Browse by Fellow

Jędrzejewska-Szmek, Joanna ; Bhalla, Upinder S. (2021) HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks PLOS Computational Biology, 17 (11). e1009621. ISSN 1553-7358

HarshaRani, G V ; Moza, S ; Ramakrishnan, N ; Bhalla, U S ; Robinson, Peter (2021) SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches Bioinformatics, 37 (16). pp. 2504-2505. ISSN 1367-4803

Bhatia, Aanchal ; Moza, Sahil ; Bhalla, Upinder S. (2020) Patterned Optogenetic Stimulation Using a DMD Projector Methods in Molecular Biology, 2191 . pp. 173-188. ISSN 1064-3745

Dwivedi, Deepanjali ; Chattarji, Sumantra ; Bhalla, Upinder S. (2019) Impaired Reliability and Precision of Spiking in Adults But Not Juveniles in a Mouse Model of Fragile X Syndrome eNeuro, 6 (6). ENEURO.0217-19.2019. ISSN 2373-2822

Bhatia, Aanchal ; Moza, Sahil ; Bhalla, Upinder Singh (2019) Precise excitation-inhibition balance controls gain and timing in the hippocampus elife, 8 . ISSN 2050-084X

Viswanath, Biju ; Rao, Naren P. ; Narayanaswamy, Janardhanan C. ; Sivakumar, Palanimuthu T. ; Kandasamy, Arun ; Kesavan, Muralidharan ; Mehta, Urvakhsh Meherwan ; Venkatasubramanian, Ganesan ; John, John P. ; Mukherjee, Odity ; Purushottam, Meera ; Kannan, Ramakrishnan ; Mehta, Bhupesh ; Kandavel, Thennarasu ; Binukumar, B. ; Saini, Jitender ; Jayarajan, Deepak ; Shyamsundar, A. ; Moirangthem, Sydney ; Vijay Kumar, K. G. ; Thirthalli, Jagadisha ; Chandra, Prabha S. ; Gangadhar, Bangalore N. ; Murthy, Pratima ; Panicker, Mitradas M. ; Bhalla, Upinder S. ; Chattarji, Sumantra ; Benegal, Vivek ; Varghese, Mathew ; Reddy, Janardhan Y. C. ; Raghu, Padinjat ; Rao, Mahendra ; Jain, Sanjeev (2018) Discovery biology of neuropsychiatric syndromes (DBNS): a center for integrating clinical medicine and basic science BMC Psychiatry, 18 (1). ISSN 1471-244X

Bhalla, Upinder S. (2017) Dendrites, deep learning, and sequences in the hippocampus Hippocampus, 29 (3). pp. 239-251. ISSN 1050-9631

Brocke, Ekaterina ; Djurfeldt, Mikael ; Bhalla, Upinder S. ; Kotaleski, Jeanette Hellgren ; Hanke, Michael (2017) Multirate method for co-simulation of electrical-chemical systems in multiscale modeling Journal of Computational Neuroscience, 42 (3). pp. 245-256. ISSN 0929-5313

Bhalla, Upinder Singh (2017) Synaptic input sequence discrimination on behavioral timescales mediated by reaction-diffusion chemistry in dendrites elife, 6 . ISSN 2050-084X

Brocke, Ekaterina ; Bhalla, Upinder S. ; Djurfeldt, Mikael ; Hellgren Kotaleski, Jeanette ; Hanke, Michael (2016) Efficient Integration of Coupled Electrical-Chemical Systems in Multiscale Neuronal Simulations Frontiers in Computational Neuroscience, 10 . ISSN 1662-5188

Gupta, Priyanka ; Bhalla, Upinder S (2016) Minority odors get equal say elife, 5 . ISSN 2050-084X

Ray, Subhasis ; Chintaluri, Chaitanya ; Bhalla, Upinder S. ; Wójcik, Daniel K. (2016) NSDF: Neuroscience Simulation Data Format Neuroinformatics, 14 (2). pp. 147-167. ISSN 1539-2791

Saucerman, Jeffrey J. ; Nair, Anu G. ; Bhalla, Upinder S. ; Hellgren Kotaleski, Jeanette (2016) Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration PLOS Computational Biology, 12 (9). e1005080. ISSN 1553-7358

Schaefer, Andreas ; Gilra, Aditya ; Bhalla, Upinder S. (2015) Bulbar Microcircuit Model Predicts Connectivity and Roles of Interneurons in Odor Coding PLoS One, 10 (5). e0098045. ISSN 1932-6203

Gupta, Priyanka ; Albeanu, Dinu F ; Bhalla, Upinder S (2015) Olfactory bulb coding of odors, mixtures and sniffs is a linear sum of odor time profiles Nature Neuroscience, 18 (2). pp. 272-281. ISSN 1097-6256

Bhattacharyya, Urvashi ; Bhalla, Upinder Singh (2015) Robust and Rapid Air-Borne Odor Tracking without Casting eNeuro, 2 (6). ENEURO.0102-15.2015. ISSN 2373-2822

Muthmann, Jens-Oliver ; Amin, Hayder ; Sernagor, Evelyne ; Maccione, Alessandro ; Panas, Dagmara ; Berdondini, Luca ; Bhalla, Upinder S. ; Hennig, Matthias H. (2015) Spike Detection for Large Neural Populations Using High Density Multielectrode Arrays Frontiers in Neuroinformatics, 9 . ISSN 1662-5196

Modi, Mehrab N ; Dhawale, Ashesh K ; Bhalla, Upinder S (2014) CA1 cell activity sequences emerge after reorganization of network correlation structure during associative learning elife, 3 . ISSN 2050-084X

Bhalla, Upinder S (2014) Molecular computation in neurons: a modeling perspective Current Opinion in Neurobiology, 25 . pp. 31-37. ISSN 0959-4388

Bhalla, Upinder S. (2014) Multiscale Modeling and Synaptic Plasticity Molecular Biology and Translational Science, 123 . pp. 351-386. ISSN 1877-1173

Sakakibara, Manabu ; Jain, Pragati ; Bhalla, Upinder S. (2014) Transcription Control Pathways Decode Patterned Synaptic Inputs into Diverse mRNA Expression Profiles PLoS One, 9 (5). e95154. ISSN 1932-6203

Parthasarathy, K. ; Bhalla, U. S. (2013) Laterality and Symmetry in Rat Olfactory Behavior and in Physiology of Olfactory Input Journal of Neuroscience, 33 (13). pp. 5750-5760. ISSN 0270-6474

Dickson, Clayton T. ; Parameshwaran, Dhanya ; Bhalla, Upinder S. (2013) Theta Frequency Background Tunes Transmission but Not Summation of Spiking Responses PLoS One, 8 (1). e55607. ISSN 1932-6203

Parameshwaran, Dhanya ; Bhalla, Upinder S. (2012) 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 . ISSN 1662-5188

Bhalla, Upinder S. (2011) Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability Neural Networks, 24 (9). pp. 943-949. ISSN 0893-6080

Bhalla, Upinder Singh (2011) Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states Biophysical Journal, 101 (1). pp. 21-32. ISSN 0006-3495

Waltemath, Dagmar ; Adams, Richard ; Beard, Daniel A. ; Bergmann, Frank T. ; Bhalla, Upinder S. ; Chelliah, Vijayalakshmi ; Cooling, Michael T. ; Cooper, Jonathan ; Crampin, Edmund J. ; Garny, Alan ; Hoops, Stefan ; Hucka, Michael ; Hunter, Peter ; Klipp, Edda ; Laibe, Camille ; Miller, Andrew K. ; Moraru, Ion ; Nickerson, David ; Nielsen, Poul ; Nikolski, Macha ; Sahle, Sven ; Sauro, Herbert M. ; Schmidt, Henning ; Snoep, Jacky L. ; Tolle, Dominic ; Wolkenhauer, Olaf ; Novère, Nicolas Le (2011) Minimum information about a simulation experiment (MIASE) PLoS Computational Biology, 7 (4). e1001122_1-e1001122_4. ISSN 1553-734X

Khan, Adil Ghani ; Parthasarathy, K. ; Bhalla, Upinder Singh (2010) Odor representations in the mammalian olfactory bulb Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2 (5). pp. 603-611. ISSN 1939-5094

Gleeson, Padraig ; Crook, Sharon ; Cannon, Robert C. ; Hines, Michael L. ; Billings, Guy O. ; Farinella, Matteo ; Morse, Thomas M. ; Davison, Andrew P. ; Ray, Subhasis ; Bhalla, Upinder S. ; Barnes, Simon R. ; Dimitrova, Yoana D. ; Silver, R. Angus (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail PLoS Computational Biology, 6 (6). pp. 1-19. ISSN 1553-734X

Dhawale, Ashesh K. ; Hagiwara, Akari ; Bhalla, Upinder S. ; Murthy, Venkatesh N. ; Albeanu, Dinu F. (2010) Non-redundant odor coding by sister mitral cells revealed by light addressable glomeruli in the mouse Nature Neuroscience, 13 (11). pp. 1404-1412. ISSN 1097-6256

Djurfeldt, Mikael ; Hjorth, Johannes ; Eppler, Jochen M. ; Dudani, Niraj ; Helias, Moritz ; Potjans, Tobias C. ; Bhalla, Upinder S. ; Diesmann, Markus ; Kotaleski, Jeanette Hellgren ; Ekeberg, Orjan (2010) Run-time interoperability between neuronal network simulators based on the music framework Neuroinformatics, 8 (1). pp. 43-60. ISSN 1539-2791

Jain, Pragati ; Bhalla, Upinder S. (2009) Signaling logic of activity-triggered dendritic protein synthesis: an mTOR gate but not a feedback switch PLoS Computational Biology, 5 (2). pp. 1-17. ISSN 1553-734X

Ramakrishnan, N. ; Bhalla, U. S. ; Tyson, J. J. (2009) Computing with proteins Computer, 42 (1). pp. 47-56. ISSN 0018-9162

Ray, Subhasis ; Bhalla, Upinder S. (2008) PyMOOSE: interoperable scripting in Python for MOOSE Frontiers in Neuroinformatics, 2 (6). pp. 1-16.

Ramakrishnan, Naren ; Bhalla, Upinder S. (2008) Memory switches in chemical reaction space PLoS Computational Biology, 4 (7). pp. 1-9. ISSN 1553-734X

Bhalla, Upinder S. (2008) How to record a million synaptic weights in a Hippocampal slice PLoS Computational Biology, 4 (6). pp. 1-14. ISSN 1553-734X

Khan, Adil G. ; Thattai, Mukund ; Bhalla, Upinder S. (2008) Odor representations in the rat olfactory bulb change smoothly with morphing stimuli Neuron, 57 (4). pp. 571-585. ISSN 0896-6273

Dhawale, Ashesh ; Bhalla, Upinder S. (2008) The network and the synapse: 100 years after Cajal HFSP Journal, 2 (1). pp. 12-16. ISSN 1955-2068

Ajay, Sriram M. ; Bhalla, Upinder S. (2007) A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity HFSP Journal, 1 (1). pp. 49-66. ISSN 1955-2068

Cannon, Robert C. ; Gewaltig, Marc-Oliver ; Gleeson, Padraig ; Bhalla, Upinder S. ; Cornelis, Hugo ; Hines, Michael L. ; Howell, Fredrick W. ; Muller, Eilif ; Stiles, Joel R. ; Wils, Stefan ; Schutter, Erik De (2007) Interoperability of neuroscience modeling software: current status and future directions Neuroinformatics, 5 (2). pp. 127-138. ISSN 1539-2791

Ajay, Sriram M. ; Bhalla, Upinder S. (2006) Synaptic plasticity in vitro and in silico: insights into an intracellular signaling maze Physiology, 21 (4). pp. 289-296. ISSN 1548-9213

Rajan, Raghav ; Clement, James P. ; Bhalla, Upinder S. (2006) Rats smell in stereo Science, 311 (5761). pp. 666-670. ISSN 0036-8075

Novere, Nicolas Le ; Finney, Andrew ; Hucka, Michael ; Bhalla, Upinder S. ; Campagne, Fabien ; Collado-Vides, Julio ; Crampin, Edmund J. ; Halstead, Matt ; Klipp, Edda ; Mendes, Pedro ; Nielsen, Poul ; Sauro, Herbert ; Shapiro, Bruce ; Snoep, Jacky L. ; Spence, Hugh D. ; Wanner, Barry L. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM) Nature Biotechnology, 23 (12). pp. 1509-1515. ISSN 1087-0156

Rajasethupathy, Priyamvada ; Vayttaden, Sharat J. ; Bhalla, Upinder S. (2005) Systems modeling: a pathway to drug discovery Current Opinion in Chemical Biology, 9 (4). pp. 400-406. ISSN 1367-5931

Hayer, Arnold ; Bhalla, Upinder S. (2005) Molecular switches at the synapse emerge from receptor and kinase traffic PLoS Computational Biology, 1 (2). pp. 137-154. ISSN 1553-734X

Harsharani, G. V. ; Vayttaden, Sharat J. ; Bhalla, Upinder S. (2005) Electronic data sources for kinetic models of cell signaling Journal of Biochemistry, 137 (6). pp. 653-657. ISSN 0021-924X

Sinha, Deepak Kumar ; Bhalla, U. S. ; Shivashankar, G. V. (2004) Kinetic measurement of ribosome motor stalling force Applied Physics Letters, 85 (20). pp. 4789-4791. ISSN 0003-6951

Ajay, Sriram M. ; Bhalla, Upinder S. (2004) A role for ERKII in synaptic pattern selectivity on the time-scale of minutes European Journal of Neuroscience, 20 (10). pp. 2671-2680. ISSN 0953-816X

Vayttaden, Sharat J. ; Ajay, Sriram M. ; Bhalla, Upinder S. (2004) A spectrum of models of signaling pathways Chembiochem, 5 (10). pp. 1365-1374. ISSN 1439-4227

Bhalla, Upinder S. (2004) Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways Biophysical Journal, 87 (2). pp. 733-744. ISSN 0006-3495

Bhalla, Upinder S. (2004) Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties Biophysical Journal, 87 (2). pp. 745-753. ISSN 0006-3495

Bhalla, Upinder S. (2004) Models of cell signaling pathways Current Opinion in Genetics & Development, 14 (4). pp. 375-381. ISSN 0959-437X

Vayttaden, Sharat Jacob ; Bhalla, Upinder Singh (2004) Developing complex signaling models using GENESIS/Kinetikit Science Signaling, 2004 (219). p. 14. ISSN 1937-9145

Vasudeva, Karan ; Bhalla, Upinder S. (2004) Adaptive stochastic-deterministic chemical kinetic simulations Bioinformatics, 20 (1). pp. 78-84. ISSN 1367-4803

Bhalla, Upinder S. (2003) Temporal computation by synaptic signaling pathways Journal of Chemical Neuroanatomy, 26 (2). pp. 81-86. ISSN 0891-0618

Bhalla, Upinder S. (2003) Managing models of signaling networks Neurocomputing, 52-54 . pp. 215-220. ISSN 0925-2312

Deshmukh, Sachin S. ; Bhalla, Upinder S. (2003) Representation of odor habituation and timing in the Hippocampus Journal of Neuroscience, 23 (5). pp. 1903-1915. ISSN 0270-6474

Bhalla, Upinder S. (2003) Understanding complex signaling networks through models and metaphors Progress in Biophysics and Molecular Biology, 81 (1). pp. 45-65. ISSN 0079-6107

Sivakumaran, Sudhir ; Hariharaputran, Sridhar ; Mishra, Jyoti ; Bhalla, Upinder S. (2003) The database of quantitative cellular signaling: management and analysis of chemical kinetic models of signaling networks Bioinformatics, 19 (3). pp. 408-415. ISSN 1367-4803

Mishra, Jyoti ; Bhalla, Upinder S. (2002) Simulations of inositol phosphate metabolism and its interaction with InsP₃-mediated calcium release Biophysical Journal, 83 (3). pp. 1298-1316. ISSN 0006-3495

Bhalla, Upinder S. (2002) Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways Biophysical Journal, 83 (2). pp. 740-752. ISSN 0006-3495

Bhalla, Upinder S. ; Ram, Prahlad T. ; Iyengar, Ravi (2002) MAP kinase phosphatase as a locus of flexibility in a Mitogen-activated protein kinase signaling network Science, 297 (5583). pp. 1018-1023. ISSN 0036-8075

Bhalla, Upinder S. (2002) Biochemical signaling networks decode temporal patterns of synaptic input Journal of Computational Neuroscience, 13 (1). pp. 49-62. ISSN 0929-5313

Bhalla, Upinder S. (2002) The chemical organization of signaling interactions Bioinformatics, 18 (6). pp. 855-863. ISSN 1367-4803

Bhalla, U. S. ; Iyengar, R. (2001) Functional modules in biological signalling networks Novartis Foundation Symposium, 239 (4-13). pp. 45-51. ISSN 1528-2511

Bhalla, Upinder S. ; Iyengar, Ravi (2001) Robustness of the bistable behavior of a biological signaling feedback loop Chaos, 11 (1). pp. 221-226. ISSN 1054-1500

Weng, Gezhi ; Bhalla, Upinder S. ; Iyengar, Ravi (1999) Complexity in biological signaling systems Science, 284 . pp. 92-96. ISSN 0036-8075

Bhalla, Upinder S. ; Iyengar, Ravi (1999) Emergent properties of networks of biological signaling pathways Science, 283 . pp. 381-387. ISSN 0036-8075

Bhalla, Upinder S. ; Bower, James M. (1997) 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 (3). pp. 221-256. ISSN 0929-5313

Olds, James L. ; Bhalla, Upinder S. ; McPhie, Donna L. ; Lester, David S. ; Bower, James M. ; Alkon, Daniel L. (1994) Lateralization of membrane-associated protein kinase C in rat piriform cortex: specific to operant training cues in the olfactory modality Behavioural Brain Research, 61 (1). pp. 37-46. ISSN 0166-4328

Bhalla, U. S. ; Bower , J. M. (1993) Exploring parameter space in detailed single neuron models: simulations of the mitral and granule cells of the olfactory bulb Journal of Neurophysiology, 69 (6). pp. 1948-1965. ISSN 0022-3077

Bhalla, Upinder S. ; Bilitch, David H. ; Bower, James M. (1992) Rallpacks: a set of benchmarks for neuronal simulators Trends in Neurosciences, 15 (11). pp. 453-458. ISSN 0166-2236