic input
    Upinder S Bhalla
    National Centre for Biological Sciences, GKVK Campus, Bangalore 560065, India
    J Comput Neurosci 13:49-62. 2002
    ..Thus the synaptic signaling network may function as a temporal decoder that transforms patterns from the time domain into the domain of chemical signaling. This may underlie different synaptic responses to different stimulus patterns...
  12. pmc Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways
    Upinder S Bhalla
    National Centre for Biological Sciences, Gandhi Krishi Vigyan Kendra Campus, Bangalore 560065, India
    Biophys J 83:740-52. 2002
    ..In the case of feedback loops, the temporal properties of the loop itself are changed. These basic tuning mechanisms may underlie specialized temporal tuning functions in more complex signaling systems in biology...
  13. ncbi request reprint The chemical organization of signaling interactions
    Upinder S Bhalla
    Neurobiology, National Centre for Biological Sciences, GKVK Campus, Bangalore 560065, India
    Bioinformatics 18:855-63. 2002
    ..The same motifs may facilitate data representation and provide functional abstraction of the chemistry...
  14. ncbi request reprint A role for ERKII in synaptic pattern selectivity on the time-scale of minutes
    Sriram M Ajay
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vignan Kendra Campus, Bangalore 560065, India
    Eur J Neurosci 20:2671-80. 2004
    ..On the basis of these combined experimental and modelling results we propose that the dynamics of PKM activation and ERKII signalling may provide a mechanism for functionally important forms of synaptic pattern selectivity...
  15. doi request reprint Laterality and symmetry in rat olfactory behavior and in physiology of olfactory input
    Kalyanasundaram Parthasarathy
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
    J Neurosci 33:5750-60. 2013
    ..Together, these results suggest that the rat olfactory system is symmetric, with highly lateralized odor flow and neuronal responses. In combination, these attributes support odor localization by differential comparison...
  16. pmc Odor representations in the rat olfactory bulb change smoothly with morphing stimuli
    Adil G Khan
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
    Neuron 57:571-85. 2008
    ..We suggest that our olfactory coding model captures many aspects of single and mixed odor representation in M/T cells...
  17. ncbi request reprint Adaptive stochastic-deterministic chemical kinetic simulations
    Karan Vasudeva
    National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore 560065, India
    Bioinformatics 20:78-84. 2004
    ..The method is fixed timestep and has first order accuracy. We compare the efficiency of this method with exact stochastic methods...
  18. pmc Simulations of inositol phosphate metabolism and its interaction with InsP(3)-mediated calcium release
    Jyoti Mishra
    National Centre for Biological Sciences, GKVK Campus, Bangalore 560065, India
    Biophys J 83:1298-316. 2002
    ..Calcium oscillations produce oscillatory responses in parts of the metabolic network and are in turn temporally modulated by the metabolism of InsP(3)...
  19. ncbi request reprint The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks
    Sudhir Sivakumaran
    National Centre for Biological Sciences, GKVK Campus, Bangalore 560065, India
    Bioinformatics 19:408-15. 2003
    ....
  20. ncbi request reprint Representation of odor habituation and timing in the hippocampus
    Sachin S Deshmukh
    National Centre for Biological Sciences, Gandhi Krishi Vignana Kendra Campus, Bangalore 560065, India
    J Neurosci 23:1903-15. 2003
    ..This may act as a neuronal substrate for habituation and for complex tasks such as odor-guided navigation...
  21. ncbi request reprint A spectrum of models of signaling pathways
    Sharat J Vayttaden
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
    Chembiochem 5:1365-74. 2004
  22. ncbi request reprint Electronic data sources for kinetic models of cell signaling
    G V HarshaRani
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
    J Biochem 137:653-7. 2005
    ..We suggest that future directions in such data sources are largely model-driven and are hinged on interoperability of data sources...
  23. ncbi request reprint Rats smell in stereo
    Raghav Rajan
    National Centre for Biological Sciences, University of Agricultural Science Gandhi Krishi Vignan Kendra Campus, Bellary Road, Bangalore, Karnataka 560065, India
    Science 311:666-70. 2006
    ..Neuronal recordings show that bulbar neurons responded differentially to stimuli from the left and stimuli from the right...
  24. pmc Signaling logic of activity-triggered dendritic protein synthesis: an mTOR gate but not a feedback switch
    Pragati Jain
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
    PLoS Comput Biol 5:e1000287. 2009
    ..We propose that these gating and stability properties may serve to suppress runaway activation of the pathway, while preserving the key role of responsiveness to multiple sources of input...
  25. pmc Theta frequency background tunes transmission but not summation of spiking responses
    Dhanya Parameshwaran
    National Centre for Biological Sciences, TIFR, Bangalore, India
    PLoS ONE 8:e55607. 2013
    ..Overall, our study suggests that although oscillations provide windows of opportunity to selectively boost transmission and EPSP size, summation of synaptic inputs remains unaffected during membrane oscillations...
  26. pmc A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity
    Sriram M Ajay
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
    HFSP J 1:49-66. 2007
    ..We propose that this propagating switch forms zones on dendrites in which plasticity is facilitated...
  27. ncbi request reprint Systems modeling: a pathway to drug discovery
    Priyamvada Rajasethupathy
    National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
    Curr Opin Chem Biol 9:400-6. 2005
    ..Systems modeling can thus fill an important niche in therapeutics by making drug discovery a faster and more systematic process...
  28. pmc Memory switches in chemical reaction space
    Naren Ramakrishnan
    Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
    PLoS Comput Biol 4:e1000122. 2008
    ..Both of these tools increased the coverage of our library of bistable systems. Thus, our systematic exploration of chemical reaction space has produced a valuable resource for investigating the key signaling motif of bistability...
  29. ncbi request reprint Synaptic plasticity in vitro and in silico: insights into an intracellular signaling maze
    Sriram M Ajay
    Temasek Life Sciences Laboratory, Singapore
    Physiology (Bethesda) 21:289-96. 2006
    ..In this review, we discuss the current state of understanding of synaptic plasticity in terms of models and experiments...
  30. ncbi request reprint Minimum information requested in the annotation of biochemical models (MIRIAM)
    Nicolas Le Novère
    European Bioinformatics Institute, Hinxton, CB10 1SD, UK
    Nat Biotechnol 23:1509-15. 2005
    ....
  31. pmc Interoperability of neuroscience modeling software: current status and future directions
    Robert C Cannon
    Textensor Limited, Edinburgh, UK
    Neuroinformatics 5:127-38. 2007
    ..cnsorg.org ). We assess the current state of interoperability of neural simulation software and explore the future directions that will enable the field to advance...