Publications

2020

Bradde, S., Nourmohammad, A., Goyal, S., & Balasubramanian, V. (2020). The size of the immune repertoire of bacteria. Proceedings of the National Academy of Sciences, 117(10), 5144-5151.
 

2019

Kang, L., & Balasubramanian, V. (2019). A geometric attractor mechanism for self-organization of entorhinal grid modules. eLife, 8, e46687.
 
Tavoni, G., Balasubramanian, V., & Gold, J. I. (2019). What is optimal in optimal inference?. Current Opinion in Behavioral Sciences, 29, 117-126.
 
Mayer, A., Balasubramanian, V., Walczak, A. M., & Mora, T. (2019). How a well-adapting immune system remembers. Proceedings of the National Academy of Sciences, 116(18), 8815-8823.
 
Singh, V., Murphy, N. R., Balasubramanian, V., & Mainland, J. D. (2019). Competitive binding predicts nonlinear responses of olfactory receptors to complex mixtures. Proceedings of the National Academy of Sciences, 116(19), 9598-9603.
 
Teşileanu, T., Cocco, S., Monasson, R., & Balasubramanian, V. (2019). Adaptation of olfactory receptor abundances for efficient coding. Elife, 8, e39279.

2018

Keinath, A. T., Epstein, R. A., & Balasubramanian, V. (2018). Environmental deformations dynamically shift the grid cell spatial metric. Elife, 7, e38169.
 
Glaze, C. M., Filipowicz, A. L., Kable, J. W., Balasubramanian, V., & Gold, J. I. (2018). A bias–variance trade-off governs individual differences in on-line learning in an unpredictable environment. Nature Human Behaviour, 2(3), 213-224.
 
Briguglio, J. J., Aizenberg, M., Balasubramanian, V., & Geffen, M. N. (2018). Cortical neural activity predicts sensory acuity under optogenetic manipulation. Journal of Neuroscience, 38(8), 2094-2105.

 

2017

Teşileanu, T., Ölveczky, B., & Balasubramanian, V. (2017). Rules and mechanisms for efficient two-stage learning in neural circuits. Elife, 6, e20944.

Krishnamurthy, K., Hermundstad, A. M., Mora, T., Walczak, A. M., & Balasubramanian, V. (2017). Disorder and the neural representation of complex odors: smelling in the real world. arXiv preprint arXiv:1707.01962.

Bradde, S., Vucelja, M., Teşileanu, T., & Balasubramanian, V. (2017). Dynamics of adaptive immunity against phage in bacterial populations. PLoS computational biology, 13(4), e1005486.

2016

Sanzeni, A, Balasubramanian V, Tiana G, Vergassola M.  2016.  Complete coverage of space favors modularity of the grid system in the brain. Physical Review E. 94(6):062409.

Prentice, J, Merel J, Balasubramanian V.  2016.  Optimal foraging and multi-scale spatial representations in the hippocampus.

2015

Balasubramanian, V.  2015.  Heterogeneity and Efficiency in the Brain. Proceedings of the IEEE. 103(8):1346-1358.

Mayer, A, Balasubramanian V, Mora T, Walczak A.  2015.  How a well-adapted immune system is organized. PNAS. 112(19):5950-5955.

Nelson, P.  2015.  Physical Models of Living Sytems.

Wei, X, Prentice J, Balasubramanian V.  2015.  A principle of economy predicts the functional architecture of grid cells'. eLife. 10.7554/eLife.0836

Prentice, JS, Homann J, Simmons KD, Tkacik G, Balasubramanian V, Nelson PC.  2015.  Spike Sorting for Multi-Electrode Array Data. Encyclopedia of Applied and Computational Mathematics.

Nelson, P, Dodson T.  2015.  A Student's Guide to MATLAB for Physical Modeling.

Nelson, P, Kinder JM.  2015.  A Student's Guide to Python for Physical Modeling.

2014

Nelson, PC.  2014.  Biological Physics: Energy, Information, Life (With new art by David Goodsell)

[Anonymous].  2014.  Biological Physics: Energy, Information, Life (With new art by David Goodsell).

Hermundstad, AM, Brown KS, Bassett DS, et al.  2014.  Structurally-constrained relationships between cognitive states in the human brain. PLoS Computational Biology. 10(5)

Briguglio, J, Hermundstad A, Conte M, Victor J*, Tkacik G*, Balasubramanian V*.  2014.  Variance predicts salience central sensory processing. eLife. 10.7554

2013

Schwab, DJ, Simmons K, Balasubamanian V.  2013.  Representing retinal ganglion cell population activiy with Restricted Boltzmann Machines. COSYNE 2013.

Prentice, JS, Homann J, Simmons KD, Tkacik G, Balasubramanian V, Nelson PC.  2013.  Spike Sorting for Multi-Electrode Array Data. Encyclopedia of Applied and Computational Mathematics.

Hermundstad, AM, Bassett DS, et al.  2013.  Structural foundations of resting-state and task-based functional connectivity in the human brain. PNAS. 110(15):6169-6174.

Idema, T, Dubuis JO, Kang L, Manning LM, Neson PC, Lubensky TC, Liu AJ.  2013.  The Syncytial Drosophila Embryo as a Mechanically Excitable Medium.. PLoS ONE. 8(10)

Beausang, JF, Shroder DY, Nelson PC, Goldman YE.  2013.  Three-dimensional Orientation and Dynamic Wobble of Myosin V by High Time Resolution Single Molecule Polarized Fluorescence. Biophysical Journal. 104:1263-1273.

Simmons, K, Prenctice J, Tkacik G, Homann J, Yee HK, Palmer SE, Nelson P, Balasubramanian V.  2013.  Transformation of stimulus correlations by the retina. PLoS Computational Biology. 9(12)

2012

Perge, JA, Niven JE, Mugnaini E, Balasubramanian V, Sterling P.  2012.  Why do axons differ in caliber? Journal of Neuroscience. 32(2):638.

Trenholm, S, Schwab D, Balasubramanian V, Awatramani G.  2012.  Lag normalization in an electrically coupled neural network. Nature Neuroscience. 16:154-156.

Neslon, PC.  2012.  Spare the (Elastic) Rod . Science. 337:1045-1046.

[Anonymous].  2012.  Spare the (Elastic) Rod<. Science. 337

2011

Little, SC, Tkacik G, Kneeland TB, Wieschaus EF, Gregor T.  2011.  The formation of the bicoid morphogen gradient requires protein movement from anteriorly localized mRNA.. PLoS Biology.

Beausang, JF, Goldman YE, Nelson PC.  2011.  Changepoint Analysis for Single-Molecule Polarized Total Internal Reflection Fluorescence Microscopy Experiments. Meth. Enzymol . 487:431-463.

Prentice, JS, Homann J, Simmons KD, Tkacik G, Balasubramanian V, Nelson P.  2011.  Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays. PLoS ONE. 6(7)> Download: MEApaper.pdf (1.24 MB)

Tkacik, G, Prentice JS, Victor J, Balasubramanian V.  2011.  Local statistics in natural scenes predict the saliency of synthetic textures. COSYNE 2011.

Tkacik, G, Garrigan P, Ratliff CP, MIlcinski G, Klein J, Sterling P, Brainard D, Balasubramanian V, Seyfarth L.  2011.  Natural images from the birthplace of the human eye. PLoS ONE. 6(6) Download: ImageDatabase.pdf (1.63 MB)

2010

Garrigan, P, Ratliff CP, Klein JM, Sterling P, Brainard D, Balasubramanian V.  2010.  >Design of a trichromatic cone array. PLoS Comput. Biol.. 6 Download: PLoS Comp Biol 2010 Garrigan.pdf (1.36 MB)

Tkacik, G.  2010.  From statistical mechanics to information theory: Understanding biophysical information processing systems. QECG 2010 Okinawa Summer School.  Download: OIST1006.4291.pdf (7.48 MB)

Tkacik, G, Prentice J, Victor J, Balasubramanian V.  2010.  Local statistics in natural scenes predict the saliency of synthetic textures. PNAS. 107(42):18149-18154. Download: PNAS-Textures.pdf (1.07 MB)

Tkacik, G, Prentice JS, Balasubramanian V, Schneidman E.  2010.  Optimal population coding by noisy spiking neurons. PNAS. 107(42):18154. Download: PNAS-OptPopCodes.pdf (972.45 KB)

Walczak, AM, Tkacik G, Bialek W.  2010.  Optimizing information flow in small genetic networks. II. Feed-forward interactions. Phys. Rev. E. 81 Download: PRE_InfoSmall_Part_II.pdf (534.98 KB)

Ratliff, CP, Borghuis BG, Kao YH, Sterling P, Balasubramanian V.  2010.  Retina is structured to process an excess of darkness in natural scenes.. PNAS. 107(40):17368-17373. Download: OnOffPNAS.pdf (582.91 KB)

2009

Tkacik, G, Bialek W.  2009.  Diffusion, dimensionality and noise in transcriptional regulation. Phys. Rev. E. 79 Download: PRE_Diffusion_dimensionality.pdf (235.11 KB)

Kryazhimskiy, S, Tkacik G, Plotkin J.  2009.  The dynamics of adaptation on correlated fitness landscapes.. PNAS. 106 Download: PNAS_Adaptive_Walks.pdf (707.16 KB)

Balasubramanian, V, Perge J, Koch K, Miller R, Sterling P.  2009.  How the optic nerve allocates space, energy capacity and information. COSYNE 2009.

Perge, JA, Koch K, Miller R, Sterling P, Balasubramanian V.  2009.  How the optic nerve allocates space, energy capacity, and information.. J. Neurosci. 29:7917-7928. Download: Journal of Neuroscience 2009 Perge.pdf (4.66 MB)

Tkacik, G, Prentice J, Victor K, Balasubramanian V.  2009.  Local fourth-order statistics in natural scenes predict the saliency of synthetic textures. COSYNE 2009.

Ratliff, C, Sterling P, Balasubramanian V.  2009.  Natural scene statistics predict that larger ganglion cells should have relatively smaller surrounds. COSYNE 2009 abstract.

Prentice, J, Tkacik G, Schneidman E, Balasubramanian V.  2009.  Optimal correlation codes in populations of noisy spiking neurons. COSYNE 2009.

Tkacik, G, Walczak A, Bialek W.  2009.  Optimizing information flow in small genetic networks.. Phys. Rev. E. 80 Download: PRE_InfoSmall_Part_I.pdf (852.56 KB)

Balasubramanian, V, Sterling P.  2009.  Receptive fields and the functional architecture in the retina. J. Physiol.. 587:2753-2767. Download: The Journal of Physiology 2009 Balasubramanian-1.pdf (928.94 KB)

Simmons, KD, Tkacik G, Prentice J, Balasubramanian V.  2009.  What is the “contrast” in contrast adaptation? COSYNE 2009.

2008

Tkacik, G, Magnasco MO.  2008.  Decoding spike timing: The differential reverse-correlation method. Bio. Systems. 93:90-100. Download: DecodingSpikeTiming.pdf (1.35 MB)

Borghuis, BG, Ratliff CP, Smith RG, Sterling P, Balasubramanian V.  2008.  Design of a neuronal array. J Neurosci. 28:3178-3189. Download: borghuis_2008.pdf (582.96 KB)

Tkacik, G, Callan CG, Bialek W.  2008.  Information capacity of genetic regulatory elements. Phys. Rev. E. 78 Download: PRE_InfoCap1.pdf (566.51 KB)

Tkacik, G, Callan CG, Bialek W.  2008.  Information flow and optimization in transcriptional regulation. PNAS. 105:12265-12270. Download: InforTranscript.pdf (1.39 MB)

Tkacik, G, Gregor T, Bialek W.  2008.  The role of input noise in transcriptional regulation. PLoS ONE. 3 Download: NoiseTranscript.pdf (340.61 KB)

2007

Garrigan, P, Ratliff CP, Brainard D, Balasubramanian V.  2007.  Chromatic statistics and information in natural images. COSYNE 2007 abstract.  Download: COSYNE_chromatic_2007.pdf (112.43 KB)

Perge, J, Koch K, Li J, Sterling P, Balasubramanian V.  2007.  Metabolic capacity of mammalian axons. COSYNE 2007 abstract.  Download: COSYNE_axons_2007.pdf (132.41 KB)

Ratliff, CP, Borghuis BG, Smith R, Sterling P, Balasubramanian V.  2007.  Natural image statistics predict organization of retinal ganglion cell arrays. COSYNE 2007 abstract.  Download: COSYNE_array_2007.pdf (113.29 KB)

2006

Koch, K, McLean J, Segev R, Freed MA, Berry MJ, Balasubramanian V, Sterling P.  2006.  How much the eye tells the brain. Curr. Biol.. 16:1428-1434. Download: Current Biology 2006 Koch.pdf (479.72 KB)

2004

Koch, K, McLean J, Berry MJ, Sterling P, Balasubramanian V, Freed MA.  2004.  Efficiency of information transmission by retinal ganglion cells. Curr. Biol.. 14:1523-1530. Download: koch_2004.pdf (309.82 KB)

2002

Balasubramanian, V, Berry MJ.  2002.  A test of metabolically efficient coding in the retina. Network. 13:531-552. Download: BalasubBerry2002.pdf (457.76 KB)

2001

Balasubramanian, V, Kimber D, Berry MJ.  2001.  Metabolically efficient information processing. Neural Comput.. 13:799-815. Download: Neural computation 2001 Balasubramanian.pdf (194.88 KB)