Publications

Journal Articles

59. Nadalin JK, Eden UT, Han X, Richardson RM, Chu CJ, Kramer MA. Application of a convolutional neural network for fully-automated detection of spike ripples in the scalp electroencephalogram. J Neurosci Methods. 2021 Jun 3:109239. doi: 10.1016/j.jneumeth.2021.109239.

58. Mount RA, Sridhar S, Hansen KR, Mohammed AI, Abdulkerim M, Kessel R, Nazer B, Gritton HJ, Han X. Distinct neuronal populations contribute to trace conditioning and extinction learning in the hippocampal CA1. Elife. 2021 Apr 12;10:e56491. doi: 10.7554/eLife.56491.

57. Hua-an Tseng, Xue Han, Distinct Spiking Patterns of Excitatory and Inhibitory Neurons and LFP Oscillations in Prefrontal Cortex During Sensory Discrimination, Frontiers in Physiology, 12 (2021).

56. Marianna K. Keaveney, Bahar Rahsepar, Hua-an Tseng, Fernando R. Fernandez, Rebecca A. Mount, Tina Ta, John A. White, Jim Berg and Xue Han, CamKIIα Positive Interneurons Identified via A microRNA Based Viral Gene Targeting Strategy, J Neurosci. 2020 Nov 5:JN-RM-2570-19. doi: 10.1523/JNEUROSCI.2570-19.2020.

55. Xiao, H. Gritton, H. Tseng, D. Zemel, X. Han, and J. Mertz, “High-contrast multifocus microscopy with a single camera and z-splitter prism,” Optica 7, 1477-1486 (2020).

54. Seth Bensussen, Sneha Shankar, Kimberley H Ching, Dana Zemel, Tina L Ta, Rebecca A Mount, Sanaya N Shroff, Howard J Gritton, Pierre Fabris, Hannah Vanbenschoten, Connor Beck, Heng-Ye Man, Xue Han, A Viral Toolbox of Genetically Encoded Fluorescent Synaptic Tags, iScience . 2020 Jun 30;23(7):101330. doi: 10.1016/j.isci.2020.101330.

53. Or A Shemesh, Changyang Linghu, Kiryl D Piatkevich, Daniel Goodwin, Orhan Tunc Celiker, Howard J Gritton, Michael F Romano, Ruixuan Gao, Chih-Chieh Jay Yu, Hua-An Tseng, Seth Bensussen, Sujatha Narayan, Chao-Tsung Yang, Limor Freifeld, Cody A Siciliano, Ishan Gupta, Joyce Wang, Nikita Pak, Young-Gyu Yoon, Jeremy FP Ullmann, Burcu Guner-Ataman, Habiba Noamany, Zoe R Sheinkopf, Won Min Park, Shoh Asano, Amy E Keating, James S Trimmer, Jacob Reimer, Andreas S Tolias, Mark F Bear, Kay M Tye, Xue Han, Misha B Ahrens, Edward S Boyden, Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator Neuron . 2020 Jun 26;S0896-6273(20)30398-6. doi: 10.1016/j.neuron.2020.05.029.

52. Sanaya N Shroff, Shoshana L Das, Hua-An Tseng, Jad Noueihed, Fernando Fernandez, John A White, Christopher S Chen, Xue Han, Voltage Imaging of Cardiac Cells and Tissue Using the Genetically Encoded Voltage Sensor Archon1, iScience. 2020 Mar 11;23(4):100974. PMID: 32299055 PMCID: PMC7160579

51. Ying Jiang, Hyeon Jeong Lee, Lu Lan, Hua-an Tseng, Chen Yang, Heng-Ye Man, Xue Han, Ji-Xin Cheng, Optoacoustic brain stimulation at submillimeter spatial precision, Nat Commun . 2020 Feb 14;11(1):881. doi: 10.1038/s41467-020-14706-1.

50. Piatkevich KD, Bensussen S, Tseng HA, Shroff SN, Lopez-Huerta VG, Park D, Jung EE, Shemesh OA, Straub C, Gritton HJ, Romano MF, Costa E, Sabatini BL, Fu Z, Boyden ES, Han X. Population imaging of neural activity in awake behaving mice. Nature. 2019 Oct 9. doi: 10.1038/s41586-019-1641-1. PubMed PMID: 31597963.

49. J Zeng, A Martin, X Han, OS Shirihai, MW Grinstaff, Biodegradable PLGA nanoparticles restore lysosomal acidity and protect neural PC-12 cells against mitochondrial toxicity, Ind. Eng. Chem. Res. 2019, 58, 31, 13910-13917

48. Gritton HJ, Howe WM, Romano MF, DiFeliceantonio AG, Kramer MA, Saligrama V, Bucklin ME, Zemel D, Han X. Unique contributions of parvalbumin and cholinergic interneurons in organizing striatal networks during movement. Nat Neurosci. 2019 Feb 25. doi: 10.1038/s41593-019-0341-3.  Matlab data analysis code used in the paper

47. Ergan S, Radwan A, Zou Z, Tseng H-a, Han X. Quantifying Human Experience in Architectural Spaces with Integrated Virtual Reality and Body Sensor Networks. Journal of Computing in Civil Engineering. 2019;33(2):04018062. doi: doi:10.1061/(ASCE)CP.1943-5487.0000812.

46. Romano M, Bucklin M, Gritton H, Mehrotra D, Kessel R, Han X. A Teensy microcontroller-based interface for optical imaging camera control during behavioral experiments. J Neurosci Methods. 2019 Apr 1. pii: S0165-0270(19)30103-7. doi: 10.1016/j.jneumeth.2019.03.019. PubMed PMID: 30946877. Related computer code for the paper.

45. Amaury Badon, Seth Bensussen, Howard J. Gritton, Mehraj R. Awal, Christopher V. Gabel, Xue Han, and Jerome Mertz, Video-rate large-scale imaging with Multi-Z confocal microscopy, Optica, Vol. 6, Issue 4, pp.389-395, 2019

44. Angela L Nocera, Sarina K Mueller, Jules R Stephan, Loretta Hing, Philip Seifert, Xue Han, Derrick T Lin, Mansoor M Amiji, Towia Libermann, Benjamin S Bleier, Exosome swarms eliminate airway pathogens and provide passive epithelial immunoprotection through nitric oxide, J Allergy Clin Immunol . 2019 Apr;143(4):1525-1535.e1. doi: 10.1016/j.jaci.2018.08.046.

43. James NM, Gritton HJ, Kopell N, Sen K, Han X., Muscarinic receptors regulate auditory and prefrontal cortical communication during auditory processing, Neuropharmacology. 2018 Oct 20. pii: S0028-3908(18)30814-1. doi: 10.1016/j.neuropharm.2018.10.027.

42.Simon P Shen, Hua-an Tseng, Kyle R Hansen, Ruofan Wu, Howard Gritton, Jennie Si, Xue Han, Automatic Cell Segmentation by Adaptive Thresholding (ACSAT) for large scale calcium imaging datasets, eNeuro, 2018  (Download Matlab Scripts on GitHub)

41. Marianna K. Keaveney, Hua-an Tseng, Tina L. Ta, Howard J. Gritton, Heng-Ye Man and Xue Han, A microRNA-based gene targeting tool for virally labeling interneurons in the rodent cortex, Cell Reports, 2018

40.Benjamin R. Pittman-Polletta, Allison Quach, Ali I. Mohammed, Michael Romano, Krishnakanth Kondabolu, Nancy J. Kopell, Xue Han, Michelle M. McCarthy, Striatal cholinergic receptor activation causes a rapid, selective, state-dependent rise in corticostriatal β activity, European Journal of Neuroscience, 2018

39. William J. Shain, Nicholas A. Vickers, Jiang Li, Xue Han, Thomas Bifano, and Jerome Mertz, Axial localization with modulated-illumination extended-depth-of-field microscopy, Biomedical Optics Express 9(4) 1771-1782, 2018

38. Xiao S, Tseng HA, Gritton H, Han X, Mertz J. Video-rate volumetric neuronal imaging using 3D targeted illumination. Sci Rep. 2018 May 21;8(1):7921.

37. Kyle R. Hansen, Gloria J. DeWalt, Ali I. Mohammed, Hua-an Tseng, Moona E. Abdulkerim, Seth Bensussen, Venkatesh Saligrama, Bobak Nazer, William D. Eldre and Xue Han, Mild Blast Injury Produces Acute Changes in Basal Intracellular Calcium Levels and Activity Patterns in Mouse Hippocampal Neurons, Journal of Neurotrauma, 2018, PubMed PMID: 29343209.  PDF for academic use (Download Matlab Scripts on GitHub) (Download Supplemental Videos)

36. Kodandaramaiah SB, Flores FJ, Holst GL, Singer AC, Han X, Brown EN, Boyden ES, Forest CR. Multi-neuron intracellular recording in vivo via interacting autopatching robots. Elife. 2018 Jan 3;7. pii: e24656. PubMed PMID: 29297466.

35. Wang G, Li S, Gilbert J, Gritton HJ, Wang Z, Li Z, Han X, Selkoe DJ, Man HY. Crucial Roles for SIRT2 and AMPA Receptor Acetylation in Synaptic Plasticity and  Memory. Cell Rep. 2017 Aug 8;20(6):1335-1347. PMID: 28793258; PMCID: PMC5584878.

34. Nocera AL, Miyake MM, Seifert P, Han X, Bleier BS. Exosomes mediate interepithelial transfer of functional P-glycoprotein in chronic rhinosinusitis with nasal polyps. Laryngoscope. 2017 Sep;127(9):E295-E300. PMID: 28485529.

33. Kunkhyen T, McCarthy EA, Korzan WJ, Doctor D, Han X, Baum MJ, Cherry JA. Optogenetic Activation of Accessory Olfactory Bulb Input to the Forebrain Differentially Modulates Investigation of Opposite versus Same-Sex Urinary Chemosignals and Stimulates Mating in Male Mice. eNeuro. 2017 Mar 23;4(2). pii: ENEURO.0010-17.2017. PMID: 28374006; PMCID: PMC5362934.

32.Zhuo JM, Tseng HA, Desai M, Bucklin ME, Mohammed AI, Robinson NT, Boyden ES, Rangel LM, Jasanoff AP, Gritton HJ, Han X. Young adult born neurons enhance hippocampal dependent performance via influences on bilateral networks. Elife. 2016 PubMed PMID: 27914197; PubMed Central PMCID: PMC5156524. PDF for academic use  (Download Matlab Scripts on GitHub) (Request Plasmids through Addgene)

31. Krishnakanth Kondabolu, Erik A Roberts, Mark Bucklin, Michelle M McCarthy, Nancy Kopell, Xue Han. Striatal Cholinergic Interneurons Generate Beta and Gamma Oscillations in the Corticostriatal Circuit and Produce Motor Deficits, PNAS 2016 May 31;113(22):E3159-68. PDF for academic use

30. Kohman RE, Cha SS, Man HY, Han X. Light-Triggered Release of Bioactive Molecules from DNA Nanostructures. Nano Letters, 2016 PDF for academic use

29. Rueckemann JW, DiMauro AJ, Rangel LM, Han X, Boyden ES, Eichenbaum H. Transient optogenetic inactivation of the medial entorhinal cortex biases the active population of hippocampal neurons. Hippocampus. 2016 PDF for academic use

28. Ali I. Mohammed, Howard J. Gritton, Hua-an Tseng, Mark E. Bucklin, Zhaojie Yao & Xue Han. An integrative approach for analyzing hundreds of neurons in task performing mice using wide-field calcium imaging  Scientific Reports, 2016 PDF  (Download Matlab package)

27. Nocera AL, Meurer AT, Miyake MM, Sadow PM, Han X, Bleier BS. Secreted P-glycoprotein is a noninvasive biomarker of chronic rhinosinusitis. Laryngoscope. 2016 Aug 31.  PMID: 27577924.

26. Nocera AL, Meurer AT, Singleton A, Simons C, BuSaba J, Tara Gass N, Han X, Bleier BS. Intact soluble P-glycoprotein is secreted by sinonasal epithelial cells. Am J Rhinol Allergy. 2016 Jul;30(4):246-9. PMID: 27456593.

25. Bleier BS, Singleton A, Nocera AL, Kocharyan A, Petkova V, Han X. P-glycoprotein regulates Staphylococcus aureus enterotoxin B-stimulated interleukin-5 and thymic stromal lymphopoietin secretion in organotypic mucosal explants. Int Forum Allergy Rhinol. 2016 Feb;6(2):169-77.  PMID: 26625351.

24. Bleier BS, Kohman RE, Guerra K, Nocera AL, Ramanlal S, Kocharyan AH, Curry WT, Han X. Heterotopic Mucosal Grafting Enables the Delivery of Therapeutic Neuropeptides Across the Blood Brain Barrier. Neurosurgery, 2015

23. Sayeg, Marianna; Weinberg, Benjamin; Cha, Susie; Goodloe, Michael; Wong, Wilson; Han, Xue. “Rationally designed microRNA-based genetic classifiers target specific neurons in the brain“. ACS Syn Bio, 2015 PDF (Request Plasmids from Addgene)

22. Bleier BS, Kocharyan A, Singleton A, Han X. Verapamil modulates interleukin-5 and interleukin-6 secretion in organotypic human sinonasal polyp explants. Int Forum Allergy Rhinol. 2015. PMID: 25330767.

21 Lam A, Hoang JD, Singleton A, Han X, Bleier BS. Itraconazole and clarithromycin inhibit P-glycoprotein activity in primary human sinonasal epithelial cells. Int Forum Allergy Rhinol. 2015. PubMed PMID: 25907295.

20. Richie E. Kohman, and Xue Han. “Light-Sensitization of DNA Nanostructures via Incorporation of Photo-Cleavable Spacers.” Chem. Commun. 2015. PMID: 25720373 PDF,  Download: caDNAno file for the spheres

19. Kohman RE, Han X, Bleier BS. Heterotopic mucosal engrafting procedure for direct drug delivery to the brain in mice. J Vis Exp. 2014. PMID: 25077554

18. Chuong, A. S., Miri, M. L.*, Busskamp, V.*, Matthews, G.A.C.*, Acker, L.C.*, Soresnsen, A.T., Young, A., Klapoetke, N. C., Henninger, M.A., Kodandaramaiah, S.B., Ogawa, M., Ramanlal, S. B., Bandler, R. C., Allen, B. D., Forest, C.R., Chow, B.Y., Han, X., Lin, Y., Tye, K.M., Roska, R., Cardin, J.A., Boyden, E. S. Noninvasive optical inhibition with a red-shifted microbial rhodopsin, Nature Neuroscience (2014) PMID: 24997763 PDF

17. Kocharyan A, Feldman R, Singleton A, Han X, Bleier BS. P-glycoprotein inhibition promotes prednisone retention in human sinonasal polyp explants. Int Forum Allergy Rhinol. 2014. PMID: 25145685.

16. Bleier BS, Nocera AL, Iqbal H, Hoang JD, Alvarez U, Feldman RE, Han X. P-glycoprotein promotes epithelial T helper 2-associated cytokine secretion in chronic sinusitis with nasal polyps. Int Forum Allergy Rhinol. (2014)

15. Bleier BS, Nocera AL, Iqbal H, Hoang JD, Feldman RE, Han X, P-glycoprotein functions as an immunomodulator in healthy human primary nasal epithelial cells, Int Forum Allergy Rhinol. (2013) PDF

14. Zhang XX, LaManna CM, Kohman RE, Mclntosh TJ, Han X, Grinstaff MW, Lipid-mediated DNA and siRNA transfection efficiency depends on peptide headgroup, Soft Matter (2013) PDF

13. Bleier BS, Kohman RE, Feldman RE, Ramanlal S, Han X, Permeabilization of the Blood-Brain Barrier via Mucosal Engrafting: Implications for Drug Delivery to the Brain, Plos One (2013) PDF

12.  Madisen L, Mao T, Koch H, Zhuo JM, Berenyi A, Fujisawa S, Hsu YW, Garcia AJ 3rd, Gu X, Zanella S, Kidney J, Gu H, Mao Y, Hooks BM, Boyden ES, Buzsáki G, Ramirez JM, Jones AR, Svoboda K, Han X, Turner EE, Zeng H. A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing. Nat Neurosci. (2012) PDF

11.  M. M. McCarthy, C. Moore-Kochlacs, X. Gu, E. S. Boyden, X. Han, and N. Kopell, Striatal origin of the pathologic beta oscillations in Parkinson’s disease, PNAS  108:11620-11625 (2011) PDF

10.  Han, X.*, Chow, B. Y.*, Zhou, H., Klapoetke, N. C., Chuong, A., Rajimehr, R., Yang, A., Baratta, M. V., Winkle, J., Desimone, R., Boyden, E. S. (2011) A high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex. Frontiers in Systems Neuroscience. 5:18. doi: 10.3389/fnsys.2011.00018 (2011) (* co-first authors) PDF

9.  Lindskog, M., Li, L., Groth R.D., Poburko, D., Thiagarajan, T.C.,  Han, X., and Tsien, R.W. Postsynaptic GluA1 enables acute retrograde enhancement of presynaptic function to coordinate adaptation to synaptic inactivity, PNAS 107:21806-11  (2010) PDF

8.  Chow, B. Y.*, Han, X.*, Dobry, A. S., Qian, X., Chuong, A. S., Li, M., Henninger, M. A., Belfort, G. M., Lin, Y., Monahan, P. E., Boyden, E. S. High-performance genetically targetable optical neural silencing by light-driven proton pumps, Nature 463:98-102. (2010), (* co-first authors) PDF

7.  Xue Han, Sherry X. Xian, and Tirin Moore, “Dynamic sensitivity of area V4 neurons during saccade preparation”, PNAS 106(31):13046-51 (2009) PDF

6.  Xue Han, Xiaofeng Qian, Jacob G. Bernstein, Hui-hui Zhou, Giovanni Talei Franzesi, Patrick Stern, Roderick T. Bronson, Ann M. Graybiel, Robert Desimone and Edward S. Boyden, “Millisecond-Timescale Optical Control of Neural Dynamics in the Nonhuman Primate Brain,” Neuron 62(2):191-8 (2009) PDF

5.  Xue Han, Xiaofeng Qian, Patrick Stern, Amy Chuong and Edward S. Boyden, “Informational lesions: optical perturbation of spike timing and neural synchrony via microbial opsin gene fusions”, Front. Mol. Neurosci 2, 12, (2009) PDF

4.  Xue Han and Edward S. Boyden. “Multiple-Color Optical Activation, Silencing, and Desynchronization of Neural Activity, with Single-Spike Temporal Resolution.” PLoS ONE, 2(3):e299. (2007) PDF

3.  Xue Han and Meyer B. Jackson. “Structural Transitions in the Synaptic SNARE Complex during Calcium triggered exocytosis.”J Cell Biol. 172(2): 281-93 (2006) PDF

2.  Xue Han and Meyer B. Jackson. “Electrostatic interactions between the syntaxin membrane anchor and neurotransmitter passing through the fusion pore.” Biophys J. 88 (3): L20-2 (2005) PDF

1.  Xue Han, Chih-Tien Wang, Jihong Bai, Edwin R. Chapman and Meyer B. Jackson. Transmembrane segments of syntaxin line the fusion pore of Ca2+-triggered exocytosis.” Science 304 (5668): 289-92 (2004) PDF

 

Review Articles
3.  Xue Han, In vivo Application of Optogenetics for Neural Circuit Analysis. ACS Chem. Neurosci. (2012) PDF

2.  Brian Y. Chow, Xue Han, Edward S. Boyden, Genetically encoded molecular tools for light-driven silencing of targeted neurons, Prog Brain Res, 196:49-61, (2012) PDF

1.  Xue Han, Optogenetics in the nonhuman primate, Prog Brain Res, 196:215-33, (2012) PDF

 

Commentaries

1. Xue Han, Control Neural Networks in “What is the Key Conceptual or Methodological Bottleneck to Controlling Neural Biology?” Cell Syst. 2020;10(6):461-462. doi:10.1016/j.cels.2020.06.001, PMID: 32585154

 

Conference Papers (Refereed)

Bernstein, J. G., Han, X., Henninger, M. A., Ko, E. Y., Qian, X., Franzesi, G. T., McConnell, J. P., Stern, P., Desimone, R., and Boyden, E. S. (2008) Prosthetic systems for therapeutic optical activation and silencing of genetically-targeted neurons. Proc Soc Photo Opt Instrum Eng, 6854:68540H.

 

Book Chapters

6. Kondabolu K, Kowalski MM, Roberts EA, Han X. Optogenetics and deep brain stimulation neurotechnologies. Handb Exp Pharmacol. 2015;228:441-50. PMID: 25977092. (2015)

5. Richie Kohman, Hua-an Tseng, and Xue Han (2014) “Optogenetics” The OMICs, Applications in Neuroscience, Oxford

4. Quach, Allison, Nicholas James, and Xue Han. (2014) “Optogenetics” Nanotechnology and Neuroscience: Nano-electronic, Photonic and Mechanical Neuronal Interfacing. Springer New York, 2014. 269-282.

3. Hua-an Tseng, Richie E. Kohman, and Xue Han. “Chapter on Optogenetics” Basic Electrophysiological Methods, Oxford University Press. (2013)

2. Chow, B. Y., Han, X., Bernstein, J. G., Monahan, P. E., Boyden, E. S. (2011) Light-Activated Ion Pumps and Channels for Temporally Precise Optical Control of Activity in Genetically Targeted Neurons, Chapter 6, Photosensitive Molecules for Controlling Biological Function, edited by James J. Chambers and Richard H. Kramer, Neuromethods Series Volume 55, 2011, DOI: 10.1007/978-1-61779-031-7, Humana Press.

1. Boyden, E. S., Han, X., Talei Franzesi, G., Chan, S., Bernstein, J., Qian, X., Li, M. (2009) New Techniques for Investigating Brain Rhythms: Optical Neural Control and Multielectrode Recording,” In: Rhythms of the Neocortex: Where Do They Come From and What Are They Good For? (Kopell N., ed.) pp. 65-75. Washington, DC: Society for Neuroscience.

 

Patents

Light-stimulated release of cargo from oligonucleotides, Xue Han, Richie Kohman and Susie Cha, U.S. Patent No. US10617759B2 (granted 2020)

Red-shifted opsin molecules and uses thereof. Amy Chuong, Nathan Klapoetke, Brian Yichiun Chow, Edward Boyden, Xue Han, US patent No. US10106584B2 (granted 2018)

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