Cell-type specialization of layer 5 excitatory neurons in tactile behavior

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King S, Maire P, Mergenthal A, Walker S, Hires SA. bioRxiv. 2024 March 17,  doi: 10.1101/2024.03.15.585205

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WhACC: Whisker Automatic Contact Classifier with expert human-level performance

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Maire P, King S, Cheung JA, Walker S, Hires SA. bioRxiv. 2023 May 22,  doi: 10.1101/2023.05.19.541544

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Goal-directed motor actions drive acetylcholine dynamics in sensory cortex

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Zou J,  Willem de Gee J, Mridha Z, Trinh S, Erskine A, Jing M, Yao J, Walker S , Li Y, McGinley M, Hires SA. bioRxiv 2021 December 23,  https://doi.org/10.1101/2021.12.21.473699 (pdf)

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Independent representations of self-motion and object location in barrel cortex output

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Cheung JA, Maire P, Kim J, Lee K, Flynn G, Hires SA. PLoS 2020 November 3, 18(11): e3000882. https://doi.
org/10.1371/journal.pbio.3000882 (pdf)

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Behavioral and neural bases of tactile shape discrimination learning in head-fixed mice

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Kim J, Erskine A, Cheung JA, Hires SA. Neuron 2020 Sep 30, doi: 10.1016/j.neuron.2020.09.012 (pdf)

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An optimized acetylcholine sensor for monitoring in vivo cholinergic activity

 

Jin M, Li Y, Zeng J, Huang P, Skirzewski M, Kljakic O, Peng W, Qian T, Tan K, Zou J, Trinh S, Wu R, Zhang S, Pan S, Hires SA, Xu M, Li H, Saksida LM, Prado VF, Bussey TJ, Prado MAM, Chen L, Cheng H, Li Y. Nature Methods 2020, doi: 10.1038/s41592-020-0953-2. (pdf)

 

The sensorimotor basis of whisker-guided anteroposterior object localization in head-fixed mice​

 

Cheung J, Maire P, Kim J, Sy J, Hires SA. Current Biology 2019, doi: 10.1016/j.cub.2019.07.068 (pdf)

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A genetically encoded fluorescent sensor for rapid and specific in vivo detection of norepinephrine.

 

Feng J, Zhang C, Lischinsky JE, Jing M, Zhou J, Wang H, Zhang Y, Dong A, Wu Z, Wu H, Chen W, Zhang P, Zou J, Hires SA, Zhu JJ, Cui G, Lin D, Du J, Li Y. Neuron. 2019 Mar 25. pii: S0896-6273(19)30172-2. (pdf)

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Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch.

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Vaxenburg R, Wyche I, Svoboda K, Efros AL, Hires SA. PLoS Comput Biol. 2018 Mar 27;14(3):e1006032. doi: 10.1371/journal.pcbi.1006032. (pdf)

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Mechanisms underlying a thalamocortical transformation during active tactile sensation.

 

Gutnisky DA, Yu J, Hires SA, To MS, Bale M, Svoboda K, Golomb D. Mechanisms underlying a thalamocortical transformation during active tactile sensation. PLoS Comput Biol. 2017;13(6):e1005576. (pdf) 

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Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation.

 

Yu J, Gutnisky DA, Hires SA, Svoboda K. Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation. Nature Neuroscience 2016; (pdf)

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Beyond cones: An improved model of whisker bending based on measured mechanics and tapering.

 

Hires SA^, Schuyler A, Sy J, Huang V, Wyche I, Wang X, Golomb D.  Beyond cones: An improved model of whisker bending based on measured mechanics and tapering. J Neurophysiol. 2016 Jun 1:jn.00511.2015. doi: 10.1152/jn.00511.2015. (pdf)

 

Neural coding during whisker-guided locomotion.

 

Sofroniew NJ, Vlasov YA, Hires SA, Freeman J, Svoboda K. Neural coding during whisker-guided locomotion. eLIFE. 2015 Dec 23;4. pii: e12559. doi: 10.7554/eLife.12559. (pdf)

 

Low-noise encoding of active touch by layer 4 in the somatosensory cortex.

 

Hires SA*, Gutnisky D*, Yu J, O'Connor DH, Svoboda K; Low-noise encoding of active touch by layer 4 in the somatosensory cortex. eLIFE 2015 Aug 6; 10.7554/eLife.06619 (pdf)

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Procedures for Behavioral Experiments in Head-Fixed Mice.

 

Guo Z; Hires SA; Li N; O'Connor D; Komiyama T; Ophir E; Huber D; Bonardi C; Morandell K; Gutnisky D; Peron S; Xu N; Cox J; Svoboda K. "Procedures for behavioral experiments in head-fixed mice". (pdf)

 

Tapered whiskers are required for active tactile sensation.

 

Hires SA, Pammer L, Svoboda K, Golomb D. Tapered whiskers are required for active tactile sensation eLife, 2013 Nov 19;2:e01350. doi: 10.7554/eLife.01350. (pdf)

 

Neural coding during active somatosensation revealed using illusory touch.

 

O'Connor DH*, Hires SA*, Guo ZV, Li N, Yu J, Sun QQ, Huber D, Svoboda K; Neural coding during active somatosensation revealed using illusory touch. Nature Neuroscience 2013 Jun 2; 16(7):958-65 (pdf)

 

Aβ induces astrocytic glutamate release, extrasynaptic NMDA receptor activation, and synaptic loss.

 

Talantova M*, Sanz-Blasco S*, Zhang X*, Xia P*, Akhtar MW, Okamoto S, Dziewczapolski G, Nakamura T, Cao G, Pratt AE, Kang YJ, Tu S, Molokanova E, McKercher SR, Hires SA, Wolosker H, Sason H, Solomon J, Powers ET, Kelly JW, Roberts AJ, Tong G, Zhang D, Nakanishi N, Chen HSV, Michael S, Masliah E, Heinemann SF, Piña-Crespo JC, Lipton SA. Aβ induces astrocytic glutamate release, extrasynaptic NMDA receptor activation, and synaptic loss Proc Natl Acad Sci U S A 2013 Jul 2;110(27):E2518-27 (pdf)

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The Mechanical Variables Underlying Object Localization along the Axis of the Whisker.

 

Pammer L*, O’Connor, DH*, Hires SA, Efros AL, Clack N, Huber D, Myers EW, Svoboda K. The mechanical variables underlying object localization along the axis of the whisker. J Neuroscience 2013 Apr 17;33(16):6726-41  (pdf)

 

An optimized fluorescent probe for visualizing glutamate neurotransmission.

 

Marvin JS, Borghuis BG, Tian L, Cichon J, Harnett MT, Akerboom J, Gordus A, Renninger S, Chen TW, Bargmann CI, Orger MB, Schreiter ER, Demb JB, Gan W, Magee JC, Hires SA, Looger LL An optimized fluorescent probe for visualizing glutamate neurotransmission. Nature Methods. 2013 Feb;10(2):162-70.  (pdf)

 

Automated Tracking of Whiskers in Videos of Head Fixed Rodents.

 

Clack NG, O'Connor DH, Huber D, Petreanu L, Hires SA, Peron S, Svoboda K, Myers EW. Automated tracking of whiskers in videos of head fixed rodents. PLoS Comput Biol. 2012 Jul; 8(7):e1002591 (pdf)

 

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators.

 

Tian L, Hires SA, Looger LL. Imaging neuronal activity with genetically encoded calcium indicators. Cold Spring Harb Protoc. 2012 Jun 1;2012(6):647-56. (pdf)

 

Concurrent Imaging of Synaptic Vesicle Recycling and Calcium Dynamics.

 

Li H, Foss SM, Dobryy YL, Park CK, Hires SA, Shaner NC, Tsien RY, Osborne LC, Voglmaier SM. Concurrent imaging of synaptic vesicle recycling and calcium dynamics. Front Mol Neurosci. 2011;4:34. Epub 2011 Nov 2. (pdf)

 

Laminar Analysis of Excitatory Local Circuits in Vibrissal Motor and Sensory Cortical Areas.

 

Hooks BM, Hires SA, Zhang YX, Huber D, Petreanu L, Svoboda K, Shepherd GM. Laminar analysis of excitatory local circuits in vibrissal motor and sensory cortical areas. PLoS Biol. 2011 Jan 4;9(1):e1000572. (pdf)

 

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators.

 

Tian L, Hires SA, Mao T, Huber D, Chiappe ME, Chalasani SH, Petreanu L, Akerboom J, McKinney SA, Schreiter ER, Bargmann CI, Jayaraman V, Svoboda K, Looger LL. Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods. 2009 Dec;6(12):875-81. Epub 2009 Nov 8. (pdf)

 

Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design.

 

Akerboom J, Rivera JD, Guilbe MM, Malavé EC, Hernandez HH, Tian L, Hires SA, Marvin JS, Looger LL, Schreiter ER. Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design. J Biol Chem. 2009 Mar 6;284(10):6455-64. Epub 2008 Dec 18. (pdf)

 

Reporting neural activity with genetically encoded calcium indicators.

 

Hires SA, Tian L, Loren Looger. Neural Activity Reporting with Genetically Encoded Calcium Indicators. Brain Cell Biology 2008 Aug;36(1-4):69-86 (pdf)

 

Optical measurement of synaptic glutamate spillover and reuptake by linker optimized glutamate-sensitive fluorescent reporters.

 

Hires SA, Zhu Y, and Tsien RY. Optical measurement of synaptic glutamate spillover and reuptake by linker optimized glutamate-sensitive fluorescent reporters. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4411-6  Supplemental Information (pdf)

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Reporting neural activity with genetically encoded calcium indicators.

 

Palmer AE, Giacomello M, Kortemme T, Hires SA, Lev-Ram V, Baker D, and Tsien RY. 2006. Ca2+ Indicators based on computationally redesigned calmodulin-peptide pairs. Chemistry & Biology 13, 521–530 (pdf)