Dengke Ma, PhD

Title(s)Associate Professor, Cardiovascular Research Inst
SchoolSchool of Medicine
Address555 Mission Bay Blvd South, #252X
San Francisco CA 94158
Phone415-502-3386
ORCID ORCID Icon0000-0002-5619-7485 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Massachusetts Institute of Technology Postdoctoral2014Department of Biology
    Johns Hopkins University School of MedicinePh.D.2009Department of Neuroscience
    Tsinghua UniversityB.S.2002Department of Physics
    Collapse Awards and Honors
    2018SKCF Faculty Scholars Program Award, Innovative Genome Institute
    2016Packard Fellowship in Science and Engineering
    2016Pew Scholar
    2016Sloan Research Fellowship
    2015  - 2018Klingenstein Fellowship in Neuroscience
    2014  - 2018NIH Pathway-to-Independent Award (K99/R00)
    2013Peter and Patricia Gruber International Research Award in Neuroscience
    2010  - 2013Helen Hey Whitney Foundation Postdoctoral Fellowship
    2009Harold M. Weintraub Graduate Student Award

    Collapse Overview 
    Collapse Overview
    We are interested in understanding the biological basis of cellular and organismic stress resilience. Many organisms in nature have evolved specialized traits to respond and adapt to severe environmental stresses, including hypothermia (cold) or hypoxia (low oxygen). For example, Arctic ground squirrels can tolerate extreme low levels of oxygen in the brain and heart during hibernation. Most nematodes, including those from the Antarctica and the common model organism C. elegans, can enter "suspended animation" states upon anoxia; they can also be frozen alive and suspend life that can be revived later virtually any long after freezing, unlike many other multicellular organisms. We use both cultured neural stem cells from hibernating Arctic ground squirrels and nematodes with extremophile-like phenotypes recapitulated in the laboratory as discovery tools to understand mechanisms of cellular and physiological resilience. Genes identified from such systems via large-scale experimental screens or computational mining often encode proteins of unusual properties that define novel mechanisms underlying cytoprotection, cellular organelle dynamics and organismic homeostasis in physiology and behaviors. Some were even acquired from extremophile microbes via horizontal gene transfers and functionally co-opted to confer stress resilience. We take advantage of findings from our research and aim to use synthetic physiology approaches to engineer biological systems that may foster new means of cytoprotection, organ transplantation, reversible cryo-preservation and therapeutics to treat ischemic, neurological and age-related disorders.

    Collapse Research 
    Collapse Research Activities and Funding
    Genetic pathway and cellular mechanism underlying organismic responses to hypoxia and hypothermia
    NIH R35GM139618Jan 1, 2021 - Dec 31, 2025
    Role: Principal Investigator
    Dissecting a Novel Genetic Pathway for Fatty Acid Desaturation and Temperature Adaptation
    NIH R01GM117461Sep 1, 2016 - Jul 31, 2021
    Role: Principal Investigator
    Control of Anoxia-Reoxygenation Responses by the O2-sensing Enzyme EGL-9 Pathway
    NIH R00HL116654May 1, 2014 - Jan 31, 2018
    Role: Principal Investigator
    Control of Anoxia-Reoxygenation Responses by the O2-sensing Enzyme EGL-9 Pathway
    NIH K99HL116654May 1, 2014 - Jan 1, 2015
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    1. Design, Synthesis and Biological Evaluation of Novel Phenyl-Substituted Naphthoic Acid Ethyl Ester Derivatives as Strigolactone Receptor Inhibitor. Int J Mol Sci. 2024 Mar 31; 25(7). Du L, Li X, Ding Y, Ma D, Yu C, Zhao H, Wang Y, Liu Z, Duan L. PMID: 38612714; PMCID: PMC11012203.
      View in: PubMed   Mentions:
    2. LPD-3 as a megaprotein brake for aging and insulin-mTOR signaling in C. elegans. Cell Rep. 2024 Mar 05; 43(3):113899. Pandey T, Wang B, Wang C, Zu J, Deng H, Shen K, do Vale GD, McDonald JG, Ma DK. PMID: 38446666.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    3. Suppressing mortality and curbing cellular damage by targeting VHL. bioRxiv. 2024 Mar 03. Jiang WI, Cao Y, Xue Y, Ji Y, Winer BY, Zhang M, Singhal NS, Pierce JT, Chen S, Ma DK. PMID: 38464138; PMCID: PMC10925324.
      View in: PubMed   Mentions:
    4. Early-life stress triggers long-lasting organismal resilience and longevity via tetraspanin. Sci Adv. 2024 Jan 26; 10(4):eadj3880. Jiang WI, De Belly H, Wang B, Wong A, Kim M, Oh F, DeGeorge J, Huang X, Guang S, Weiner OD, Ma DK. PMID: 38266092; PMCID: PMC10807809.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    5. Early-life stress triggers long-lasting organismal resilience and longevity via tetraspanin. bioRxiv. 2023 Dec 17. Jiang WI, De Belly H, Wang B, Wong A, Kim M, Oh F, DeGeorge J, Huang X, Guang S, Weiner OD, Ma DK. PMID: 37546737; PMCID: PMC10402089.
      View in: PubMed   Mentions:
    6. Acquired stress resilience through bacteria-to-nematode interdomain horizontal gene transfer. EMBO J. 2023 Dec 11; 42(24):e114835. Pandey T, Kalluraya CA, Wang B, Xu T, Huang X, Guang S, Daugherty MD, Ma DK. PMID: 37953666; PMCID: PMC10711659.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    7. Natural product P57 induces hypothermia through targeting pyridoxal kinase. Nat Commun. 2023 09 26; 14(1):5984. Wang R, Xiao L, Pan J, Bao G, Zhu Y, Zhu D, Wang J, Pei C, Ma Q, Fu X, Wang Z, Zhu M, Wang G, Gong L, Tong Q, Jiang M, Hu J, He M, Wang Y, Li T, Liang C, Li W, Xia C, Li Z, Ma DK, Tan M, Liu JY, Jiang W, Luo C, Yu B, Dang Y. PMID: 37752106; PMCID: PMC10522591.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    8. Acquired stress resilience through bacteria-to-nematode horizontal gene transfer. bioRxiv. 2023 Aug 21. Pandey T, Kalluraya C, Wang B, Xu T, Huang X, Guang S, Daugherty MD, Ma DK. PMID: 37662235; PMCID: PMC10473587.
      View in: PubMed   Mentions:
    9. LPD-3 as a megaprotein brake for aging and insulin-mTOR signaling in C. elegans. bioRxiv. 2023 Jul 17. Pandey T, Wang B, Wang C, Zu J, Deng H, Shen K, do Vale GD, McDonald JG, Ma DK. PMID: 36824874; PMCID: PMC9949100.
      View in: PubMed   Mentions:
    10. Bridge-Like Lipid Transfer Proteins (BLTPs) in C. elegans: From Genetics to Structures and Functions. Contact (Thousand Oaks). 2023 Jan-Dec; 6:25152564231186489. Pandey T, Zhang J, Wang B, Ma DK. PMID: 37455813; PMCID: PMC10345909.
      View in: PubMed   Mentions: 1  
    11. Stress-Induced Phenoptosis: Mechanistic Insights and Evolutionary Implications. Biochemistry (Mosc). 2022 Dec; 87(12):1504-1511. Pandey T, Ma DK. PMID: 36717459.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    12. GPCR signaling regulates severe stress-induced organismic death in Caenorhabditis elegans. Aging Cell. 2023 01; 22(1):e13735. Wang C, Long Y, Wang B, Zhang C, Ma DK. PMID: 36415159; PMCID: PMC9835589.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    13. A conserved megaprotein-based molecular bridge critical for lipid trafficking and cold resilience. Nat Commun. 2022 11 10; 13(1):6805. Wang C, Wang B, Pandey T, Long Y, Zhang J, Oh F, Sima J, Guo R, Liu Y, Zhang C, Mukherjee S, Bassik M, Lin W, Deng H, Vale G, McDonald JG, Shen K, Ma DK. PMID: 36357390; PMCID: PMC9649747.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    14. Co-opted genes of algal origin protect C. elegans against cyanogenic toxins. Curr Biol. 2022 11 21; 32(22):4941-4948.e3. Wang B, Pandey T, Long Y, Delgado-Rodriguez SE, Daugherty MD, Ma DK. PMID: 36223775; PMCID: PMC9691542.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    15. Abstract TP251: CRISPR-engineered Mouse Neural Cells Expressing An Optimized Manf Variant Reveals Mechanisms Of MANF Neuroprotection. Stroke. 2022 Feb 1; 53(Suppl_1):atp251-atp251. Llera LT, Singhal SN, Ma MD. .
      View in: Publisher Site   Mentions:
    16. Ethacrynic acid targets GSTM1 to ameliorate obesity by promoting browning of white adipocytes. Protein Cell. 2021 06; 12(6):493-501. Cui Z, Liu Y, Wan W, Xu Y, Hu Y, Ding M, Dou X, Wang R, Li H, Meng Y, Li W, Jiang W, Li Z, Li Y, Tan M, Ma DK, Ding Y, Liu JO, Luo C, Yu B, Tang Q, Dang Y. PMID: 32399897; PMCID: PMC8160069.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    17. The C. elegans homolog of human panic-disorder risk gene TMEM132D orchestrates neuronal morphogenesis through the WAVE-regulatory complex. Mol Brain. 2021 03 16; 14(1):54. Wang X, Jiang W, Luo S, Yang X, Wang C, Wang B, Dang Y, Shen Y, Ma DK. PMID: 33726789; PMCID: PMC7962252.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    18. The conserved autoimmune-disease risk gene TMEM39A regulates lysosome dynamics. Proc Natl Acad Sci U S A. 2021 02 09; 118(6). Luo S, Wang X, Bai M, Jiang W, Zhang Z, Chen Y, Ma DK. PMID: 33531362; PMCID: PMC8017986.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    19. The conserved transmembrane protein TMEM-39 coordinates with COPII to promote collagen secretion and regulate ER stress response. PLoS Genet. 2021 02; 17(2):e1009317. Zhang Z, Luo S, Barbosa GO, Bai M, Kornberg TB, Ma DK. PMID: 33524011; PMCID: PMC7901769.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    20. Cytoprotection by a naturally occurring variant of ATP5G1 in Arctic ground squirrel neural progenitor cells. Elife. 2020 10 14; 9. Singhal NS, Bai M, Lee EM, Luo S, Cook KR, Ma DK. PMID: 33050999; PMCID: PMC7671683.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    21. Nucleolus localization of SpyCas9 affects its stability and interferes with host protein translation in mammalian cells. Genes Dis. 2022 May; 9(3):731-740. Tan R, Du W, Liu Y, Cong X, Bai M, Jiang C, Li Z, Tan M, Ma DK, Huang Q, Jiang W, Dang Y. PMID: 35782966; PMCID: PMC9243344.
      View in: PubMed   Mentions: 2  
    22. Resilience to Injury: A New Approach to Neuroprotection? Neurotherapeutics. 2020 04; 17(2):457-474. Singhal NS, Sun CH, Lee EM, Ma DK. PMID: 31997268; PMCID: PMC7283435.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    23. Broadly conserved roles of TMEM131 family proteins in intracellular collagen assembly and secretory cargo trafficking. Sci Adv. 2020 02; 6(7):eaay7667. Zhang Z, Bai M, Barbosa GO, Chen A, Wei Y, Luo S, Wang X, Wang B, Tsukui T, Li H, Sheppard D, Kornberg TB, Ma DK. PMID: 32095531; PMCID: PMC7015688.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    24. Neuronal GDPGP1 and glycogen metabolism: friend or foe? J Cell Biol. 2020 02 03; 219(2). Singhal NS, Lee EM, Ma DK. PMID: 31971543; PMCID: PMC7041681.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    25. Abstract TP110: Dissecting the Optimized Cytoprotective Responses of Arctic Ground Squirrels With CRISPR. Stroke. 2020 Feb 1; 51(Suppl_1). Lee LE, Singhal SN, Bai BM, Ma MD. .
      View in: Publisher Site   Mentions:
    26. MDT-15/MED15 permits longevity at low temperature via enhancing lipidostasis and proteostasis. PLoS Biol. 2019 08; 17(8):e3000415. Lee D, An SWA, Jung Y, Yamaoka Y, Ryu Y, Goh GYS, Beigi A, Yang JS, Jung GY, Ma DK, Ha CM, Taubert S, Lee Y, Lee SV. PMID: 31408455; PMCID: PMC6692015.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    27. VHL-1 inactivation and mitochondrial antioxidants rescue C. elegans dopaminergic neurodegeneration. Protein Cell. 2019 08; 10(8):610-614. Chen S, Luo S, Zhang Z, Ma DK. PMID: 30945137; PMCID: PMC6626599.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    28. Abstract TP136: Mitochondrial Mechanisms of Resilience Revealed by Arctic Ground Squirrel Neural Cells. Stroke. 2019 Feb 1; 50(Suppl_1). Singhal SN, Bai BM, Luo LS, Ma MD. .
      View in: Publisher Site   Mentions:
    29. WDR-23 and SKN-1/Nrf2 Coordinate with the BLI-3 Dual Oxidase in Response to Iodide-Triggered Oxidative Stress. G3 (Bethesda). 2018 11 06; 8(11):3515-3527. Xu Z, Hu Y, Deng Y, Chen Y, Hua H, Huang S, Nie Q, Pan Q, Ma DK, Ma L. PMID: 30166349; PMCID: PMC6222583.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    30. The receptor tyrosine kinase HIR-1 coordinates HIF-independent responses to hypoxia and extracellular matrix injury. Sci Signal. 2018 10 02; 11(550). Vozdek R, Long Y, Ma DK. PMID: 30279166.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    31. A genetic program mediates cold-warming response and promotes stress-induced phenoptosis in C. elegans. Elife. 2018 04 17; 7. Jiang W, Wei Y, Long Y, Owen A, Wang B, Wu X, Luo S, Dang Y, Ma DK. PMID: 29664006; PMCID: PMC5903861.
      View in: PubMed   Mentions: 21     Fields:    Translation:Animals
    32. Conserved roles of C. elegans and human MANFs in sulfatide binding and cytoprotection. Nat Commun. 2018 03 01; 9(1):897. Bai M, Vozdek R, Hnízda A, Jiang C, Wang B, Kuchar L, Li T, Zhang Y, Wood C, Feng L, Dang Y, Ma DK. PMID: 29497057; PMCID: PMC5832864.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    33. Prolyl 4-hydroxylase 2 promotes B-cell lymphoma progression via hydroxylation of Carabin. Blood. 2018 03 22; 131(12):1325-1336. Jiang W, Zhou X, Li Z, Liu K, Wang W, Tan R, Cong X, Shan J, Zhan Y, Cui Z, Jiang L, Li Q, Shen S, Bai M, Cheng Y, Li B, Tan M, Ma DK, Liu JO, Dang Y. PMID: 29437589; PMCID: PMC5865229.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    34. Multiple excitatory and inhibitory neural signals converge to fine-tune Caenorhabditis elegans feeding to food availability. FASEB J. 2016 Feb; 30(2):836-48. Dallière N, Bhatla N, Luedtke Z, Ma DK, Woolman J, Walker RJ, Holden-Dye L, O'Connor V. PMID: 26514165; PMCID: PMC4714553.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    35. Warm up and cool down! Oncotarget. 2015 Oct 13; 6(31):30449-50. Wang T, Ma D. PMID: 26387141; PMCID: PMC4741542.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    36. Acyl-CoA Dehydrogenase Drives Heat Adaptation by Sequestering Fatty Acids. Cell. 2015 May 21; 161(5):1152-1163. Ma DK, Li Z, Lu AY, Sun F, Chen S, Rothe M, Menzel R, Sun F, Horvitz HR. PMID: 25981666; PMCID: PMC4441829.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    37. CYP-13A12 of the nematode Caenorhabditis elegans is a PUFA-epoxygenase involved in behavioural response to reoxygenation. Biochem J. 2014 Nov 15; 464(1):61-71. Keller J, Ellieva A, Ma DK, Ju J, Nehk E, Konkel A, Falck JR, Schunck WH, Menzel R. PMID: 25138176.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    38. Cytochrome P450 drives a HIF-regulated behavioral response to reoxygenation by C. elegans. Science. 2013 Aug 02; 341(6145):554-8. Ma DK, Rothe M, Zheng S, Bhatla N, Pender CL, Menzel R, Horvitz HR. PMID: 23811225; PMCID: PMC3969381.
      View in: PubMed   Mentions: 22     Fields:    Translation:Animals
    39. The neurobiology of sensing respiratory gases for the control of animal behavior. Front Biol (Beijing). 2012 Jun; 7(3):246-253. Ma DK, Ringstad N. PMID: 22876258; PMCID: PMC3412401.
      View in: PubMed   Mentions: 6  
    40. CYSL-1 interacts with the O2-sensing hydroxylase EGL-9 to promote H2S-modulated hypoxia-induced behavioral plasticity in C. elegans. Neuron. 2012 Mar 08; 73(5):925-40. Ma DK, Vozdek R, Bhatla N, Horvitz HR. PMID: 22405203; PMCID: PMC3305813.
      View in: PubMed   Mentions: 58     Fields:    
    41. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci. 2011 Aug 28; 14(10):1345-51. Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H. PMID: 21874013; PMCID: PMC3183401.
      View in: PubMed   Mentions: 341     Fields:    Translation:AnimalsCells
    42. Bridging Environment and DNA: Activity-Induced Epigenetic Modification in the Adult Brain. Two Faces of Evil: Cancer and Neurodegeneration. 2011 Jan 1; 113-123. Ma MD, Guo GJ, Ming MG, Song SH. .
      View in: Publisher Site   Mentions:
    43. Epigenetic choreographers of neurogenesis in the adult mammalian brain. Nat Neurosci. 2010 Nov; 13(11):1338-44. Ma DK, Marchetto MC, Guo JU, Ming GL, Gage FH, Song H. PMID: 20975758; PMCID: PMC3324277.
      View in: PubMed   Mentions: 150     Fields:    Translation:HumansAnimalsCells
    44. Oxysterols drive dopaminergic neurogenesis from stem cells. Cell Stem Cell. 2009 Oct 02; 5(4):343-4. Ma DK, Ming GL, Song H. PMID: 19796609; PMCID: PMC6188706.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    45. Activity-dependent extrinsic regulation of adult olfactory bulb and hippocampal neurogenesis. Ann N Y Acad Sci. 2009 Jul; 1170:664-73. Ma DK, Kim WR, Ming GL, Song H. PMID: 19686209; PMCID: PMC2729764.
      View in: PubMed   Mentions: 80     Fields:    Translation:Animals
    46. Molecular genetic analysis of FGFR1 signalling reveals distinct roles of MAPK and PLCgamma1 activation for self-renewal of adult neural stem cells. Mol Brain. 2009 Jun 08; 2:16. Ma DK, Ponnusamy K, Song MR, Ming GL, Song H. PMID: 19505325; PMCID: PMC2700800.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    47. Adult neural stem cells in the mammalian central nervous system. Cell Res. 2009 Jun; 19(6):672-82. Ma DK, Bonaguidi MA, Ming GL, Song H. PMID: 19436263; PMCID: PMC2738865.
      View in: PubMed   Mentions: 140     Fields:    Translation:HumansCells
    48. DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation. Cell Cycle. 2009 May 15; 8(10):1526-31. Ma DK, Guo JU, Ming GL, Song H. PMID: 19377292; PMCID: PMC2738863.
      View in: PubMed   Mentions: 83     Fields:    Translation:HumansAnimalsCells
    49. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science. 2009 Feb 20; 323(5917):1074-7. Ma DK, Jang MH, Guo JU, Kitabatake Y, Chang ML, Pow-Anpongkul N, Flavell RA, Lu B, Ming GL, Song H. PMID: 19119186; PMCID: PMC2726986.
      View in: PubMed   Mentions: 458     Fields:    Translation:AnimalsCells
    50. G9a and Jhdm2a regulate embryonic stem cell fusion-induced reprogramming of adult neural stem cells. Stem Cells. 2008 Aug; 26(8):2131-41. Ma DK, Chiang CH, Ponnusamy K, Ming GL, Song H. PMID: 18535151; PMCID: PMC4059405.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    51. Cellular niches for endogenous neural stem cells in the adult brain. CNS Neurol Disord Drug Targets. 2007 Oct; 6(5):336-41. Jordan JD, Ma DK, Ming GL, Song H. PMID: 18045162.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    52. Disrupted-In-Schizophrenia 1 regulates integration of newly generated neurons in the adult brain. Cell. 2007 Sep 21; 130(6):1146-58. Duan X, Chang JH, Ge S, Faulkner RL, Kim JY, Kitabatake Y, Liu XB, Yang CH, Jordan JD, Ma DK, Liu CY, Ganesan S, Cheng HJ, Ming GL, Lu B, Song H. PMID: 17825401; PMCID: PMC2002573.
      View in: PubMed   Mentions: 318     Fields:    Translation:AnimalsCells
    53. Glial influences on neural stem cell development: cellular niches for adult neurogenesis. Curr Opin Neurobiol. 2005 Oct; 15(5):514-20. Ma DK, Ming GL, Song H. PMID: 16144763.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansAnimalsCells
    54. Adult neural stem cells and repair of the adult central nervous system. J Hematother Stem Cell Res. 2003 Dec; 12(6):671-9. Goh EL, Ma D, Ming GL, Song H. PMID: 14977476.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
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