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Items: 1 to 50 of 104

1.

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.

Bedbrook CN, Yang KK, Robinson JE, Mackey ED, Gradinaru V, Arnold FH.

Nat Methods. 2019 Oct 14. doi: 10.1038/s41592-019-0583-8. [Epub ahead of print]

PMID:
31611694
2.

Low- and high-thermogenic brown adipocyte subpopulations coexist in murine adipose tissue.

Song A, Dai W, Jang MJ, Medrano L, Li Z, Zhao H, Shao M, Tan J, Li A, Ning T, Miller MM, Armstrong B, Huss JM, Zhu Y, Liu Y, Gradinaru V, Wu X, Jiang L, Scherer PE, Wang QA.

J Clin Invest. 2019 Oct 1. pii: 129167. doi: 10.1172/JCI129167. [Epub ahead of print]

3.

Proceedings of the Sixth Deep Brain Stimulation Think Tank Modulation of Brain Networks and Application of Advanced Neuroimaging, Neurophysiology, and Optogenetics.

Ramirez-Zamora A, Giordano J, Boyden ES, Gradinaru V, Gunduz A, Starr PA, Sheth SA, McIntyre CC, Fox MD, Vitek J, Vedam-Mai V, Akbar U, Almeida L, Bronte-Stewart HM, Mayberg HS, Pouratian N, Gittis AH, Singer AC, Creed MC, Lazaro-Munoz G, Richardson M, Rossi MA, Cendejas-Zaragoza L, D'Haese PF, Chiong W, Gilron R, Chizeck H, Ko A, Baker KB, Wagenaar J, Harel N, Deeb W, Foote KD, Okun MS.

Front Neurosci. 2019 Sep 12;13:936. doi: 10.3389/fnins.2019.00936. eCollection 2019.

4.

Optical dopamine monitoring with dLight1 reveals mesolimbic phenotypes in a mouse model of neurofibromatosis type 1.

Robinson JE, Coughlin GM, Hori AM, Cho JR, Mackey ED, Turan Z, Patriarchi T, Tian L, Gradinaru V.

Elife. 2019 Sep 23;8. pii: e48983. doi: 10.7554/eLife.48983. [Epub ahead of print]

5.

Publisher Correction: Systemic AAV vectors for widespread and targeted gene delivery in rodents.

Challis RC, Kumar SR, Chan KY, Challis C, Beadle K, Jang MJ, Kim HM, Rajendran PS, Tompkins JD, Shivkumar K, Deverman BE, Gradinaru V.

Nat Protoc. 2019 Aug;14(8):2597. doi: 10.1038/s41596-019-0155-5.

PMID:
31312046
6.

The Serotonergic Raphe Promote Sleep in Zebrafish and Mice.

Oikonomou G, Altermatt M, Zhang RW, Coughlin GM, Montz C, Gradinaru V, Prober DA.

Neuron. 2019 Aug 21;103(4):686-701.e8. doi: 10.1016/j.neuron.2019.05.038. Epub 2019 Jun 24.

PMID:
31248729
7.

Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies.

Rajendran PS, Challis RC, Fowlkes CC, Hanna P, Tompkins JD, Jordan MC, Hiyari S, Gabris-Weber BA, Greenbaum A, Chan KY, Deverman BE, Münzberg H, Ardell JL, Salama G, Gradinaru V, Shivkumar K.

Nat Commun. 2019 Apr 26;10(1):1944. doi: 10.1038/s41467-019-09770-1.

8.

TRIM9-Mediated Resolution of Neuroinflammation Confers Neuroprotection upon Ischemic Stroke in Mice.

Zeng J, Wang Y, Luo Z, Chang LC, Yoo JS, Yan H, Choi Y, Xie X, Deverman BE, Gradinaru V, Gupton SL, Zlokovic BV, Zhao Z, Jung JU.

Cell Rep. 2019 Apr 9;27(2):549-560.e6. doi: 10.1016/j.celrep.2018.12.055.

9.

Systemic AAV vectors for widespread and targeted gene delivery in rodents.

Challis RC, Ravindra Kumar S, Chan KY, Challis C, Beadle K, Jang MJ, Kim HM, Rajendran PS, Tompkins JD, Shivkumar K, Deverman BE, Gradinaru V.

Nat Protoc. 2019 Feb;14(2):379-414. doi: 10.1038/s41596-018-0097-3. Erratum in: Nat Protoc. 2019 Aug;14(8):2597.

PMID:
30626963
10.

Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy.

Mano T, Albanese A, Dodt HU, Erturk A, Gradinaru V, Treweek JB, Miyawaki A, Chung K, Ueda HR.

J Neurosci. 2018 Oct 31;38(44):9330-9337. doi: 10.1523/JNEUROSCI.1677-18.2018. Review.

11.

Two-Photon Microscopy with a Double-Wavelength Metasurface Objective Lens.

Arbabi E, Li J, Hutchins RJ, Kamali SM, Arbabi A, Horie Y, Van Dorpe P, Gradinaru V, Wagenaar DA, Faraon A.

Nano Lett. 2018 Aug 8;18(8):4943-4948. doi: 10.1021/acs.nanolett.8b01737. Epub 2018 Jul 23.

PMID:
30016110
12.

Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors.

Patriarchi T, Cho JR, Merten K, Howe MW, Marley A, Xiong WH, Folk RW, Broussard GJ, Liang R, Jang MJ, Zhong H, Dombeck D, von Zastrow M, Nimmerjahn A, Gradinaru V, Williams JT, Tian L.

Science. 2018 Jun 29;360(6396). pii: eaat4422. doi: 10.1126/science.aat4422. Epub 2018 May 31.

13.

Hydrogel-Tissue Chemistry: Principles and Applications.

Gradinaru V, Treweek J, Overton K, Deisseroth K.

Annu Rev Biophys. 2018 May 20;47:355-376. doi: 10.1146/annurev-biophys-070317-032905. Review.

14.

The Neuropeptide Tac2 Controls a Distributed Brain State Induced by Chronic Social Isolation Stress.

Zelikowsky M, Hui M, Karigo T, Choe A, Yang B, Blanco MR, Beadle K, Gradinaru V, Deverman BE, Anderson DJ.

Cell. 2018 May 17;173(5):1265-1279.e19. doi: 10.1016/j.cell.2018.03.037.

15.

Viral Strategies for Targeting the Central and Peripheral Nervous Systems.

Bedbrook CN, Deverman BE, Gradinaru V.

Annu Rev Neurosci. 2018 Jul 8;41:323-348. doi: 10.1146/annurev-neuro-080317-062048. Epub 2018 Apr 25. Review.

PMID:
29709207
16.

Deep tissue optical focusing and optogenetic modulation with time-reversed ultrasonically encoded light.

Ruan H, Brake J, Robinson JE, Liu Y, Jang M, Xiao C, Zhou C, Gradinaru V, Yang C.

Sci Adv. 2017 Dec 8;3(12):eaao5520. doi: 10.1126/sciadv.aao5520. eCollection 2017 Dec.

17.

Overriding sleep.

Gradinaru V.

Science. 2017 Oct 27;358(6362):457. doi: 10.1126/science.aap9535. No abstract available.

PMID:
29074759
18.

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization.

Bedbrook CN, Yang KK, Rice AJ, Gradinaru V, Arnold FH.

PLoS Comput Biol. 2017 Oct 23;13(10):e1005786. doi: 10.1371/journal.pcbi.1005786. eCollection 2017 Oct.

19.

Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?

Greenbaum A, Jang MJ, Challis C, Gradinaru V.

BMC Biol. 2017 Sep 25;15(1):87. doi: 10.1186/s12915-017-0421-3.

20.

The Jellyfish Cassiopea Exhibits a Sleep-like State.

Nath RD, Bedbrook CN, Abrams MJ, Basinger T, Bois JS, Prober DA, Sternberg PW, Gradinaru V, Goentoro L.

Curr Biol. 2017 Oct 9;27(19):2984-2990.e3. doi: 10.1016/j.cub.2017.08.014. Epub 2017 Sep 21.

21.

Dopaminergic dysfunction in neurodevelopmental disorders: recent advances and synergistic technologies to aid basic research.

Robinson JE, Gradinaru V.

Curr Opin Neurobiol. 2018 Feb;48:17-29. doi: 10.1016/j.conb.2017.08.003. Epub 2017 Aug 30. Review.

22.

Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems.

Chan KY, Jang MJ, Yoo BB, Greenbaum A, Ravi N, Wu WL, Sánchez-Guardado L, Lois C, Mazmanian SK, Deverman BE, Gradinaru V.

Nat Neurosci. 2017 Aug;20(8):1172-1179. doi: 10.1038/nn.4593. Epub 2017 Jun 26.

23.

Dorsal Raphe Dopamine Neurons Modulate Arousal and Promote Wakefulness by Salient Stimuli.

Cho JR, Treweek JB, Robinson JE, Xiao C, Bremner LR, Greenbaum A, Gradinaru V.

Neuron. 2017 Jun 21;94(6):1205-1219.e8. doi: 10.1016/j.neuron.2017.05.020. Epub 2017 Jun 8.

24.

Global Representations of Goal-Directed Behavior in Distinct Cell Types of Mouse Neocortex.

Allen WE, Kauvar IV, Chen MZ, Richman EB, Yang SJ, Chan K, Gradinaru V, Deverman BE, Luo L, Deisseroth K.

Neuron. 2017 May 17;94(4):891-907.e6. doi: 10.1016/j.neuron.2017.04.017.

25.

Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow.

Greenbaum A, Chan KY, Dobreva T, Brown D, Balani DH, Boyce R, Kronenberg HM, McBride HJ, Gradinaru V.

Sci Transl Med. 2017 Apr 26;9(387). pii: eaah6518. doi: 10.1126/scitranslmed.aah6518.

PMID:
28446689
26.

Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins.

Bedbrook CN, Rice AJ, Yang KK, Ding X, Chen S, LeProust EM, Gradinaru V, Arnold FH.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2624-E2633. doi: 10.1073/pnas.1700269114. Epub 2017 Mar 10.

27.

Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore.

Herwig L, Rice AJ, Bedbrook CN, Zhang RK, Lignell A, Cahn JKB, Renata H, Dodani SC, Cho I, Cai L, Gradinaru V, Arnold FH.

Cell Chem Biol. 2017 Mar 16;24(3):415-425. doi: 10.1016/j.chembiol.2017.02.008. Epub 2017 Mar 2.

28.

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease.

Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK.

Cell. 2016 Dec 1;167(6):1469-1480.e12. doi: 10.1016/j.cell.2016.11.018.

29.

Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling.

DePas WH, Starwalt-Lee R, Van Sambeek L, Ravindra Kumar S, Gradinaru V, Newman DK.

MBio. 2016 Sep 27;7(5). pii: e00796-16. doi: 10.1128/mBio.00796-16.

30.

Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation.

Pan M, Reid MA, Lowman XH, Kulkarni RP, Tran TQ, Liu X, Yang Y, Hernandez-Davies JE, Rosales KK, Li H, Hugo W, Song C, Xu X, Schones DE, Ann DK, Gradinaru V, Lo RS, Locasale JW, Kong M.

Nat Cell Biol. 2016 Oct;18(10):1090-101. doi: 10.1038/ncb3410. Epub 2016 Sep 12.

31.

Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors.

Treweek JB, Gradinaru V.

Curr Opin Biotechnol. 2016 Aug;40:193-207. doi: 10.1016/j.copbio.2016.03.012. Epub 2016 Jul 6. Review.

32.

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.

Shah S, Lubeck E, Schwarzkopf M, He TF, Greenbaum A, Sohn CH, Lignell A, Choi HM, Gradinaru V, Pierce NA, Cai L.

Development. 2016 Aug 1;143(15):2862-7. doi: 10.1242/dev.138560. Epub 2016 Jun 24.

33.

Cholinergic Mesopontine Signals Govern Locomotion and Reward through Dissociable Midbrain Pathways.

Xiao C, Cho JR, Zhou C, Treweek JB, Chan K, McKinney SL, Yang B, Gradinaru V.

Neuron. 2016 Apr 20;90(2):333-47. doi: 10.1016/j.neuron.2016.03.028.

34.

Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain.

Deverman BE, Pravdo PL, Simpson BP, Kumar SR, Chan KY, Banerjee A, Wu WL, Yang B, Huber N, Pasca SP, Gradinaru V.

Nat Biotechnol. 2016 Feb;34(2):204-9. doi: 10.1038/nbt.3440. Epub 2016 Feb 1.

35.

Neuroscience: Fluorescent boost for voltage sensors.

Gradinaru V, Flytzanis NC.

Nature. 2016 Jan 28;529(7587):469-70. doi: 10.1038/529469a. No abstract available.

PMID:
26819038
36.

Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation.

Skennerton CT, Ward LM, Michel A, Metcalfe K, Valiente C, Mullin S, Chan KY, Gradinaru V, Orphan VJ.

Front Microbiol. 2015 Dec 23;6:1425. doi: 10.3389/fmicb.2015.01425. eCollection 2015.

37.

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.

Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V.

Nat Protoc. 2015 Nov;10(11):1860-1896. doi: 10.1038/nprot.2015.122. Epub 2015 Oct 22.

38.

Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo.

Bedbrook CN, Kato M, Ravindra Kumar S, Lakshmanan A, Nath RD, Sun F, Sternberg PW, Arnold FH, Gradinaru V.

Chem Biol. 2015 Aug 20;22(8):1108-21. doi: 10.1016/j.chembiol.2015.06.020. Epub 2015 Jul 23.

39.

Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons.

Flytzanis NC, Bedbrook CN, Chiu H, Engqvist MK, Xiao C, Chan KY, Sternberg PW, Arnold FH, Gradinaru V.

Nat Commun. 2014 Sep 15;5:4894. doi: 10.1038/ncomms5894.

40.

Directed evolution of a far-red fluorescent rhodopsin.

McIsaac RS, Engqvist MK, Wannier T, Rosenthal AZ, Herwig L, Flytzanis NC, Imasheva ES, Lanyi JK, Balashov SP, Gradinaru V, Arnold FH.

Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13034-9. doi: 10.1073/pnas.1413987111. Epub 2014 Aug 25.

41.

Single-cell phenotyping within transparent intact tissue through whole-body clearing.

Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen CK, Lubeck E, Shah S, Cai L, Gradinaru V.

Cell. 2014 Aug 14;158(4):945-958. doi: 10.1016/j.cell.2014.07.017. Epub 2014 Jul 31.

42.

Bioelectronic medicines: a research roadmap.

Birmingham K, Gradinaru V, Anikeeva P, Grill WM, Pikov V, McLaughlin B, Pasricha P, Weber D, Ludwig K, Famm K.

Nat Rev Drug Discov. 2014 Jun;13(6):399-400. doi: 10.1038/nrd4351. Review. No abstract available.

PMID:
24875080
43.

Optogenetic delay of status epilepticus onset in an in vivo rodent epilepsy model.

Sukhotinsky I, Chan AM, Ahmed OJ, Rao VR, Gradinaru V, Ramakrishnan C, Deisseroth K, Majewska AK, Cash SS.

PLoS One. 2013 Apr 24;8(4):e62013. doi: 10.1371/journal.pone.0062013. Print 2013.

44.

Structural and molecular interrogation of intact biological systems.

Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K.

Nature. 2013 May 16;497(7449):332-7. doi: 10.1038/nature12107. Epub 2013 Apr 10.

45.

Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins.

Mattis J, Tye KM, Ferenczi EA, Ramakrishnan C, O'Shea DJ, Prakash R, Gunaydin LA, Hyun M, Fenno LE, Gradinaru V, Yizhar O, Deisseroth K.

Nat Methods. 2011 Dec 18;9(2):159-72. doi: 10.1038/nmeth.1808.

46.

Leptin regulates the reward value of nutrient.

Domingos AI, Vaynshteyn J, Voss HU, Ren X, Gradinaru V, Zang F, Deisseroth K, de Araujo IE, Friedman J.

Nat Neurosci. 2011 Nov 13;14(12):1562-8. doi: 10.1038/nn.2977.

47.

Dynamics of retrieval strategies for remote memories.

Goshen I, Brodsky M, Prakash R, Wallace J, Gradinaru V, Ramakrishnan C, Deisseroth K.

Cell. 2011 Oct 28;147(3):678-89. doi: 10.1016/j.cell.2011.09.033. Epub 2011 Oct 20.

48.

Amygdala circuitry mediating reversible and bidirectional control of anxiety.

Tye KM, Prakash R, Kim SY, Fenno LE, Grosenick L, Zarabi H, Thompson KR, Gradinaru V, Ramakrishnan C, Deisseroth K.

Nature. 2011 Mar 17;471(7338):358-62. doi: 10.1038/nature09820. Epub 2011 Mar 9.

49.

Cholinergic interneurons control local circuit activity and cocaine conditioning.

Witten IB, Lin SC, Brodsky M, Prakash R, Diester I, Anikeeva P, Gradinaru V, Ramakrishnan C, Deisseroth K.

Science. 2010 Dec 17;330(6011):1677-81. doi: 10.1126/science.1193771.

50.

Global and local fMRI signals driven by neurons defined optogenetically by type and wiring.

Lee JH, Durand R, Gradinaru V, Zhang F, Goshen I, Kim DS, Fenno LE, Ramakrishnan C, Deisseroth K.

Nature. 2010 Jun 10;465(7299):788-92. doi: 10.1038/nature09108.

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