Research Publications

  • Bhalla US. HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Comput Biol 2021 Nov 29;17(11):e1009621. https://doi.org/10.1371/journal.pcbi.1009621
  • G V HarshaRani, S Moza, N Ramakrishnan, Bhalla US. SWITCHES: Searchable web interface for topologies of CHEmical switches. Bioinformatics 2021 Jan 18;btab006. DOI: 10.1093/bioinformatics/btab006.
  • Bhatia A, Moza S, Bhalla US.Optogenetic Stimulation Using a DMD Projector.Methods Mol Biol. 2021;2191:173-188. DOI: 10.1007/978-1-0716-0830-2_11.
  • Dwivedi D, Chattarji S, Bhalla US. Impaired Reliability and Precision of Spiking in Adults But Not Juveniles in a Mouse Model of Fragile X Syndrome. eNeuro. 2019 Dec 3;6(6):ENEURO.0217-19.2019. doi: 10.1523/ENEURO.0217-19.2019.
  • Bhatia A, Moza S, Bhalla US. Precise excitation-inhibition balance controls gain and timing in the hippocampus.2019 Apr 25;8.doi: 10.7554/eLife.43415.
  • D Singh, Bhalla US. Subunit exchange enhances information retention by CaMKII in dendritic spines. 2018 Jul 19; doi: http://dx.doi.org/10.1101/372748.
  • Biju Viswanath, Naren P. Rao, Janardhanan C. Narayanaswamy, Palanimuthu T. Sivakumar, Arun Kandasamy, Muralidharan Kesavan, Urvakhsh Meherwan Mehta, Ganesan Venkatasubramanian, John P. John, Odity Mukherjee, Meera Purushottam, Ramakrishnan Kannan, Bhupesh Mehta, Thennarasu Kandavel, B. Binukumar, Jitender Saini, Deepak Jayarajan, A. Shyamsundar, Sydney Moirangthem, K. G. Vijay Kumar, Jagadisha Thirthalli, Prabha S. Chandra, Bangalore N. Gangadhar, Pratima Murthy, Mitradas M. Panicker, Bhalla US, Sumantra Chattarji, Vivek Benegal, Mathew Varghese, Janardhan Y. C. Reddy, Padinjat Raghu, Mahendra Rao and Sanjeev Jain. Discovery biology of neuropsychiatric syndromes (DBNS): a center for integrating clinical medicine and basic science. 2018 Jul 26; https://doi.org/10.1186/s12888-018-1674-2
  • DT Vooturi, K Kothapalli, Bhalla US. Parallelizing Hines Matrix Solver in Neuron Simulations on GPU. 2018 Feb 08 doi: 10.1109/HiPC.2017.00051
  • Bhalla US. Dendrites, deep learning, and sequences in the hippocampus. Hippocampus. 2017 Oct 12. doi: 10.1002/hipo.22806
  • Bhalla US. Synaptic input sequence discrimination on behavioral timescales mediated by reaction-diffusion chemistry in dendrites. Elife. 2017 Apr 19;6. pii: e25827. doi: 10.7554/eLife.25827.
  • Brocke E, Djurfeldt M, Bhalla US, Kotaleski JH, Hanke M. Multirate method for co-simulation of electrical-chemical systems in multiscale modeling.J Comput Neurosci. 2017 Jun;42(3):245-256. doi: 10.1007/s10827-017-0639-7. Epub 2017 Apr 7.
  • Brocke E, Bhalla US, Djurfeldt M, Hellgren Kotaleski J, Hanke M.  Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations. Front Comput Neurosci. 2016 Sep 12;10:97. doi: 10.3389/fncom.2016.00097.
  • Nair AG, Bhalla US, Hellgren Kotaleski J.  Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration. PLoS Comput Biol. 2016 Sep 1;12(9):e1005080. doi: 10.1371/journal.pcbi.1005080.
  • Gupta P, Bhalla US. Minority odors get equal say. Elife. 2016 Jun23:5. pii: e18037. doi: 10.7554/eLife. 18037.
  • Muthmann JO, Amin H, Sernagor E, Maccione A, Panas D, Berdondini L, Bhalla US, Hennig MH. Spike Detection for Large Neural Populations Using High Density Multielectrode Arrays. Front Neuroinform. 2015 Dec 18;9:28. doi: 10.3389/fninf.2015.00028. eCollection 2015.
  • Bhattacharyya U, Singh Bhalla U. Robust and Rapid Air-Borne Odor Tracking without Casting(1,2,3). eNeuro. 2015 Dec 7;2(6). pii: ENEURO.0102-15.2015. doi:10.1523/ENEURO.0102-15.2015. eCollection 2015 Nov-Dec.
  • Ray S, Chintaluri C, Bhalla US, Wójcik DK. NSDF: Neuroscience Simulation Data Format. Neuroinformatics. 2015 Nov 19. [Epub ahead of print]
  • Gilra A, Bhalla U S. Bulbar microcircuit model predicts connectivity and roles of interneurons in odor coding. PLoS One. 2015 May 5;10(5):e0098045. doi: 10.1371/journal.pone.0098045. eCollection 2015.
  • Gupta P, albeanu DF, Bhalla U S. Olfactory bulb coding of odors, mixtures and sniffs is a linear sum of odor time profiles. Nat Neurosci. 2015 Feb: 18(2):272-81. doi:10.1038/nn.3913. Epub 2015 Jan 12.
  • Jain P,  Bhalla U S. Transcription control pathways decode patterned synaptic inputs into diverse mRNA expression profiles. PLoS One. 2014 May 1;9(5):e95154. doi: 10.1371/journal.pone.0095154. eCollection 2014.
  • Bhalla U S. Molecular computation in neurons: a modeling perspective. Curr Opin Neurobiol. 2014 Apr;25:31-7. doi: 10.1016/j.conb.2013.11.006. Epub 2013 Dec 12.
  • Modi MN, Dhawale Ak, Bhalla U S. CA1 cell activity sequences emerge after reorganization of network correlation structure during associative learning. Elife (Cambridge). 2014 Mar 25;3:e01982. doi: 10.7554/eLife.01982.
  • Bhalla U S. Multiscale modeling and synaptic plasticity. Prog Mol Biol Transl Sci. 2014;123:351-86. doi: 10.1016/B978-0-12-397897-4.00012-7.
  • Parthasarathy K,  Bhalla U S. Laterality and symmetry in rat olfactory behavior and in physiology of olfactory input.  J Neurosci. 2013 Mar 27;33(13):5750-60. doi: 10.1523/JNEUROSCI.1781-12.2013.
  • Parameshwaran D, Bhalla U S. Theta frequency background tunes transmission but not summation of spiking respones. PLoS One. 2013;8(1):e55607. doi: 10.1371/journal.pone.0055607. Epub 2013 Jan 31.
  • Parameshwaran D, Bhalla U S. Summation in the Hippocampal CA3-CA1 Network Remains Robustly Linear Following Inhibitory Modulation and Plasticity, but Undergoes Scaling and Offset Transformations.  Front Comput Neurosci. 2012;6:71. doi: 10.3389/fncom.2012.00071. Epub 2012 Sep 25
  • Khan, A.G Sarangi, M, & Bhalla U S. Rats track odour trails accurately using a multi-layered strategy with near-optimal sampling(2012),
  • Khan, A.G Sarangi, M, & Bhalla, U.S. Rats track odour trails accurately using a multi-layered strategy with near-optimal sampling(2012),  Nature Communications, 3:703
  • Bhalla US. Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable States (2011).Biophys J. 2011 Jul 6;101(1):21-32
  • Bhalla US. Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability (2011). Neural Netw. 2011 May 10
  • Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US,, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N(2011). Minimum Information About a Simulation Experiment (MIASE).PLoS Comput Biol. 2011 Apr;7(4):e1001122
  • Dhawale AK, Hagiwara A, Bhalla, U.S, Murthy VN, Albeanu DF (2010).Non-redundant odor coding by sister mitral cells revealed by light addressable glomeruli in the mouse. Nat Neurosci. 2010 Nov;13(11):1306-7
  • Khan, A.G., Parthasarathy, K. and Bhalla, U.S. (2010). Odor representations in the mammalian olfactory bulb. Wiley Interdiscip Rev Syst Biol Med. 2010 Sep-Oct;2(5):603-11
  • Gleeson, P., Crook, S., Cannon, R., Hines, M., Billings, G.O., Farinella, M., Morse, T.M., Davison, A.P., Ray, S., Bhalla, U.S., Barnes, S.R., Dimitrova, Y.D., R Angus, Silver, A. and Neuro,M.L.(2010). A language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Computational BiologyPLoS Comput Biol. 2010 Jun 17;6(6):e1000815
  • Djurfeldt ,M., Hjorth, J., Eppler, J.M., Dudani, N., Helias, M., Potjans, T.C.,Bhalla, U.S., Diesmann, M., Kotaleski, J.H.and Ekeberg, O. (2010). Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics, 8, 43-60
  • Jain P, and Bhalla, U.S. Signaling logic of activity-triggered dendritic protein synthesis: an mTOR gate but not a feedback switch. PLoS Comput Biol. 2009 Feb;5(2):e1000287. Epub 2009 Feb 13
  • Ray S., and Bhalla, U.S. PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinformatics. 2008;2:6. Epub 2008 Dec 19
  • Ramakrishnan, N., and Bhalla, U.S. Memory Switches in Chemical Reaction Space. PLoS Comput. Biol. 2008, 4(7)
  • Bhalla, U.S. How to Record a Million Synaptic Weights in a Hippo campal Slice. PLoS Comput. Biol. 2008, 4(6) .
  • Khan, A.G., Thattai, M., and Bhalla, U.S. Odor Representations in the Rat Olfactory Bulb Change Smoothly with Morphing Stimuli.
    Neuron. 57(4):571-85, 2008.
  • Ajay, S.M. and Bhalla, U.S. A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity.
    HFSP Journal. 1(1):49-66, 2007 .
  • Cannon, R.C., Gewaltig, M.O., Bhalla, U.S., Cornelis, H., Gleeson, P., Hines, M.L., Howell, F.W., Muller, E., Stiles, J.R. Wils, S., De Schutter, E. Interoperability of neuroscience modeling software:
    current status and future directions. Neuroinformatics. 5(2) 2007.
  • Rajan R, Clement JP, Bhalla, U.S. Rats smell in stereo.
    Science. 2006, 311(5761):666-670.. (PDF file and supplementary material)
  • Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Minimum information requested in the annotation of biochemical models (MIRIAM)
    Nat Biotechnol. 2005 23(12):1509-15..
  • Hayer A, Bhalla US. Molecular switches at the synapse emerge from receptor and kinase traffic.
    PLoS Comput. Biol. 2005 1(2). (Demonstration simulations and supplementary material)
  • Ajay SM, Bhalla US. A role for ERKII in synaptic pattern selectivity on the time-scale of minutes.
    Eur J Neurosci. 2004 Nov;20(10):2671-80.
  • Sinha, D, Bhalla, US and Shivashankar, GV. Kinetic measurement of ribosome motor stalling force.
    App. Phys. Lett 2004. 85(20):4789-4791. (Demonstration simulations and supplementary material)
  • Bhalla US. Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties.
    Biophys J. 2004 Aug;87(2):745-53. (Demonstration simulations and supplementary material)
  • Bhalla US. Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways.
    Biophys J. 2004 Aug;87(2):733-44. (Demonstration simulations and supplementary material)
  • Vayttaden SJ, Bhalla US. Developing complex signaling models using GENESIS/Kinetikit.
    Sci STKE. 2004 Feb 03;2004(219):p14. (Supplementary Material: Download STKE Demo)
  • Vasudeva K, Bhalla US. Adaptive stochastic-deterministic chemical kinetic simulations.
    Bioinformatics. 2004 Jan 01;20(1):78-84. (Demonstration simulations and supplementary material)
  • Bhalla US. Temporal computation by synaptic signaling pathways.
    J Chem Neuroanat. 2003 Oct;26(2):81-6. (PDF files)
  • Deshmukh SS., Bhalla US. Representation of odor habituation and timing in the hippocampus.
    J Neurosci. 2003 Mar 01;23(5):1903-15. (PDF file)
  • Sivakumaran S., Hariharaputran S., Mishra J., Bhalla U.S. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.
    Bioinformatics. 2003 Feb 12;19(3):408-15. (PDF file)
  • Mishra J., Bhalla US. Simulations of inositol phosphate metabolism and its interaction with InsP3 mediated calcium release.
    Biophys J. 2002 Sep;83(3):1298-1316. (PDF file)
  • Bhalla US, Ram PT., Iyengar R. MAP kinase phosphatase as a locus of flexibility in a mitogen- activated protein kinase signaling network.
    Science. 2002 Aug 09; 297:1018-1023. (PDF file) (Demonstration simulations and supplementary material)
  • Bhalla, U.S. Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways.
    Biophys J. 2002 Aug;83(2):740-752. (PDF file) (Demonstration simulations and supplementary material)
  • Bhalla US. Biochemical signaling networks decode temporal patterns of synaptic input.
    J Comput Neurosci. 2002 Jul-Aug;13(1):49-62.
  • Bhalla U.S. The chemical organization of signaling interactions.
    Bioinformatics. 2002 Jun18(6):855-63. (PDF file)
  • Bhalla US. and Iyengar R. Robustness of the bistable behavior of a biological signaling feedback loop.
    Chaos. 2001 Mar;11(1):221-226.
  • Bhalla US., Iyengar R. Emergent properties of networks of biological signaling pathways.
    Science. 1999 Jan 15;283(5400):381-7. (PDF file) (Demonstration simulations and supplementary material)
  • Bhalla US., Bower JM. Multiday recordings from olfactory bulb neurons in awake freely moving rats: spatially and temporally organized variability in odorant response properties.
    J Comput Neurosci. 1997 jul; 4(3):221-256.
  • Olds JL, Bhalla US, McPhie DL, Lester DS, Bower JM, Alkon DL. Lateralization of membrane-associated protein kinase C in rat piriform cortex: specific to operant training cues in the olfactory modality.
    Behav Brain Res. 1994 Mar 31;61(1):37-46.
  • Bhalla US., Bower JM. Exploring parameter space in detailed single neuron models : Simulations of the mitral and granule cells of the olfactory bulb.
    J Neurophysiol. 1993 Jun;69(6):1948-65. (PDF files)
  • Bhalla US., Bower JM. Genesis : a neuronal simulation system. Neural Systems: Analysis and Modeling, pp 95-102, Ed. Eeckman, F.H. Kluwer Academic Publishers, Norwell, 1993.
  • Wilson, M.A., Bhalla, U.S, Uhley, J.D, Bower, J.M. GENESIS : A system for simulating neural networks. Advances in Neural Information Processing Systems1, pp 485-492 Ed. Touretzky., 1989.

Review Articles

  1. Viswan NA, Bhalla US.Understanding molecular signaling cascades in neural disease using multi-resolution models.
    Curr Opin Neurobiol. 2023 Dec;83:102808. doi: 10.1016/j.conb.2023.102808. Epub 2023 Nov 14.

  2. Asopa A, Bhalla US.A computational view of short-term plasticity and its implications for E-I balance.
    Curr Opin Neurobiol. 2023 Aug;81:102729. doi: 10.1016/j.conb.2023.102729. Epub 2023 May 26.

  3. Pulikkottil VV, Somashekar BP, Bhalla US. Computation, wiring, and plasticity in synaptic clusters. Curr Opin Neurobiol. 2021 Sep 9;70:101-112. doi: 10.1016/j.conb.2021.08.001.
  4. Dwivedi D, Bhalla US. Physiology and Therapeutic Potential of SK, H, and M Medium AfterHyperPolarization Ion Channels. Front Mol Neurosci. 2021 Jun 3;14:658435. doi: 10.3389/fnmol.2021.658435. eCollection 2021.
  5. Viswan NA, HarshaRani GV, Stefan MI, Bhalla US. FindSim: A Framework for Integrating Neuronal Data and Signaling Models. Front Neuroinform. 2018 Jun 26;12:38. doi: 10.3389/fninf.2018.00038. eCollection 2018.
  6. G.V. HarshaRani, Bhalla, U.S. Database of Quantitative Cellular Signaling (DOQCS). Encyclopedia of System Biology 2013, pp 534-537
  7. Ramakrishnan, N.,Bhalla, U.S. and Tyson JJ. Computing with Proteins Computer ssue Date:January 2009 (vol .42 no.1) pp. 47-56 (PDF file)
  8. Dhawale, A., and Bhalla, U.S. The network and the synapse: 100 years after Cajal. HFSP Journal.Volume 2, Issue 1, pp. 12-16 (February 2008) (PDF file)
  9. Rajasethupathy P, Vayttaden SJ, Bhalla US. Systems modeling: a pathway to drug discovery. Curr Opin Chem Biol. 2005
  10. HarshaRani GV, Vayttaden SJ, Bhalla US. Electronic data sources for kinetic models of cell signaling. Journal of Biochemistry(Tokyo) 2005 Vol.137, No.6
    (Demonstration simulations and supplementary material)
  11. Vayttaden SJ, Ajay SM, Bhalla US. A spectrum of models of signaling pathways. Chembiochem. 2004 Oct 4;5(10):1365-74.
    (Demonstration simulations and supplementary material)
  12. Bhalla US. Models of cell signaling pathways. Curr Opin Genet Dev. (2004 Aug) 14(4):375-81. (PDF files)
  13. Bhalla US. Understanding complex signaling networks through models and metaphors. Prog Biophys Mol Biol. 2003 Jan;81(1):45-65. (PDF file)
  14. Bhalla US. Managing models of signaling networks. Neurocomputing 2003;52-54:215-220. (PDF file)
  15. Bhalla US., Bilitch DH., Bower JM. Rallpacks : A set of benchmarks for neural simulators. Trends Neurosci. 1992 Nov;15(11)453-8. Erratum in: Trends Neurosci 1993.
  16. Bhalla US, Iyengar R. Functional modules in biological signalling networks. Novartis Found Symp. 2001:239:4-13; discussion 13-5, 45-51.
  17. Weng G, Bhalla US, Iyengar R. Complexity in Biological Signaling Systems. Science 1999 Apr 02;284(5411):92-96. (PDF file)
  18. Bhalla US. Contemporary Issues in olfaction: Meeting report. Current Science 76(11): 1416-1420, 1999.

Book Chapters

  1. Bhalla, U.S. (2009). Molecules, networks and memory. In: Systems Biology: The Challenge of Complexity. Ed. S. Nakanishi, R. Kageyama and D. Watanabe. Springer, Tokyo, 2009.
  2. Bhalla US. Use of Kinetikit and GENESIS for modeling signaling pathways. In Methods in Enzymology. 2002;345:3-23 Ed. J.D. Hildebrandt and R. Iyengar.
  3. Bhalla US. Simulations of biochemical signaling. In Computational Neuroscience: Realistic Modeling for Experimentalists2001. Ed. E. De Schutter. CRC
  4. Bhalla US. The network within: signaling pathways. In The Book of GENESIS 2nd. Edition. Exploring Realistic Neural Models with the General Neural Simulation System. 1998Ed. J. M. Bower and D. Beeman. Springer Verlag
  5. Bhalla US. Advanced Xodus Techniques: Simulation visualization. In: The Book of GENESIS. Exploring Realistic Neural Models with the General Neural Simulation System. 1995,1998 Ed.J. M. Bower and D. Beeman. Springer Verlag.

Book Reviews

  • Bhalla US. Theoretical Neuroscience: Computational and Mathematical Modelling of Neural Systems. Peter Dayan and L.F. Abbott. In Current Science 82(10), 2002. (PDF files)
  • Bhalla US. Modeling in the Neurosciences: From Ionic Channels To Neural Networks. Roman R.Poznanski (ed.)., Harwood Academic Publishers. In Current Science 76(11): 1504-1502.