Liwang JK, Kronman FA, Minteer JA, Wu Y, Vanselow DJ, Ben-Simon Y, Taormina M, Parmaksiz D, Way SW, Zeng H, Tasic B, Ng L, Kim Y
epDevAtlas: Mapping GABAergic cells and microglia in postnatal mouse brains
bioRxivv, 2023
https://doi.org/10.1101/2023.11.24.568585
Kronman FA, Liwang JK, Betty R, Vanselow DJ, Wu Y, Tustison NJ, Bhandiwad A, Manjila SB, Minteer JA, Shin D, Lee CH, Patil R, Duda JT, Puelles L, Gee JC, Zhang J, Ng L, Kim Y
Developmental Mouse Brain Common Coordinate Framework
bioRxiv, 2023
https://doi.org/10.1101/2023.09.14.557789
Stamenkovic S, Schmid F , Weitermann N, Takasaki K, Bonney SK, Sosa MJ, Li Y, Benett HC, Kim Y, Waters J, Shih AY
Impaired drainage through capillary-venous networks contributes to aged-related white matter loss
bioRxiv, 2024
https://www.biorxiv.org/content/10.1101/2024.02.11.579849v1
Stouffer KM, Trouve A, Younes L, Kunst M, Ng L, Zeng H, Anant M, Fan J, Kim Y, Miller MI
A Universal Method for Crossing Molecular and Atlas Modalities using Simplex-Based Image Varifolds and Quadratic Programming
bioRxiv, 2023
https://www.biorxiv.org/content/10.1101/2023.03.28.534622v1
Xue J, Thompson JR, Brawner AT, Yelhekar TD, Newmaster KT, Qiu Q, Cooper YA, Yu CR, Ahmed-Braimah YH, Kim Y, Lin Y
Spatiotemporal Mapping and Molecular Basis of Whole-brain Circuit Maturation
bioRxiv, 2024
https://www.biorxiv.org/content/10.1101/2024.01.03.572456v1
Bennett HC, Zhang Q, Wu Y, Chon U, Pi H, Drew PJ, Kim Y
Aging drives cerebrovascular network remodeling and functional changes in the mouse brain
bioRxiv, 2023
https://doi.org/10.1101/2023.05.23.541998
BICCN Data Ecosytem Collaboration, Hawrylycz MJ, Martone ME, Hof PR, Lein ES, Regev A, Ascoli GAA, Bjaalie JG, Dong H, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Kim Y, Liu Y, Miller JA, Mitra PP, Mukamel E, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Ropelewski A, Scheuermann RH, Tan SZK, Tickle T, Tilgner H, Varghese M, Wester B, White O, Aevermann B, Allemang D, Ament S, Athey TL, Baker PM, Baker C, Baker KS, Bandrowski A, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding S, Dolbeare T, Ecker JR, Fang R, Fillion-Robin J, Fliss JP, Gee J, Gillespie T, Gouwens N, Halchenko YO, Harris N, Herb BR, Hintiryan H, Hood G, Horvath S, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Markuhar A, Mathews J, Mathews KL, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Ng L, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Thompson CL, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zeng H, Zhang G, Zhang YR, Zheng JW, Zingg B
A guide to the BRAIN Initiative Cell Census Network data ecosystem
Plos Biology (2023)
https://www.biorxiv.org/content/10.1101/2022.10.26.513573
Liwang JK, Bennett HC, Pi H, Kim Y
A high-resolution cell type and cerebrovasculature mapping pipeline in the whole mouse brain using serial two-photon tomography
STAR protocols (2023)
https://star-protocols.cell.com/protocols/2373
Manjila S, Betty R, Kim Y.
Missing pieces in decoding the brain oxytocin puzzle: Functional insights from mouse brain wiring diagrams
Frontiers in Neuroscience, (2022)
https://doi.org/10.3389/fnins.2022.1044736
Yuan-ting Wu, Hannah C. Bennett, Uree Chon, Daniel J. Vanselow, Qingguang Zhang, Rodrigo Munoz-Castaneda, Keith C. Cheng, Pavel Osten, Patrick J. Drew, Yongsoo Kim.
Quantitative relationship between cerebrovascular network and neuronal cell types in mice
Cell Reports, (2022)
https://doi.org/10.1016/j.celrep.2022.110978
Son S, Manjila S, Newmaster KT, Wu T, Vanselow DJ, Ciarletta M, Todd TE, Cheng KC, Kim Y.
Wiring diagram of the oxytocin system in the mouse brain.
Journal of Neuroscience (2022)
https://www.jneurosci.org/content/early/2022/05/20/JNEUROSCI.0307-22.2022
Bennett HC, Kim Y
Advances in studying whole mouse brain vasculature using high-resolution 3D light microscopy imaging
Neurophotonics (2022)
https://doi.org/10.1117/1.NPh.9.2.021902
Newmaster KT, Kronman FA, Wu Y, Kim Y
Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain
Frontier in Neuroanatomy (2022)
https://www.frontiersin.org/articles/10.3389/fnana.2021.787601/full
Muñoz-Castañeda R, Zingg B, Matho KS, Wang Q, Chen X, Foster NN, Narasimhan A, Li A, Hirokawa KE, Huo B, Bannerjee S, Korobkova L, Park CS, Park Y, Bienkowski MS, Chon U, Wheeler DW, Li X, Wang Y, 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 J, Kondo H, Kuang X, Lesnar P, Li X, Li Y, Lin M, Liu L, Lo D, Mizrachi J, Mok S, Naeemi M, Nicovich PR, Palaniswamy R, Palmer J, Qi X, Shen E, Sun Y, Tao H, Wakemen W, Wang Y, Xie P, Yao S, Yuan J, Zhu M, Ng L, Zhang LI, Lim BK, Hawrylycz M, Gong H, Gee JC, Kim Y, Peng H, Chuang K, Yang XW, Luo Q, Mitra PP, Zador AM, Zeng H, Ascoli GA, Huang ZJ, Osten P, Harris JA, Dong H
Cellular Anatomy of the Mouse Primary Motor Cortex
Nature (2021)
https://www.nature.com/articles/s41586-021-03970-w
Cui Q, Du X, Chang I, Pamukcu A, Lilascharoen V, Berceau B, Garcia D, Hong D, Chon U, Narayanan A, Kim Y, Lim B, Chan S
Striatal Direct Pathway Targets Npas1+ Pallidal Neurons
Journal of Neuroscience. (2021)
https://pubmed.ncbi.nlm.nih.gov/33731445/
Bennett HC, Kim Y
Pericytes Across the Lifetime in the Central Nervous System
Frontier in Cellular Neuroscience, (2021)
https://www.frontiersin.org/articles/10.3389/fncel.2021.627291/full
Chon U, LaFever BJ, Nguyen U, Kim Y#, Imamura F#
Topographically distinct projection patterns of early- and late-generated projection neurons in the mouse olfactory bulb
eNeuro, (2020)
https://pubmed.ncbi.nlm.nih.gov/33158934/
#Corresponding authors
Jefferson SJ, Feng M, Chon U, Guo Y, Kim Y, Luscher B. Disinhibition of somatostatin interneurons confers resilience to stress in male but not female mice.
Neurobiology of Stress, (2020)
https://pubmed.ncbi.nlm.nih.gov/33344694/
Newmaster K, Nolan ZT, Chon U, Vanselow DJ, Weit AR, Tabbaa M, Hidema S, Nishimori K, Hammock EAD, Kim Y.
Quantitative Cellular-Resolution Map of the Oxytocin Receptor in Postnatally Developing Mouse Brains.
Nature Communications, (2020)
https://www.ncbi.nlm.nih.gov/pubmed/32313029
Chon U, Vanselow DJ, Cheng KC, Kim Y. Enhanced and Unified Anatomical Labeling for a Common Mouse Brain Atlas
Nature Communications:, 2019
https://www.ncbi.nlm.nih.gov/pubmed/31699990
Zhao C, Son S, Kim Y, Prince J.
iSMORE: an iterative self super-resolution algorithm (2019)
Simulation and Synthesis in Medical Imaging. (Conference Paper)
https://link.springer.com/chapter/10.1007/978-3-030-32778-1_14
Abecassis Z, Berceau B, Win P, Garcia D, Xenias H, Cui Q, Pamucku A, Hernández V, Chon U, Lim BK, Kim Y, Justice N, Awatramani R, Chan S.
Npas1+-Nkx2.1+ Neurons Are an Integral Part of the Cortico-pallido-cortical Loop. (2019)
Journal of Neuroscience
https://www.ncbi.nlm.nih.gov/pubmed/31811030
Zhang XM, Anwar S, Kim Y, Brown J, Comte I, Cai H, Cai NN, Wade-Martins R, Szele FG.
The A30P α-synuclein mutation decreases subventricular zone proliferation (2019)
Human Molecular Genetics
https://www.ncbi.nlm.nih.gov/pubmed/31267130
Kelly SM, Raudales R, He M, Lee J, Kim Y, Gibb LG, Wu P, Matho P, Osten P, Graybiel AM, Huang ZJ. Radial glial lineage progression and differential intermediate progenitor amplification underlie striatal compartments and circuit organization (2018). Neuron.
https://www.ncbi.nlm.nih.gov/pubmed/30017396
Hoerder-Suabedissen A, Hayashi S, Upton L, Nolan Z, Casas-Torremocha D, Grant E, Viswanathan S, Kanold PO, Clasca F, Kim Y, Zoltan Molnar. Subset of cortical layer 6b neurons selectively innervates higher order thalamic nuclei in mice (2018). Cerebral Cortex.
https://www.ncbi.nlm.nih.gov/pubmed/29481606
Selected for a cover image
He M, Tucciarone J, Lee S, Nigro MJ, Kim Y, Levine JM, Kelly SM, Krugikov I, Wu P, Chen Y, Gong L, Hou Y, Osten P, Rudy B, Huang ZJ. Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex. (2016). Neuron
http://www.ncbi.nlm.nih.gov/pubmed/27618674
Kim Y#, Perova Z#, Mirrione MM#, Pradhan K, Henn FA, Shea S, Osten P, Li B. Whole-brain mapping of neuronal activity in the learned helplessness model of depression (2016). Front Neural Circuits, 10:3, #Equal contribution.
http://www.ncbi.nlm.nih.gov/pubmed/26869888
Jeong M#, Kim Y#, Kim J, Ferrante DD, Mitra PP, Osten P, Kim D. Comparative three dimensional connectome map of motor cortical projections in the mouse brain (2016). Scientific Reports, 6:20072, # Equal contribution
http://www.ncbi.nlm.nih.gov/pubmed/26830143
Kim Y, Umadevi Venkataraju K, Pradhan K, Mende C, Taranda J, Turaga SC, Arganda-Carreras I, Ng L, Hawrylycz MJ, Rockland K, Seung HS, Osten P. Mapping social behavior-induced brain activation at cellular resolution in the mouse (2015). Cell Reports 10(2):292-305.
http://www.ncbi.nlm.nih.gov/pubmed/25558063
Selected as one of the best 11 papers published in Cell Reports in 2015
Ragan T, Kadiri L, Umadevi Venkataraju K, Bahlmann K, Sutin J, Taranda J, Arganda-Carreras I, Kim Y, Seung HS, Osten P. Serial two-photon tomography: an automated method for ex-vivo mouse brain imaging (2012). Nature Methods15;9(3):255-8
http://www.ncbi.nlm.nih.gov/pubmed/22245809
Comte I, Kim Y, Young CC, Bolam PJ, van der Harg JM, Hockberger P, Poirier F, Szele FG. Galectin-3 maintains cell motility from the subventricular zone to the olfactory bulb (2011) Journal of Cell Science 124(Pt 14):2438-47
http://www.ncbi.nlm.nih.gov/pubmed/21693585
James R, Kim Y, Hockberger P, Szele FG. SVZ neuroblast cell migration: lessons from quantitative 2-photon microscopy (2011). Frontiers in Neuroscience. 5:30
http://www.ncbi.nlm.nih.gov/pubmed/21472025
Walker AS, Goings GE, Kim Y, Miller RJ, Chenn A, Szele FG. Transgenic nestin reporter mouse labels multiple central nervous system precursor cells (2011). Neural Plasticity, 2010:894374
http://www.ncbi.nlm.nih.gov/pubmed/21527990
Martinez-Molina N, Kim Y, Hockberger P, Szele FG. Rostral Migratory Stream Neuroblasts Turn and Change Directions in Stereotypic Patterns. (2011) Cell Adhesion and Migration 5(1):83-95
http://www.ncbi.nlm.nih.gov/pubmed/21045564
Kim Y, Wang W, Comte I, Pastrana E, Tran PB, Brown J, Miller R, Doetsch F, Molnar Z, Szele FG. Dopamine stimulates postnatal murine subventricular zone neurogenesis via the D3 receptor (2010). Journal of Neurochemistry 114:750-760
http://www.ncbi.nlm.nih.gov/pubmed/20477937
Kim Y, Comte I, Szabo G, Hockberger P, Szele FG. Adult mouse subventricular zone stem and progenitor cells are static and epidermal growth factor receptor negatively regulates neuroblast migration (2009). Plos One 4:e8122
http://www.ncbi.nlm.nih.gov/pubmed/19956583
Kim Y, Szele FG. Activation of subventricular zone stem cells after neuronal injury (2008). Cell and Tissue Research 331:337-345. 2008
http://www.ncbi.nlm.nih.gov/pubmed/17694326
Nam SC, Kim Y, Dryanovski D, Walker A, Goings G, Woolfrey K, Kang SS, Chu C, Chenn A, Erdelyi F, Szabo G, Hockberger P, Szele FG. Dynamic features of postnatal subventricular zone cell motility: a two-photon time-lapse study (2007). Journal of Comparative Neurology 505:190-208
http://www.ncbi.nlm.nih.gov/pubmed/17853439