Publications (ORCID: 0000-0001-8624-0168)

 * Equal Contribution | † Corresponding | Google Scholar link

Manuscripts in revision

  • El Mesaoudi A, Lundby JMB, De Jong N, Luo Y, Lin L, Kim DW†. STAT1 sets microglial neutral-lipid content independently of lipid-handling transcriptional programs. bioRxiv doi.org/10.64898/2026.08.15.745002.

  • Sejer S, Pedersen MM, Lundby JMB, De Jong N, Kim DW†. Population-specific transcriptional-state remodeling of cortical and hypothalamic neurons in Alzheimer's disease. bioRxiv /doi.org/10.64898/2026.08.15.745006.

Original Articles

2026

  • Murlanova K, Novototskaya-Vlasova K, Huseynov S, Pletnikova O, Howell RD, Jouroukhin Y, Kim DW, Jenson AES, Lee J, Qin C, Thompson SR, Saraf V, Morales MJ, Gomez EC, Margolis RL, Nucifora Jr FC, Rosario SR, Pieper AA, Withers HG, Haj-Dahmane S, Kim J, Pletnikov MV. NPAS3-regulated astrocyte mitochondrial bioenergetics is required for cognition. Science Advances. 2026 Jun 19;12(25):eadt2527.PMID: 42308317.

  • Yea Jh, Bian Q, Cheng YH, Yu EY, Tan Y, Kim DW, Wan H, Yoo S, Blackshaw S, Cahan P. Signaling and transcriptional networks governing late synovial joint development. Developmental Biology. 2026 Jun 4:S0012-1606(26)00118-1. PMID: 42248342.

  • Chandler PW, Lee SS, Duncan LH, Kim DW, Wu M, and Blackshaw S. Molecularly distinct subtypes of Lhx6-positive neurons of the zona incerta differentially regulate sleep pressure and recovery sleep. iScience. 29 (4), 115403 (2026). PMID: 41993694

‍2025

  • Manning E, Chinnaiya K, Kim DW, Blackshaw S, Placzek M, Place E. Resolving forebrain developmental organization by analysis of differential growth patterns. Nature Communications 2025 Dec 21. PMID: 41423470

  • Kim DW*†, Duncan LH*, Xu J, Chang M, Sejer S, Terrillion CE, Kanold P, Blackshaw S†. Decoding Gene Networks Governing Hypothalamic and Prethalamic Neuron Development. Cell Reports.PMID: 40512619

  • Lee SS, Liu Q, Cheng AHR, Kim DW, Boudreau DM, Mehta A, Keles M, Fejfer R, Palmer I, Park KH, Muenzberg H, Harris TD, Graves AR, Blackshaw S, Wu MW. Sleep need-dependent plasticity of a thalamic circuit 2 generates persistence of sleep drive. Science  Jun 19;388(6753):eadm8203 (2025). PMID: 40536979

‍ 2024

  • Kim DW†, Kim S, Han J, Belday K, Li E, Mahoney N, Blackshaw S, Rajaii F†. Transcriptomic profiling of thyroid eye disease orbital fat demonstrates differences in adipogenecity and IGF1-R pathway. https://insight.jci.org/articles/view/182352. Accepted at JCI Insight (Oct/2024)

  • Placzek M, Chinnaiya K, Kim DW, Blackshaw S. Control of tuberal hypothalamic development and its implications in metabolic disorders. Review paper. Nature Reviews Endocrinology(2024). PMID: 39313573

  • Liu Q, Xiong J, Kim DW, Lee SS, Bell B, Alexandre C, Blackshaw S, Latremoliere A, Wu M. An Amygdalar Local Oscillator Coordinates Cellular and Behavioral Rhythms. Neuron Sep 18:S0896-6273(24)00609-3 (2024). PMID: 39303704

  • Hong I*†, Kim J*, Hainmuelle T*; Kim DW, Johnson RC, Park SH, Limjunyawong N, Yang Z, Cheon D, Hwang T, Agarwal A, Cholvin T, Krienen F, McCarroll S, Dong X, Leopold D, Blackshaw S, Bergles D, Bartos M, Brown SP, Huganir RL†. Calcium-permeable AMPA receptors govern PV neuron feature selectivity. Nature Oct 2. doi: 10.1038/s41586-024-08027-2 (2024). PMID: 39358515

2023

  • Bell B*, Liu Q*, Kim DW, Lee S, Liu Q, Blum I, Wang A, Bedont J, Chang A, Issa H, Cohen J, Blackshaw S, Wu M. A Clock-Dependent Brake for Rhythmic Arousal in the Dorsomedial Hypothalamus. Nature Communications Oct 11;14(1):6381 (2023). PMID: 37821426

  • Hoang T*†, Kim DW*†, Appel H, Ozawa M, Zheng S, Yu M, Peachey NS, Kim J, and Blackshaw S†. Ptbp1 deletion does not induce astrocyte-to-neuron conversion.Nature Jun;618(7964):E1-E7 (2023). PMID: 37286658

  • Chinnaiya K, Burbridge S, Jones A, K,  Kim DW, Place E, Manning E, Groves I, Sun C, Towers M, Blackshaw S, Placzek M. A neuroepithelial wave of BMP signalling drives anteroposterior specification of the tuberal hypothalamus. eLife 12: e83133 (2023). PMID: 36718990

Until 2022

  • Kim DW, Tu K, Wei A, Lau A, Gonzalez-Gil A, Cao T, Braunstein K, Ling JP, Troncoso JC, Wong PC, Blackshaw S, Schnaar RL, Li T. Amyloid-beta and tau pathologies are both necessary to induce novel stage-specific microglia subtypes during Alzheimer’s disease progression.Molecular Neurodegeneration Dec 17;17(1):83 (2022). PMID: 36536457

  • Hoang T*†, Kim DW*†, Appel H, Pannullo NA, Leavey P, Ozawa M, Zheng S, Yu M, Peachey NS, and Blackshaw S†. Genetic loss of function of Ptbp1 does not induce glia-to-neuron conversion in retina.Cell Reports 39 (11), 110849 (2022). PMID: 35705053

  • Kim DW*, Place E*, Chinnaiya K*, Manning E, Sun C, Dai W, Ohyama K, Burbridge S, Placzek M, Blackshaw S. Single cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamus. Cell Reports 38 (3), 110251 (2022). Featured cover image. PMID: 35045288

  • Kim J*, Kim DW*, Lee A*, Mason M, Jouroukhin Y, Woo H, Yolken RH, Pletnikov MV. Homeostatic regulation of neuronal excitability by probiotics in male germ-free mice. Journal of Neuroscience Research 100 (2), 444-460 (2022). PMID: 34935171

  • Place E, Manning L, Kim DW, Kinjo A, Nakamura G, Ohyama K. SHH and NOTCH regulate SOX9+ progenitors to govern arcuate POMC neurogenesis. Frontiers in Neuroscience Aug 11;16:855288 (2022). PMID: 36033614

  • Price PD, Droguett DHP, Taylor JA, Kim DW, Place ES, Rogers TF, Mank JE, Cooney CR, Wright AE. Reply to Fraser: The importance of developmental context and evolutionary timeframe in gene expression evolution. Nature Ecology and Evolution(Matters Arising) Dec;6(12):1838-1839 (2022). PMID: 36344678

  • Price PD, Droguett DHP, Taylor JA, Kim DW, Place ES, Rogers TF, Mank JE, Cooney CR, Wright AE. Detecting signatures of selection on gene expression. Nature Ecology and Evolution6 (7), 1035-1045 (2022). PMID: 35551249

  • Moore A*, Chinnaiya K*, Kim DW, Brown S, Stewart I, Robins S, Dowsett G, Muir C, Travaglio M, Leis JE, Ebling F, Blackshaw S, Furley A, Placzek M. The neural cell adhesion molecule NrCAM regulates development of hypothalamic tanycytes. Frontiers in Neuroscience 7;16:832961 (2022). PMID: 35464310

  • Kim DW, Taneja K, Hoang T, Santiago CP, McCulley TJ, Merbs SL, Mahoney NR, Blackshaw S, Rajaii F. Transcriptomic profiling of control and thyroid-associated orbitopathy (TAO) orbital fat and TAO orbital fibroblasts undergoing adipogenesis. Investigative Ophthalmology & Visual Science 62 (9), 24-24 (2021). PMID: 34269815

  • Kim DW, Liu K, Wang Z, Zhang S, Bathini A, Brown M, Lin S, Washington P, Sun C, Lindtner S, Lee B, Wang H, Shimogori T, Rubenstein J, Blackshaw S. Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6-expressing GABAergic neurons. Communications Biology 4 (1), 1-16 (2021). PMID: 33479483

  • Lyu P*, Hoang T*, Santiago P*, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza D, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, Blackshaw S. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell fate specification in the mammalian retina. Cell Reports 37 (7), 109994 (2021). PMID: 34788628

  • Bell B*, Wang A*,Kim DW, Blackshaw S, Wu M. Characterization of mWake expression in the murine brain. Journal of Comparative Neurology529 (8), 1954-1987 (2021). PMID: 33140455

  • Weir K, Kim DW, Blackshaw S. A potential role for somatostatin signaling in regulating retinal neurogenesis. Scientific Reports 11 (1), 1-12 (2021). PMID: 34040115

  • Brodie-Kommit J, Clark B, Shi Q, Shiau F, Kim DW, Langel J, Sheely C, Schmidt T, Glaser T, Bader T, Zhao H, Singer J, Blackshaw S, Hattar S. Atoh7-independent specification of retinal ganglion cell identity. Science Advances 7 (11), eabe4983 (2021). PMID: 33712461

  • Rajaii F, Kim DW, Pan J, Mahoney N, Eberhardt C, Qian J, Blackshaw S. Temperature and species-dependent regulation of browning in retrobulbar fat. Scientific Reports 11 (1), 1-11 (2021). PMID: 33542375

  • Jager P, Moore G, Calpin P, Durmishi X, Salgarella I, Menage L, Kita Y, Wang Y, Kim DW, Blackshaw S, Schultz S, Brickley S, Shimogori T, Delogu A. Dual midbrain and forebrain origins of thalamic inhibitory interneurons. eLife 10, e59272 (2021). PMID: 33522480

  • Kim DW, Washington PW, Wang ZQ, Lin SH, Sun C, Ismail BT, Wang H, Jiang L, Blackshaw S. The cellular and molecular landscape of hypothalamus patterning and differentiation from embryonic to late postnatal development. Nature Communications 11 (1), 1-11 (2020). PMID: 32868762

  • Hoang T*, Wang J*, Boyd P, Wang F, Santiago C, Jiang L, Lahne M, Yoo S, Todd L, Saez C, Keuthan C, Palazzo I, Squires N, Campbell W, Jia M, Rajaii F, Parayil T, Trinh V, Kim DW, Wang G, Ash J, Fischer A, Hyde D, Qian J, Blackshaw S. Gene regulatory networks controlling vertebrate retinal regeneration. Science 370, 6519 (2020). PMID: 33004674

  • Bian Q, Cheng YH, Wilson JP, Su EY, Kim DW, Wang H, Yoo S, Blackshaw S, Cahan P. A single cell transcriptional atlas of early synovial joint development. Development 147 (14), dev185777 (2020). PMID: 32580935

  • Hu MW, Kim DW, Liu S, Zack DJ, Blackshaw S, Qian J. PanoView: An iterative clustering for single-cell RNA sequencing data. PLOS computational biology 15 (8), e1007040 (2019). PMID: 31469823

  • Yoo S*, Cha D*, Kim DW, Hoang TV, Blackshaw S. Tanycyte-independent control of hypothalamic leptin signalling. Front Neurosci 13, 240 (2019). PMID: 30941008

  • Newman EA, Kim DW, Wan J, Wang J, Qian J, Blackshaw S. Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes. Developmental biology 439 (2), 102-111  (2018). PMID: 29679559

  • Liu K, Kim J*, Kim DW*, Zhang YS*, Bao H, Denaxa M, Lim S, Kim E, Liu C, Wickersham IR, Pachnis V, Hattar S, Song J, Brown SP, Blackshaw S. Lhx6-positive GABAergic neurons of the zona incerta promote sleep. Nature 548 (7669), 582-587(2017).* Co-second authors. PMID: 28847002

  • Kim DW, Glendining KA, Grattan DR, Jasoni CL. Maternal obesity leads to increased proliferation and numbers of astrocytes in the developing fetus and neonatal mouse hypothalamus. International Journal of Developmental Neuroscience 53, 18-25 (2016). PMID: 27326907

  • Kim DW, Glendining KA, Grattan DR, Jasoni CL. Maternal obesity in the mouse compromises the blood-brain barrier in the arcuate nucleus of offspring. Endocrinology157 (6), 2229-2242 (2016) (highlighted in News & Views, Endocrinology, Volume 157, Issue 6. 'Programming the brain from the womb: maternal obesity perturbs the hypothalamic blood-brain barrier'). PMID: 27054554

  • Sanders TR*, Kim DW*, Glendining KA, Jasoni CL. Maternal obesity and IL6 lead to aberrant developmental gene expression and deregulated neurite growth in the fetal arcuate nucleus. Endocrinology 155 (7), 2566-2577 (2014). PMID: 24773340

  • Kim DW, Young SL, Grattan DR, Jasoni CL. Obesity during pregnancy disrupts placental morphology, cell proliferation, and inflammation in a sex-specific manner across gestation in the mouse. Biology of Reproduction 90 (6), 130, 1-11 (2014). PMID: 24829026

Reviews / Editoral Comments / Book Chapters

  • El Mesaoudi A, Kim DW†. Microglial state transitions are constrained by developmental and metabolic checkpoints. Review paper. Frontiers in Cellular Neuroscience. PMID: 42222058.

  • Placzek M, Chinnaiya K, Kim DW, Blackshaw S. Control of tuberal hypothalamic development and its implications in metabolic disorders. Review paper. Nature Reviews Endocrinology(2024). PMID: 39313573

  • El Mesaoudi A†,Kim DW, Traiffort E. Smoothened signaling in microglia: canonical or not, and does it promote or limit inflammation? Letter to the Editor. Acta Pharmacological Sinica. PMID: 42557293

  • Kim DW. Editorial: Expanding the glial frontiers: development, function and pathophysiology. Frontiers in Cellular Neuroscience. PMID: 42110582

  • Kim DW, Blackshaw S. A supersonic synchronizer: Shh signaling controls the core mammalian circadian clock. Science (2023).Perspective. PMID: 37262151

  • Kim DW, Blackshaw S. Winding the clock: development of hypothalamic neural circuitry controlling circadian timing and sleep. In Masterclass in Developmental Neuroendocrinology, 105-127, Springer (2020).Book Chapter (https://link.springer.com/chapter/10.1007/978-3-030-40002-6_5)

  • Jasoni CL, Sanders TR*, Kim DW*. Do all roads lead to Rome? The role of neuro-immune interactions before birth in the programming of offspring obesity. Frontiers in Neuroscience 8, 455 (2015). PMID: 25691854