Publications

Selected Publications

(* indicates equal contributors, # indicates co-corresponding authors)

  1. Kim YS*#, Gillespie SM*, Geraghty AC, Yalçın B, Ivec AE, Yang A, Mancusi R, Hysinger J, Reed J, Drexler R, Quezada M, Malacon K, Woo P, Byun YG, Mount C, Lam M, Pan Y, Zuchero JB, Trotter J, Monje M#, Neuroligin-3 interaction with CSPG4 regulates normal and malignant glial precursors through mechanotransduction, Nature Neuroscience (in press)
  2. Tajima S*, Kim YS*, Fukuda M, Jo YJ, Wang PY, Paggi JM, Inoue M, Byrne EFX, Kishi KE, Nakamura S, Ramakrishnan C, Takaramoto S, Nagata T, Konno M, Sugiura M, Katayama K, Matsui TE, Yamashita K, Kim S, Ikeda H, Kim J, Kandori H, Dror RO, Inoue K, Deisseroth K#, Kato HE#, Structural basis for ion selectivity in potassium-selective channelrhodopsins, Cell, 186, 1-20 (2023)
  3. Kishi KE*, Kim YS*, Fukuda M*, Inoue M*, Kusakizako T*, Wang PY*, Ramakrishnan C, Byrne EFX, Thadhani E, Paggi JM, Matsui TE, Yamashita K, Nagata T, Konno M, Quirin S, Lo M, Benster T, Uemura T, Liu K, Shibata M, Nomura N, Iwata S, Nureki O, Dror RO, Inoue K, Deisseroth K#, Kato HE#, Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine, Cell, 185, 1-18 (2022)
  4. Fenno LE*, Ramakrishnan C*, Kim YS*, Evans KE, Lo M, Vesuna S, Inoue M, Cheung KYM, Yuen E, Pichamoorthy N, Hong A and Deisseroth K, Comprehensive dual- and triple-feature intersectional single-vector delivery of diverse functional payloads to cells of behaving mammals, Neuron, 107, 1-18 (2020)
  5. Liu J*, Kim YS*, Richardson C*, Tom A*, Ramakrishnan C, Birey F, Katsumata T, Chen S, Wang C, Wang X, Joubert L, Jiang Y, Wang H, Fenno LE, Tok JBH, Pasca SP, Bao Z# and Deisseroth K#, Genetically-targeted Chemical Assembly of Functional Materials in Living Cells, Tissues and Animals, Science 367 (6484) (2020)
  6. Marshel JH*, Kim YS*, Machado TA*, Quirin S*, Benson B, Kadmon J, Raja C, Chibukhchyan A, Ramakrishnan C, Inoue M, Shane JC, McKnight DJ, Yoshizawa S, Kato HE, Ganguli S and Deisseroth K, Cortical Layer-specific Critical Dynamics Triggering Perception, Science 365 (6453) (2019)
  7. Kim YS*, Kato HE*#, Yamashita K, Ito S, Inoue K, Ramakrishnan C, Fenno LE, Evans KE, Paggi JM, Dror RO, Kandori H, Kobilka BK and Deisseroth K#, Crystal structure of the natural anion-conducting channelrhodopsin GtACR1, Nature 561 (7723), 343-348 (2018)
  8. Kato HE*#, Kim YS*, Paggi JM, Evans KE, Allen WE, Richardson C, Inoue K, Ito S, Ramakrishnan C, Fenno LE, Yamashita K, Hilger D, Lee SY, Berndt A, Shen K, Kandori H, Dror RO, Kobilka BK and Deisseroth K#, Structural mechanisms of selectivity and gating in anion channelrhodopsins, Nature 561 (7723), 349-354 (2018)

Other Publications

  1. Tomaio JN, Fleury S, Bilder A, Nacimba J, Lakshman A, Kim YS, Fenno LE, Ramakrishnan C, Deisseroth K, Mingote S, Evidence for age-related vulnerability in dopamine–glutamate projections to the lateral entorhinal cortex, bioRxiv, 2025.10.06.680552 (2025).
  2. Savchuk S, Gentry KM, Wang W, Carleton E, Biagi-Junior CAO, Luthria K, Yalçın B, Ni L, Farnsworth HC, Davis RA, Drexler R, Melms JC, Liu Y, Acosta-Alvarez L, Hartmann GG, Pavarino EC, LaBelle J, Woo PJ, Toland AM, Qu F, Kim YS, Filbin MG, Krasnow MA, Ligon KL, Izar B, Sage J, Sabatini BL, Monje M, and Venkatesh HS, Neuronal activity-dependent mechanisms of small cell lung cancer pathogenesis, Nature, 1–11 (2025).
  3. McGovern DJ, Phillips A, Ly A, Prévost ED, Ward L, Siletti K, Kim YS, Fenno LE, Ramakrishnan C, Deisseroth K, Baratta MV, Ford CP, Root DH, Salience signaling and stimulus scaling of ventral tegmental area glutamate neuron subtypes, Journal of Neuroscience, 45(27), 1-18 (2025)
  4. Drexler R, Drinnenberg A, Gavish A, Yalçın B, Shamardani K, Rogers AE, Mancusi R, Trivedi V, Taylor KR, Kim YS, Woo PJ, Soni N, Su M, Ravel A, Tatlock E, Midler A, Wu SH, Ramakrishnan C, Chen R, Ayala-Sarmiento AE, Rincon Fernandez Pacheco D, Siverts L, Daigle TL, Tasic B, Zeng H, Breunig JJ, Deisseroth K, Monje M#, Cholinergic neuronal activity promotes diffuse midline glioma growth through muscarinic signaling, Cell, 188, 1-18 (2025)
  5. Barron T, Yalçın B, Su M, Byun YG, Gavish A, Shamardani K, Xu H, Ni L, Soni N, Mehta V, Maleki Jahan S, Kim YS, Taylor KR, Keough MB, Quezada MA, Geraghty AC, Mancusi R, Vo LT, Herrera Castañeda E, Woo PJ, Petritsch CK, Vogel H, Kaila K, Monje M#, GABAergic neuron-to-glioma synapses in diffuse midline gliomas, Nature, 639, 1060-1068 (2025)
  6. Kishi K, Kim YS, Fukuda M, Inoue M, Kusakizako T, Wang P, Ramakrishnan C, Thadhani E, Paggi J, Matsui T, Yamashita K, Nagat T, Cryo-EM structural analysis and tool design of pump-like channelrhodopsin ChRmine, Protein Science, 32(12), 2023.
  7. Buck S, Xue X, Fenno LE, Weisel F, Ramakrishnan C, Kim YS, Deisseroth K, Awatramani R, Watson A, Logan R, Freyberg Z, Intersectional and Transcriptomic Approaches for Probing Molecular Mechanisms of Dopamine Neuron Resilience in Distinct Dopamine Neuron Subpopulations, Neuropsychopharmacology, 48, 293-294 (2023)
  8. Taylor KR, Barron T, Hui A, Spitzer A, Yalcin B, Ivec AE, Geraghty A, Zhang H, Hartmann G, Arzt M, Gillespie SM, Kim YS, Jahan SM, Shamardani K, Su M, Ni L, Du P, Woo PJ, Silva-Torres A, Venkatesh HS, Mancusi R, Ponnuswami A, Mulinyawe S, Keough MB, Chau I, Aziz-Bose R, Tirosh I, Suva ML, Monje M, Glioma synapses recruit mechanisms of adaptive plasticity, Nature, 623 (7986) (2023)
  9. Azcorra M, Gaertner Z, Davidson C, He Q, Kim H, Nagappan S, Hayes CK, Ramakrishnan C, Fenno LE, Kim YS, Deisseroth K, Longnecker R, Awatramani R, Dombeck DA, Unique functional responses differentially map onto genetic subtypes of dopamine neurons, Nature Neuroscience, 26 (10) (2023)
  10. Yang A, Jude KM, Lai B, Minot M, Kocyla AM, Glassman CR, Nishimiya D, Kim YS, Reddy ST, Khan AA, Garcia KC, Deploying protein-protein interactions through synthetic coevolution and machine learning, Science, 381 (6656) (2023)
  11. Hsueh B*, Chen R*, Jo YJ, Tang D, Raffiee M, Kim YS, Inoue M, Randles S, Ramakrishnan C, Patel S, Kim DK, Liu TX, Kim SH, Tan L, Mortazavi L, Codero A, Shi J, Zhao M, Ho T, Crow A, Wang Yoo AC, Raja C, Evans K, Bernstein D, Zeineh M, Gouban M, Deisseroth K, Cardiogenic control of affective behavioral state, Nature, 615 (7951), 292-299 (2023)
  12. Fan LZ, Kim DK, Jennings JH, Tian H, Wang PY, Ramakrishnan C, Randles S, Sun Y, Thadhani E, Kim YS, Quirin S, Giocomo L, Cohen AE, Deisseroth K, All-optical physiology resolves a synaptic basis for behavioral timescale plasticity, Cell, 186 (1-17) (2023)
  13. Rossi MA, Basiri ML, Liu Y, Hashikawa Y, Hashikawa K, Fenno LE, Kim YS, Ramakrishnan C, Deisseroth K and Stuber GD, Transcriptional and functional divergence in lateral hypothalamic glutamate neurons projecting to the lateral habenula and ventral tegmental area, Neuron, 109 (23) (2021)
  14. Pereira Luppi M, Azcorra M, Caronia-Brown G, Poulin JF, Gaertner Z, Gatica S, Moreno-Ramos OA, Nouri N, Dubois M, Ma YC, Ramakrishnan C, Fenno L, Kim YS, Deisseroth K, Cicchetti F, Dombeck DA, Awatramani R, Sox6 expression distinguishes dorsally and ventrally biased dopamine neurons in the substantia nigra with distinctive properties and embryonic origins, Cell Reports, 37(6) (2021)
  15. Chen R*, Gore F*, Nguyen QA, Ramakrishnan C, Patel S, Kim SH, Raffiee M, Kim YS, Hsueh B, Krook-Magnusson E, Solstesz I, and Deisseroth K, Deep brain optogenetics without intracranial surgery, Nature Biotechnology, 39 (2) (2021)
  16. Root DH, Barker DJ, Estrin DJ, Miranda-Barrientos JA, Liu B, Zhang S, Wang H-L, Vautier F, Ramakrishnan C, Kim YS, Fenno LE, Deisseroth K, Morales M, Distinct Signaling by Ventral Tegmental Area Glutamate, GABA, and Combinatorial Glutamate-GABA Neurons in Motivated Behavior, Cell Reports, 32 (9) (2020)
  17. Rovira-Esteban L, Gunduz-Cinar O, Bukalo O, Limoges A, Brockway E, Muller K, Fenno LE, Kim YS, Andrási T, Ramakrishnan C, Deisseroth K, Holmes A, Hajos N, Excitation of diverse classes of cholecystokinin interneurons in the basolateral amygdala facilitates fear extinction, eNeuro 6 (6) (2019)
  18. Hafner G, Witte M, Guy J, Subhashini N, Fenno LE, Ramakrishnan C, Kim YS, Deisseroth K, Callaway EM, Oberhuber M, Conzelmann K-K, Staiger JF, Mapping Brain-Wide Afferent Inputs of Parvalbumin-Expressing GABAergic Neurons in Barrel Cortex Reveals Local and Long-Range Circuit Motifs, Cell Reports, 28 (13) (2019)