Hong Wei Dong, M.D., Ph.D.
Director - B.R.A.I.N.


The long-term objective of my research is to map the interconnections among all delineated regions of the C57Bl/6 mouse brain, to generate a corresponding comprehensive connectome map that represents the connections in a common neuroanatomic frame, and to understand how the different brain regions assemble into functional networks based on their connections to affect behavioral output ( By integrating connectomics with genetics, 3D high resolution imaging, and artificial intelligence, we hope to uncover the fundamental architecture and functional organization of the central nervous system. A second major direction of my research is to classify cell types of the mouse brain and spinal cord based on their anatomic locations, neuronal connectivity, neuronal morphology, and their molecular and physiological properties. Identifying and enumerating cell types in the nervous system will allow for their selective manipulation and a better understanding of an individual cell's function in health and disease. The derived knowledge and technologies from our work can be directly applied to characterize connectivity disruptions that potentially underlie symptomatology in mouse models of neurodegenerative diseases such as Alzheimer’s and Huntington’s Disease. Finally, my lab also is dedicated to developing microscopy and histological technologies for mapping connections of the human brain at the axonal and cellular resolution as part of our motivation to advance toward translational research.


Macroscale connections of the mouse lateral preoptic area and anterior lateral hypothalamic area.
Hahn JD; Gao L; Boesen T; Gou L; Hintiryan H; Dong HW;
J Comp Neurol. 2022-May-1;
PMID: 35579973   DOI:
Cross-modal coherent registration of whole mouse brains
Qu L; Li Y; Xie P; Liu L; Wang Y; Wu J; Liu Y; Wang T; Li L; Guo K; Wan W; Ouyang L; Xiong F; Kolstad AC; Wu Z; Xu F; Zheng Y; Gong H; Luo Q; Bi G; Dong H; Hawrylycz M; Zeng H; Peng H;
Nat Methods. 2021-Dec-1;
PMID: 34887551   DOI:
A multimodal cell census and atlas of the mammalian primary motor cortex
BRAIN Initiative Cell Census Network (BICCN)
Nature. 2021-Oct-6; 598(7879):86-102
PMID: 34616075   DOI:
Cellular anatomy of the mouse primary motor cortex
Muñoz-Castañeda R; Zingg B; Matho KS; Chen X; Wang Q; Foster NN; Li A; Narasimhan A; Hirokawa KE; Huo B; Bannerjee S; Korobkova L; Park CS; Park YG; Bienkowski MS; Chon U; Wheeler DW; Li X; Wang Y; Naeemi M; Xie P; Liu L; Kelly K; An X; Attili SM; Bowman I; Bludova A; Cetin A; Ding L; Drewes R; D'Orazi F; Elowsky C; Fischer S; Galbavy W; Gao L; Gillis J; Groblewski PA; Gou L; Hahn JD; Hatfield JT; Hintiryan H; Huang JJ; Kondo H; Kuang X; Lesnar P; Li X; Li Y; Lin M; Lo D; Mizrachi J; Mok S; Nicovich PR; Palaniswamy R; Palmer J; Qi X; Shen E; Sun YC; Tao HW; Wakemen W; Wang Y; Yao S; Yuan J; Zhan H; Zhu M; Ng L; Zhang LI; Lim BK; Hawrylycz M; Gong H; Gee JC; Kim Y; Chung K; Yang XW; Peng H; Luo Q; Mitra PP; Zador AM; Zeng H; Ascoli GA; Josh Huang Z; Osten P; Harris JA; Dong HW;
Nature. 2021-Oct-6; 598(7879):159-166
PMID: 34616071   DOI:
The mouse cortico-basal ganglia-thalamic network
Foster NN; Barry J; Korobkova L; Garcia L; Gao L; Becerra M; Sherafat Y; Peng B; Li X; Choi JH; Gou L; Zingg B; Azam S; Lo D; Khanjani N; Zhang B; Stanis J; Bowman I; Cotter K; Cao C; Yamashita S; Tugangui A; Li A; Jiang T; Jia X; Feng Z; Aquino S; Mun HS; Zhu M; Santarelli A; Benavidez NL; Song M; Dan G; Fayzullina M; Ustrell S; Boesen T; Johnson DL; Xu H; Bienkowski MS; Yang XW; Gong H; Levine MS; Wickersham I; Luo Q; Hahn JD; Lim BK; Zhang LI; Cepeda C; Hintiryan H; Dong HW;
Nature. 2021-Oct-6; 598(7879):188-194
PMID: 34616074   DOI:
High-throughput mapping of a whole rhesus monkey brain at micrometer resolution
Xu F; Shen Y; Ding L; Yang CY; Tan H; Wang H; Zhu Q; Xu R; Wu F; Xiao Y; Xu C; Li Q; Su P; Zhang LI; Dong HW; Desimone R; Xu F; Hu X; Lau PM; Bi GQ;
Nat Biotechnol. 2021-Jul-26;
PMID: 34312500   DOI:
Organization of the inputs and outputs of the mouse superior colliculus
Benavidez NL, Bienkowski MS, Zhu M, Garcia LH, Fayzullina M, Gao L, Bowman I, Gou L, Khanjani N, Cotter KR, Korobkova L, Becerra M, Cao C, Song MY, Zhang B, Yamashita S, Tugangui AJ, Zingg B, Rose K, Lo D, Foster NN, Boesen T, Mun HS, Aquino S, Wickersham IR, Ascoli GA, Hintiryan H, Dong HW
Nature Communications. 2021-Jun-28; 12(1):4004
PMID: 34183678   DOI: 10.1038/s41467-021-24241-2
Connectivity characterization of the mouse basolateral amygdalar complex
Hintiryan H; Bowman I; Johnson DL; Korobkova L; Zhu M; Khanjani N; Gou L; Gao L; Yamashita S; Bienkowski MS; Garcia L; Foster NN; Benavidez NL; Song MY; Lo D; Cotter KR; Becerra M; Aquino S; Cao C; Cabeen RP; Stanis J; Fayzullina M; Ustrell SA; Boesen T; Tugangui AJ; Zhang ZG; Peng B; Fanselow MS; Golshani P; Hahn JD; Wickersham IR; Ascoli GA; Zhang LI; Dong HW;
Nat Commun. 2021-May-17; 12(1):2859
PMID: 34001873   DOI:
An open access mouse brain flatmap and upgraded rat and human brain flatmaps based on current reference atlases
Hahn JD; Swanson LW; Bowman I; Foster NN; Zingg B; Bienkowski MS; Hintiryan H; Dong HW;
J Comp Neurol. 2021-Feb-1; 529(3):576-594
PMID: 32511750   DOI:
Homologous laminar organization of the mouse and human subiculum.
Bienkowski MS; Sepehrband F; Kurniawan ND; Stanis J; Korobkova L; Khanjani N; Clark K; Hintiryan H; Miller CA; Dong HW;
Sci Rep. 2021-Feb-1; 11(1):3729
PMID: 33580088   DOI:
Brainwide Genetic Sparse Cell Labeling to Illuminate the Morphology of Neurons and Glia with Cre-Dependent MORF Mice
Veldman MB; Park CS; Eyermann CM; Zhang JY; Zuniga-Sanchez E; Hirano AA; Daigle TL; Foster NN; Zhu M; Langfelder P; Lopez IA; Brecha NC; Zipursky SL; Zeng H; Dong HW; Yang XW;
Neuron. 2020-Oct-1; 108(1):111-127.e6
PMID: 32795398   DOI:
Extrastriate connectivity of the mouse dorsal lateral geniculate thalamic nucleus
Bienkowski MS; Benavidez NL; Wu K; Gou L; Becerra M; Dong HW;
J Comp Neurol. 2019-May-1; 527(9):1419-1442
PMID: 30620046   DOI:
Precise segmentation of densely interweaving neuron clusters using G-Cut
Li R; Zhu M; Li J; Bienkowski MS; Foster NN; Xu H; Ard T; Bowman I; Zhou C; Veldman MB; Yang XW; Hintiryan H; Zhang J; Dong HW;
Nat Commun. 2019-Apr-1; 10(1):1549
PMID: 30948706   DOI:
Integration of gene expression and brain-wide connectivity reveals the multiscale organization of mouse hippocampal networks
Bienkowski MS; Bowman I; Song MY; Gou L; Ard T; Cotter K; Zhu M; Benavidez NL; Yamashita S; Abu-Jaber J; Azam S; Lo D; Foster NN; Hintiryan H; Dong HW;
Nat Neurosci. 2018-Nov-1; 21(11):1628-1643
PMID: 30297807   DOI:
Input-output organization of the mouse claustrum
Zingg B; Dong HW; Tao HW; Zhang LI;
J Comp Neurol. 2018-Oct-1; 526(15):2428-2443
PMID: 30252130   DOI:
The mouse cortico-striatal projectome
Hintiryan H; Foster NN; Bowman I; Bay M; Song MY; Gou L; Yamashita S; Bienkowski MS; Zingg B; Zhu M; Yang XW; Shih JC; Toga AW; Dong HW;
Nat Neurosci. 2016-Aug-1; 19(8):1100-14
PMID: 27322419   DOI:
BAMS2 workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections
Bota M; Talpalaru S; Hintiryan H; Dong HW; Swanson LW;
J Comp Neurol. 2014-Oct-1; 522(14):3160-76
PMID: 24668342   DOI:
Neural networks of the mouse neocortex
Zingg B; Hintiryan H; Gou L; Song MY; Bay M; Bienkowski MS; Foster NN; Yamashita S; Bowman I; Toga AW; Dong HW;
Cell. 2014-Feb-1; 156(5):1096-111
PMID: 24581503   DOI:
Comprehensive connectivity of the mouse main olfactory bulb: analysis and online digital atlas
Hintiryan H; Gou L; Zingg B; Yamashita S; Lyden HM; Song MY; Grewal AK; Zhang X; Toga AW; Dong HW;
Front Neuroanat. 2012-Aug-7; 6:30
PMID: 22891053   DOI:
Genetic dissection of an amygdala microcircuit that gates conditioned fear
Haubensak W; Kunwar PS; Cai H; Ciocchi S; Wall NR; Ponnusamy R; Biag J; Dong HW; Deisseroth K; Callaway EM; Fanselow MS; Lüthi A; Anderson DJ;
Nature. 2010-Nov-1; 468(7321):270-6
PMID: 21068836   DOI:
Compensation in the neural circuitry of fear conditioning awakens learning circuits in the bed nuclei of the stria terminalis
Poulos AM; Ponnusamy R; Dong HW; Fanselow MS;
Proc Natl Acad Sci U S A. 2010-Aug-1; 107(33):14881-6
PMID: 20679237   DOI:
Genomic-anatomic evidence for distinct functional domains in hippocampal field CA1
Dong HW; Swanson LW; Chen L; Fanselow MS; Toga AW;
Proc Natl Acad Sci U S A. 2009-Jul-1; 106(28):11794-9
PMID: 19561297   DOI:
From gene networks to brain networks.
Bota M; Dong HW; Swanson LW;
Nat Neurosci. 2003-Aug-1; 6(8):795-9
PMID: 12886225   
Brain architecture management system.
Bota M; Dong HW; Swanson LW;
Neuroinformatics. 0-Dec; 3(1):15-48
PMID: 15897615