Upinder Singh Bhalla - Publications

Affiliations: 
National Center for Biological Sciences, Bengaluru, Karnataka, India 
Area:
Olfactory coding, computational neuroscience
Website:
http://www.ncbs.res.in/bhalla

81 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Viswan NA, Bhalla US. Understanding molecular signaling cascades in neural disease using multi-resolution models. Current Opinion in Neurobiology. 83: 102808. PMID 37972535 DOI: 10.1016/j.conb.2023.102808  0.794
2023 Asopa A, Bhalla US. A computational view of short-term plasticity and its implications for E-I balance. Current Opinion in Neurobiology. 81: 102729. PMID 37245258 DOI: 10.1016/j.conb.2023.102729  0.773
2023 Ananthamurthy KG, Bhalla US. Synthetic Data Resource and Benchmarks for Time Cell Analysis and Detection Algorithms. Eneuro. 10. PMID 36823166 DOI: 10.1523/ENEURO.0007-22.2023  0.742
2022 Eriksson O, Bhalla US, Blackwell KT, Crook SM, Keller D, Kramer A, Linne ML, Saudargienė A, Wade RC, Hellgren Kotaleski J. Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. Elife. 11. PMID 35792600 DOI: 10.7554/eLife.69013  0.556
2021 Bhatia A, Moza S, Bhalla US. Correction: Precise excitation-inhibition balance controls gain and timing in the hippocampus. Elife. 10. PMID 34165427 DOI: 10.7554/eLife.71338  0.756
2021 Bhatia A, Moza S, Bhalla US. Patterned Optogenetic Stimulation Using a DMD Projector. Methods in Molecular Biology (Clifton, N.J.). 2191: 173-188. PMID 32865745 DOI: 10.1007/978-1-0716-0830-2_11  0.767
2019 Bhatia A, Moza S, Bhalla US. Precise excitation-inhibition balance controls gain and timing in the hippocampus. Elife. 8. PMID 31021319 DOI: 10.7554/Elife.43415  0.784
2019 Bhatia A, Moza S, Bhalla US. Author response: Precise excitation-inhibition balance controls gain and timing in the hippocampus Elife. DOI: 10.7554/Elife.43415.030  0.759
2018 Singh D, Bhalla US. Subunit exchange enhances information retention by CaMKII in dendritic spines. Elife. 7. PMID 30418153 DOI: 10.7554/eLife.41412  0.314
2018 Viswan NA, HarshaRani GV, Stefan MI, Bhalla US. FindSim: A Framework for Integrating Neuronal Data and Signaling Models. Frontiers in Neuroinformatics. 12: 38. PMID 29997492 DOI: 10.3389/Fninf.2018.00038  0.8
2017 Bhalla US. Dendrites, Deep Learning, and Sequences in the Hippocampus. Hippocampus. PMID 29024221 DOI: 10.1002/hipo.22806  0.347
2017 Bhalla US. Synaptic input sequence discrimination on behavioral timescales mediated by reaction-diffusion chemistry in dendrites. Elife. 6. PMID 28422010 DOI: 10.7554/eLife.25827  0.381
2017 Brocke E, Djurfeldt M, Bhalla US, Kotaleski JH, Hanke M. Multirate method for co-simulation of electrical-chemical systems in multiscale modeling. Journal of Computational Neuroscience. PMID 28389716 DOI: 10.1007/S10827-017-0639-7  0.369
2016 Brocke E, Bhalla US, Djurfeldt M, Hellgren Kotaleski J, Hanke M. Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations. Frontiers in Computational Neuroscience. 10: 97. PMID 27672364 DOI: 10.3389/Fncom.2016.00097  0.345
2016 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 Computational Biology. 12: e1005080. PMID 27584878 DOI: 10.1371/journal.pcbi.1005080  0.321
2015 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. Frontiers in Neuroinformatics. 9: 28. PMID 26733859 DOI: 10.3389/Fninf.2015.00028  0.33
2015 Ray S, Chintaluri C, Bhalla US, Wójcik DK. NSDF: Neuroscience Simulation Data Format. Neuroinformatics. PMID 26585711 DOI: 10.1007/S12021-015-9282-5  0.783
2015 Gilra A, Bhalla US. Bulbar microcircuit model predicts connectivity and roles of interneurons in odor coding. Plos One. 10: e0098045. PMID 25942312 DOI: 10.1371/Journal.Pone.0098045  0.8
2015 Gupta P, Albeanu DF, Bhalla US. Olfactory bulb coding of odors, mixtures and sniffs is a linear sum of odor time profiles. Nature Neuroscience. 18: 272-81. PMID 25581362 DOI: 10.1038/Nn.3913  0.752
2014 Jain P, Bhalla US. Transcription control pathways decode patterned synaptic inputs into diverse mRNA expression profiles. Plos One. 9: e95154. PMID 24787753 DOI: 10.1371/Journal.Pone.0095154  0.761
2014 Bhalla US. Molecular computation in neurons: a modeling perspective. Current Opinion in Neurobiology. 25: 31-7. PMID 24709598 DOI: 10.1016/j.conb.2013.11.006  0.401
2014 Modi MN, Dhawale AK, Bhalla US. CA1 cell activity sequences emerge after reorganization of network correlation structure during associative learning. Elife. 3: e01982. PMID 24668171 DOI: 10.7554/Elife.01982  0.772
2014 Bhalla US. Multiscale modeling and synaptic plasticity. Progress in Molecular Biology and Translational Science. 123: 351-86. PMID 24560151 DOI: 10.1016/B978-0-12-397897-4.00012-7  0.359
2014 Modi MN, Dhawale AK, Bhalla US. Author response: CA1 cell activity sequences emerge after reorganization of network correlation structure during associative learning Elife. DOI: 10.7554/Elife.01982.019  0.758
2013 Parthasarathy K, Bhalla US. Laterality and symmetry in rat olfactory behavior and in physiology of olfactory input. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 33: 5750-60. PMID 23536088 DOI: 10.1523/JNEUROSCI.1781-12.2013  0.562
2013 Parameshwaran D, Bhalla US. Theta frequency background tunes transmission but not summation of spiking responses. Plos One. 8: e55607. PMID 23383242 DOI: 10.1371/journal.pone.0055607  0.794
2013 Muthmann J, Amin H, Maccione A, Sernagor E, Berdondini L, Hennig MH, Bhalla US. Estimating the fraction of falsely detected spikes in high density microelectrode array recordings based on correlations Bmc Neuroscience. 14. DOI: 10.1186/1471-2202-14-S1-P25  0.33
2012 Parameshwaran D, Bhalla US. Summation in the Hippocampal CA3-CA1 Network Remains Robustly Linear Following Inhibitory Modulation and Plasticity, but Undergoes Scaling and Offset Transformations. Frontiers in Computational Neuroscience. 6: 71. PMID 23055964 DOI: 10.3389/fncom.2012.00071  0.8
2012 Khan AG, Sarangi M, Bhalla US. Rats track odour trails accurately using a multi-layered strategy with near-optimal sampling. Nature Communications. 3: 703. PMID 22426224 DOI: 10.1038/ncomms1712  0.518
2011 Bhalla US. Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states. Biophysical Journal. 101: 21-32. PMID 21723811 DOI: 10.1016/j.bpj.2011.05.037  0.336
2011 Bhalla US. Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability. Neural Networks : the Official Journal of the International Neural Network Society. 24: 943-9. PMID 21616637 DOI: 10.1016/j.neunet.2011.05.001  0.376
2011 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, et al. Minimum Information About a Simulation Experiment (MIASE). Plos Computational Biology. 7: e1001122. PMID 21552546 DOI: 10.1371/Journal.Pcbi.1001122  0.639
2011 Muthmann O, Hennig MH, Bhalla US. Inferring ion channel densities from spike data Bmc Neuroscience. 12. DOI: 10.1186/1471-2202-12-S1-P12  0.373
2010 Dhawale AK, Hagiwara A, Bhalla US, Murthy VN, Albeanu DF. Non-redundant odor coding by sister mitral cells revealed by light addressable glomeruli in the mouse. Nature Neuroscience. 13: 1404-12. PMID 20953197 DOI: 10.1038/Nn.2673  0.787
2010 Khan AG, Parthasarathy K, Bhalla US. Odor representations in the mammalian olfactory bulb. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 603-11. PMID 20836051 DOI: 10.1002/Wsbm.85  0.659
2010 Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. Plos Computational Biology. 6: e1000815. PMID 20585541 DOI: 10.1371/Journal.Pcbi.1000815  0.807
2010 Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Kotaleski JH, Ekeberg O. Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics. 8: 43-60. PMID 20195795 DOI: 10.1007/S12021-010-9064-Z  0.799
2010 Gilra A, Bhalla US. Biophysical model of odor representation and processing in the rat olfactory bulb Bmc Neuroscience. 11. DOI: 10.1186/1471-2202-11-S1-P63  0.788
2009 Jain P, Bhalla US. Signaling logic of activity-triggered dendritic protein synthesis: an mTOR gate but not a feedback switch. Plos Computational Biology. 5: e1000287. PMID 19242559 DOI: 10.1371/Journal.Pcbi.1000287  0.763
2009 Dudani N, Ray S, George S, Bhalla US. Multiscale modeling and interoperability in MOOSE Bmc Neuroscience. 10: 54. DOI: 10.1186/1471-2202-10-S1-P54  0.78
2008 Dhawale A, Bhalla US. The network and the synapse: 100 years after Cajal. Hfsp Journal. 2: 12-6. PMID 19404449 DOI: 10.2976/1.2835214  0.797
2008 Ray S, Bhalla US. PyMOOSE: Interoperable Scripting in Python for MOOSE. Frontiers in Neuroinformatics. 2: 6. PMID 19129924 DOI: 10.3389/Neuro.11.006.2008  0.799
2008 Bhalla US. How to record a million synaptic weights in a hippocampal slice. Plos Computational Biology. 4: e1000098. PMID 18566658 DOI: 10.1371/journal.pcbi.1000098  0.394
2008 Khan AG, Thattai M, Bhalla US. Odor representations in the rat olfactory bulb change smoothly with morphing stimuli. Neuron. 57: 571-85. PMID 18304486 DOI: 10.1016/j.neuron.2008.01.008  0.554
2008 Ray S, Deshpande R, Dudani N, Bhalla US. A general biological simulator: the multiscale object oriented simulation environment, MOOSE Bmc Neuroscience. 9: 93. DOI: 10.1186/1471-2202-9-S1-P93  0.752
2008 Bhalla US, Madhavan R, Dhawale A, Modi M, Deshpande R, Dudani N, Ray S. Large-scale synapse-level neuronal wiring diagrams in silico and in vitro Bmc Neuroscience. 9. DOI: 10.1186/1471-2202-9-S1-P20  0.753
2007 Ajay SM, Bhalla US. A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity. Hfsp Journal. 1: 49-66. PMID 19404460 DOI: 10.2976/1.2721383/10.2976/1  0.375
2007 Cannon RC, Gewaltig MO, Gleeson P, Bhalla US, Cornelis H, Hines ML, Howell FW, Muller E, Stiles JR, Wils S, De Schutter E. Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics. 5: 127-38. PMID 17873374 DOI: 10.1007/S12021-007-0004-5  0.571
2006 Ajay SM, Bhalla US. Synaptic plasticity in vitro and in silico: insights into an intracellular signaling maze. Physiology (Bethesda, Md.). 21: 289-96. PMID 16868318 DOI: 10.1152/physiol.00009.2006  0.392
2006 Rajan R, Clement JP, Bhalla US. Rats smell in stereo. Science (New York, N.Y.). 311: 666-70. PMID 16456082 DOI: 10.1126/science.1122096  0.504
2005 Le Novère 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, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology. 23: 1509-15. PMID 16333295 DOI: 10.1038/Nbt1156  0.631
2005 Hayer A, Bhalla US. Molecular switches at the synapse emerge from receptor and kinase traffic. Plos Computational Biology. 1: 137-54. PMID 16110334 DOI: 10.1371/journal.pcbi.0010020  0.317
2005 Rajasethupathy P, Vayttaden SJ, Bhalla US. Systems modeling: a pathway to drug discovery. Current Opinion in Chemical Biology. 9: 400-6. PMID 16006180 DOI: 10.1016/j.cbpa.2005.06.008  0.758
2005 HarshaRani GV, Vayttaden SJ, Bhalla US. Electronic data sources for kinetic models of cell signaling. Journal of Biochemistry. 137: 653-7. PMID 16002985 DOI: 10.1093/jb/mvi083  0.784
2004 Ajay SM, Bhalla US. A role for ERKII in synaptic pattern selectivity on the time-scale of minutes. The European Journal of Neuroscience. 20: 2671-80. PMID 15548210 DOI: 10.1111/j.1460-9568.2004.03725.x  0.384
2004 Vayttaden SJ, Ajay SM, Bhalla US. A spectrum of models of signaling pathways. Chembiochem : a European Journal of Chemical Biology. 5: 1365-74. PMID 15457536 DOI: 10.1002/cbic.200400127  0.773
2004 Bhalla US. Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties. Biophysical Journal. 87: 745-53. PMID 15298883 DOI: 10.1529/biophysj.104.040501  0.369
2004 Bhalla US. Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways. Biophysical Journal. 87: 733-44. PMID 15298882 DOI: 10.1529/biophysj.104.040469  0.307
2004 Bhalla US. Models of cell signaling pathways. Current Opinion in Genetics & Development. 14: 375-81. PMID 15261653 DOI: 10.1016/j.gde.2004.05.002  0.374
2004 Vayttaden SJ, Bhalla US. Developing complex signaling models using GENESIS/Kinetikit. Science's Stke : Signal Transduction Knowledge Environment. 2004: pl4. PMID 14872097 DOI: 10.1126/stke.2192004pl4  0.799
2004 Vasudeva K, Bhalla US. Adaptive stochastic-deterministic chemical kinetic simulations. Bioinformatics (Oxford, England). 20: 78-84. PMID 14693812 DOI: 10.1093/bioinformatics/btg376  0.309
2003 Bhalla US. Temporal computation by synaptic signaling pathways. Journal of Chemical Neuroanatomy. 26: 81-6. PMID 14599656 DOI: 10.1016/S0891-0618(02)00105-9  0.403
2003 Deshmukh SS, Bhalla US. Representation of odor habituation and timing in the hippocampus. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 23: 1903-15. PMID 12629195 DOI: 10.1523/Jneurosci.23-05-01903.2003  0.614
2003 Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics (Oxford, England). 19: 408-15. PMID 12584128 DOI: 10.1093/Bioinformatics/Btf860  0.701
2003 Bhalla US. Understanding complex signaling networks through models and metaphors. Progress in Biophysics and Molecular Biology. 81: 45-65. PMID 12475569 DOI: 10.1016/S0079-6107(02)00046-9  0.38
2003 Bhalla US. Managing models of signaling networks Neurocomputing. 52: 215-220. DOI: 10.1016/S0925-2312(02)00737-3  0.36
2002 Mishra J, Bhalla US. Simulations of inositol phosphate metabolism and its interaction with InsP(3)-mediated calcium release. Biophysical Journal. 83: 1298-316. PMID 12202356 DOI: 10.1016/S0006-3495(02)73901-5  0.505
2002 Bhalla US, Ram PT, Iyengar R. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science (New York, N.Y.). 297: 1018-23. PMID 12169734 DOI: 10.1126/science.1068873  0.503
2002 Bhalla US. Biochemical signaling networks decode temporal patterns of synaptic input. Journal of Computational Neuroscience. 13: 49-62. PMID 12154335 DOI: 10.1023/A:1019644427655  0.37
2002 Bhalla US. Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways. Biophysical Journal. 83: 740-52. PMID 12124261 DOI: 10.1016/S0006-3495(02)75205-3  0.37
2002 Bhalla US. The chemical organization of signaling interactions. Bioinformatics (Oxford, England). 18: 855-63. PMID 12075021 DOI: 10.1093/Bioinformatics/18.6.855  0.313
2002 Bhalla US. Use of Kinetikit and GENESIS for modeling signaling pathways. Methods in Enzymology. 345: 3-23. PMID 11665614 DOI: 10.1016/S0076-6879(02)45003-3  0.348
2001 Bhalla US, Iyengar R. Robustness of the bistable behavior of a biological signaling feedback loop. Chaos (Woodbury, N.Y.). 11: 221-226. PMID 12779455 DOI: 10.1063/1.1350440  0.525
2001 Bhalla US, Iyengar R. Functional modules in biological signalling networks. Novartis Foundation Symposium. 239: 4-13; discussion 13-. PMID 11529315 DOI: 10.1002/0470846674.Ch2  0.533
1999 Weng G, Bhalla US, Iyengar R. Complexity in biological signaling systems. Science (New York, N.Y.). 284: 92-6. PMID 10102825 DOI: 10.1126/science.284.5411.92  0.497
1999 Bhalla US, Iyengar R. Emergent properties of networks of biological signaling pathways. Science (New York, N.Y.). 283: 381-7. PMID 9888852 DOI: 10.1126/science.283.5400.381  0.545
1997 Bhalla US, Bower JM. Multiday recordings from olfactory bulb neurons in awake freely moving rats: spatially and temporally organized variability in odorant response properties. Journal of Computational Neuroscience. 4: 221-56. PMID 9257234 DOI: 10.1023/A:1008819818970  0.578
1994 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. Behavioural Brain Research. 61: 37-46. PMID 8031495 DOI: 10.1016/0166-4328(94)90006-X  0.568
1993 Bhalla US, Bower JM. Exploring parameter space in detailed single neuron models: simulations of the mitral and granule cells of the olfactory bulb. Journal of Neurophysiology. 69: 1948-65. PMID 7688798 DOI: 10.1152/JN.1993.69.6.1948  0.568
1993 Bhalla US, Bilitch DH, Bower JM. Erratum: Rallpacks: A set of benchmarks for neuronal simulators (TINS (Vol. 15) (pp. 453-458)) Trends in Neurosciences. 16. DOI: 10.1016/0166-2236(93)90048-Q  0.337
1992 Bhalla US, Bilitch DH, Bower JM. Rallpacks: a set of benchmarks for neuronal simulators. Trends in Neurosciences. 15: 453-8. PMID 1281353 DOI: 10.1016/0166-2236(92)90009-W  0.59
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