Publications

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

 * Equal Contribution | † Corresponding | Google Scholar link

As a Group Leader:

Reviews

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

During Postdoctoral Fellow:

First/Co-First/Co-Corresponding papers 

• 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

• 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

• 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

• 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

Co-author papers 

• 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

• 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

• 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 Evolution 6 (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

• 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 Neurology 529 (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

• 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 

Reviews

• 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) 

During PhD:

First/Co-First papers 

• 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. Endocrinology 157 (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

• 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 

Manuscripts in revision:

• 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. bioRxiv: doi.org/10.1101/2023.07.20.549908.

• 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. bioRxiv: doi.org/10.1101/2024.03.08.584151

• 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. bioRxiv: doi.org/10.1101/2021.08.25.457383