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Daniel Lim, MD, PhD

TitleAssociate Professor
SchoolUCSF School of Medicine
DepartmentNeurological Surgery
Address35 Medical Center way
San Fancisco CA 94143
Phone415-476-8138
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    Collapse Biography 
    Collapse Education and Training
    University of California, BerkeleyB.A.1994MCB
    Rockefeller UniversityPh.D.2001
    Cornell Medical SchoolM.D.2002
    University of California, San FranciscoResidency2008Neurological Surgery
    Collapse Awards and Honors
    National Institutes of Health2009  - 2014NIH Director's New Innovator Award
    Sontag Foundation2009  - 2013Distinguished Researcher Award
    U.S. National Academy of Sciences2010Kavli Fellow

    Collapse Research 
    Collapse Research Activities and Funding
    Functional long noncoding RNAs in human glioma
    NIH/NINDS R21NS101395Apr 1, 2017 - Mar 31, 2019
    Role: Principal Investigator
    Long noncoding RNA regulation of neural stem cells
    NIH/NINDS R01NS091544Feb 15, 2016 - Jan 31, 2021
    Role: Principal Investigator
    Chromatin-based regulation of neural stem cells
    VA I01BX000252Oct 1, 2009 - Sep 30, 2022
    Role: Principal Investigator
    Chromatin-based cellular memory in neural stem cells
    NIH DP2OD006505Sep 30, 2009 - Jun 30, 2014
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
    Collapse Global Health
    Collapse Featured Publications

    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.
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    1. Nowakowski TJ, Bhaduri A, Pollen AA, Alvarado B, Mostajo-Radji MA, Di Lullo E, Haeussler M, Sandoval-Espinosa C, Liu SJ, Velmeshev D, Ounadjela JR, Shuga J, Wang X, Lim D, West JA, Leyrat AA, Kent WJ, Kriegstein AR. Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science. 2017 Dec 08; 358(6368):1318-1323. PMID: 29217575.
      View in: PubMed
    2. Cebrián-Silla A, Alfaro-Cervelló C, Herranz-Pérez V, Kaneko N, Park DH, Sawamoto K, Alvarez-Buylla A, Lim D, García-Verdugo JM. Unique Organization of the Nuclear Envelope in the Post-natal Quiescent Neural Stem Cells. Stem Cell Reports. 2017 Jul 11; 9(1):203-216. PMID: 28648897.
      View in: PubMed
    3. Rolston JD, Lim D. In Reply: Thalamotomy-Like Effects from Partial Removal of a Ventral Intermediate Nucleus Deep Brain Stimulator Lead in a Patient With Essential Tremor. Neurosurgery. 2017 May 01; 80(5):E256. PMID: 28368504.
      View in: PubMed
    4. Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim D. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science. 2017 01 06; 355(6320). PMID: 27980086.
      View in: PubMed
    5. Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim D, Diaz A. Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol. 2016 Nov 25; 12(11):889. PMID: 27888226.
      View in: PubMed
    6. Cohen-Pfeffer JL, Gururangan S, Lester T, Lim D, Shaywitz AJ, Westphal M, Slavc I. Intracerebroventricular Delivery as a Safe, Long-Term Route of Drug Administration. Pediatr Neurol. 2017 Feb; 67:23-35. PMID: 28089765.
      View in: PubMed
    7. Delgado RN, Lu C, Lim D. Maintenance of neural stem cell regional identity in culture. Neurogenesis (Austin). 2016; 3(1):e1187321. PMID: 27606338; PMCID: PMC4973606 [Available on 05/09/17].
    8. Lim D, Alvarez-Buylla A. The Adult Ventricular-Subventricular Zone (V-SVZ) and Olfactory Bulb (OB) Neurogenesis. Cold Spring Harb Perspect Biol. 2016 May 02; 8(5). PMID: 27048191.
      View in: PubMed
    9. Diaz A, Liu SJ, Sandoval C, Pollen A, Nowakowski TJ, Lim D, Kriegstein A. SCell: integrated analysis of single-cell RNA-seq data. Bioinformatics. 2016 Jul 15; 32(14):2219-20. PMID: 27153637; PMCID: PMC4937196 [Available on 07/15/17].
    10. Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim D. Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol. 2016 Apr 14; 17:67. PMID: 27081004; PMCID: PMC4831157.
    11. Rowland NC, Kalia SK, Kalia LV, Larson PS, Lim D, Bankiewicz KS. Merging DBS with viral vector or stem cell implantation: "hybrid" stereotactic surgery as an evolution in the surgical treatment of Parkinson's disease. Mol Ther Methods Clin Dev. 2016; 3:15051. PMID: 26817024; PMCID: PMC4714520.
    12. Ramos AD, Attenello FJ, Lim D. Uncovering the roles of long noncoding RNAs in neural development and glioma progression. Neurosci Lett. 2016 Jun 20; 625:70-9. PMID: 26733304.
      View in: PubMed
    13. Rolston JD, Ramos AD, Heath S, Englot DJ, Lim D. Thalamotomy-Like Effects From Partial Removal of a Ventral Intermediate Nucleus Deep Brain Stimulator Lead in a Patient With Essential Tremor: Case Report. Neurosurgery. 2015 Nov; 77(5):E831-6; discussion E836-7. PMID: 26200771.
      View in: PubMed
    14. Delgado RN, Lim D. Embryonic Nkx2.1-expressing neural precursor cells contribute to the regional heterogeneity of adult V-SVZ neural stem cells. Dev Biol. 2015 Nov 15; 407(2):265-74. PMID: 26387477; PMCID: PMC4663161 [Available on 11/15/16].
    15. Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim D, Leyrat AA, West JA, Kriegstein AR. Molecular identity of human outer radial glia during cortical development. Cell. 2015 Sep 24; 163(1):55-67. PMID: 26406371; PMCID: PMC4583716.
    16. Lim D. Transcriptional and epigenetic insights from stem cells and developing tissues. Development. 2015 Aug 01; 142(15):2549-53. PMID: 26243867.
      View in: PubMed
    17. Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz CC, Salinas RD, Zarabi H, Kriegstein AR, Lim D. The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. Cell Stem Cell. 2015 Apr 02; 16(4):439-447. PMID: 25800779; PMCID: PMC4388801.
    18. Rowland NC, Starr PA, Larson PS, Ostrem JL, Marks WJ, Lim D. Combining cell transplants or gene therapy with deep brain stimulation for Parkinson's disease. Mov Disord. 2015 Feb; 30(2):190-5. PMID: 25521796.
      View in: PubMed
    19. Potts MB, Siu JJ, Price JD, Salinas RD, Cho MJ, Ramos AD, Hahn J, Margeta M, Oldham MC, Lim D. Analysis of Mll1 deficiency identifies neurogenic transcriptional modules and Brn4 as a factor for direct astrocyte-to-neuron reprogramming. Neurosurgery. 2014 Oct; 75(4):472-82; discussion 482. PMID: 24887289; PMCID: PMC4420187.
    20. Lim D, Alvarez-Buylla A. Adult neural stem cells stake their ground. Trends Neurosci. 2014 Oct; 37(10):563-71. PMID: 25223700; PMCID: PMC4203324.
    21. Price JD, Park KY, Chen J, Salinas RD, Cho MJ, Kriegstein AR, Lim D. The Ink4a/Arf locus is a barrier to direct neuronal transdifferentiation. J Neurosci. 2014 Sep 10; 34(37):12560-7. PMID: 25209293; PMCID: PMC4160784.
    22. Park DH, Hong SJ, Salinas RD, Liu SJ, Sun SW, Sgualdino J, Testa G, Matzuk MM, Iwamori N, Lim D. Activation of neuronal gene expression by the JMJD3 demethylase is required for postnatal and adult brain neurogenesis. Cell Rep. 2014 Sep 11; 8(5):1290-9. PMID: 25176653; PMCID: PMC4201382.
    23. Silvestrini MT, Yin D, Martin AJ, Coppes VG, Mann P, Larson PS, Starr PA, Zeng X, Gupta N, Panter SS, Desai TA, Lim D. Interventional magnetic resonance imaging-guided cell transplantation into the brain with radially branched deployment. Mol Ther. 2015 Jan; 23(1):119-29. PMID: 25138755; PMCID: PMC4426791.
    24. Andersen RE, Lim D. An ingredient for the elixir of youth. Cell Res. 2014 Dec; 24(12):1381-2. PMID: 25112712; PMCID: PMC4260342.
    25. Benitah SA, Bracken A, Dou Y, Huangfu D, Ivanova N, Koseki H, Laurent L, Lim D, Meshorer E, Pombo A, Sander M, Xu GL. Stem cell epigenetics: looking forward. Cell Stem Cell. 2014 Jun 05; 14(6):706-9. PMID: 25032261.
      View in: PubMed
    26. Hwang WW, Salinas RD, Siu JJ, Kelley KW, Delgado RN, Paredes MF, Alvarez-Buylla A, Oldham MC, Lim D. Distinct and separable roles for EZH2 in neurogenic astroglia. Elife. 2014 May 27; 3:e02439. PMID: 24867641; PMCID: PMC4032491.
    27. Cheng JS, Lim D, Chang EF, Barbaro NM. A review of percutaneous treatments for trigeminal neuralgia. Neurosurgery. 2014 Mar; 10 Suppl 1:25-33; discussion 33. PMID: 24509496.
      View in: PubMed
    28. Gonzales-Roybal G, Lim D. Chromatin-based epigenetics of adult subventricular zone neural stem cells. Front Genet. 2013 Oct 08; 4:194. PMID: 24115953; PMCID: PMC3792351.
    29. Cheng JS, Lim D, Chang EF, Barbaro NM. A Review of Percutaneous Treatments for Trigeminal Neuralgia. Neurosurgery. 2013 Sep 23. PMID: 24064481.
      View in: PubMed
    30. Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim D. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell. 2013 May 02; 12(5):616-28. PMID: 23583100; PMCID: PMC3662805.
    31. Potts MB, Silvestrini MT, Lim D. Devices for cell transplantation into the central nervous system: Design considerations and emerging technologies. Surg Neurol Int. 2013; 4(Suppl 1):S22-30. PMID: 23653887; PMCID: PMC3642746.
    32. Silvestrini MT, Yin D, Coppes VG, Mann P, Martin AJ, Larson PS, Starr PA, Gupta N, Panter SS, Desai TA, Lim D. Radially branched deployment for more efficient cell transplantation at the scale of the human brain. Stereotact Funct Neurosurg. 2013; 91(2):92-103. PMID: 23343609; PMCID: PMC3739996.
    33. Lim D, Chan MF, Childs C. Surrogate consent for critical care research: exploratory study on public perception and influences on recruitment. Crit Care. 2013 Jan 15; 17(1):R5. PMID: 23320945; PMCID: PMC4057109.
    34. Gupta N, Henry RG, Strober J, Kang SM, Lim D, Bucci M, Caverzasi E, Gaetano L, Mandelli ML, Ryan T, Perry R, Farrell J, Jeremy RJ, Ulman M, Huhn SL, Barkovich AJ, Rowitch DH. Neural stem cell engraftment and myelination in the human brain. Sci Transl Med. 2012 Oct 10; 4(155):155ra137. PMID: 23052294; PMCID: PMC3893824.
    35. Potts MB, Lim D. An old drug for new ideas: metformin promotes adult neurogenesis and spatial memory formation. Cell Stem Cell. 2012 Jul 06; 11(1):5-6. PMID: 22770236; PMCID: PMC3468946.
    36. Diaz A, Park K, Lim D, Song JS. Normalization, bias correction, and peak calling for ChIP-seq. Stat Appl Genet Mol Biol. 2012 Mar 31; 11(3):Article 9. PMID: 22499706; PMCID: PMC3342857.
    37. Crowell AL, Ryapolova-Webb ES, Ostrem JL, Galifianakis NB, Shimamoto S, Lim D, Starr PA. Oscillations in sensorimotor cortex in movement disorders: an electrocorticography study. Brain. 2012 Feb; 135(Pt 2):615-30. PMID: 22252995; PMCID: PMC3281473.
    38. Sugiarto S, Persson AI, Munoz EG, Waldhuber M, Lamagna C, Andor N, Hanecker P, Ayers-Ringler J, Phillips J, Siu J, Lim D, Vandenberg S, Stallcup W, Berger MS, Bergers G, Weiss WA, Petritsch C. Asymmetry-defective oligodendrocyte progenitors are glioma precursors. Cancer Cell. 2011 Sep 13; 20(3):328-40. PMID: 21907924; PMCID: PMC3297490.
    39. Johnston MA, Lim D. Keeping them quiet: BMPs maintain adult neural stem cell quiescence. Cell Stem Cell. 2010 Jul 02; 7(1):9-10. PMID: 20621042.
      View in: PubMed
    40. Oh MC, Lim D. Novel treatment strategies for malignant gliomas using neural stem cells. Neurotherapeutics. 2009 Jul; 6(3):458-64. PMID: 19560736.
      View in: PubMed
    41. Lim D, Larson PS. Intraoperative MRI in functional neurosurgery. Preface. Neurosurg Clin N Am. 2009 Apr; 20(2):xi. PMID: 19555874.
      View in: PubMed
    42. Roskom J, Swistowski A, Zeng X, Lim D. Future directions: use of interventional MRI for cell-based therapy of Parkinson disease. Neurosurg Clin N Am. 2009 Apr; 20(2):211-8. PMID: 19555884.
      View in: PubMed
    43. Lim D, Huang YC, Swigut T, Mirick AL, Garcia-Verdugo JM, Wysocka J, Ernst P, Alvarez-Buylla A. Chromatin remodelling factor Mll1 is essential for neurogenesis from postnatal neural stem cells. Nature. 2009 Mar 26; 458(7237):529-33. PMID: 19212323; PMCID: PMC3800116.
    44. Lim D, Tarapore P, Chang E, Burt M, Chakalian L, Barbaro N, Chang S, Lamborn KR, McDermott MW. Safety and feasibility of switching from phenytoin to levetiracetam monotherapy for glioma-related seizure control following craniotomy: a randomized phase II pilot study. J Neurooncol. 2009 Jul; 93(3):349-54. PMID: 19169651; PMCID: PMC2687520.
    45. Silber J, Lim D, Petritsch C, Persson AI, Maunakea AK, Yu M, Vandenberg SR, Ginzinger DG, James CD, Costello JF, Bergers G, Weiss WA, Alvarez-Buylla A, Hodgson JG. miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells. BMC Med. 2008 Jun 24; 6:14. PMID: 18577219; PMCID: PMC2443372.
    46. Lim D, Cha S, Mayo MC, Chen MH, Keles E, VandenBerg S, Berger MS. Relationship of glioblastoma multiforme to neural stem cell regions predicts invasive and multifocal tumor phenotype. Neuro Oncol. 2007 Oct; 9(4):424-9. PMID: 17622647; PMCID: PMC1994099.
    47. Lim D, Khandhar SM, Heath S, Ostrem JL, Ringel N, Starr P. Multiple target deep brain stimulation for multiple sclerosis related and poststroke Holmes' tremor. Stereotact Funct Neurosurg. 2007; 85(4):144-9. PMID: 17259750.
      View in: PubMed
    48. Lim D, Huang YC, Alvarez-Buylla A. The adult neural stem cell niche: lessons for future neural cell replacement strategies. Neurosurg Clin N Am. 2007 Jan; 18(1):81-92, ix. PMID: 17244556.
      View in: PubMed
    49. Lim D, Suárez-Fariñas M, Naef F, Hacker CR, Menn B, Takebayashi H, Magnasco M, Patil N, Alvarez-Buylla A. In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis. Mol Cell Neurosci. 2006 Jan; 31(1):131-48. PMID: 16330219.
      View in: PubMed
    50. Palma V, Lim D, Dahmane N, Sánchez P, Brionne TC, Herzberg CD, Gitton Y, Carleton A, Alvarez-Buylla A, Ruiz i Altaba A. Sonic hedgehog controls stem cell behavior in the postnatal and adult brain. Development. 2005 Jan; 132(2):335-44. PMID: 15604099; PMCID: PMC1431583.
    51. Alvarez-Buylla A, Lim D. For the long run: maintaining germinal niches in the adult brain. Neuron. 2004 Mar 04; 41(5):683-6. PMID: 15003168.
      View in: PubMed
    52. Caporaso GL, Lim D, Alvarez-Buylla A, Chao MV. Telomerase activity in the subventricular zone of adult mice. Mol Cell Neurosci. 2003 Aug; 23(4):693-702. PMID: 12932448.
      View in: PubMed
    53. Tramontin AD, García-Verdugo JM, Lim D, Alvarez-Buylla A. Postnatal development of radial glia and the ventricular zone (VZ): a continuum of the neural stem cell compartment. Cereb Cortex. 2003 Jun; 13(6):580-7. PMID: 12764031.
      View in: PubMed
    54. Naef F, Lim D, Patil N, Magnasco M. DNA hybridization to mismatched templates: a chip study. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Apr; 65(4 Pt 1):040902. PMID: 12005798.
      View in: PubMed
    55. Lim D, Flames N, Collado L, Herrera DG. Investigating the use of primary adult subventricular zone neural precursor cells for neuronal replacement therapies. Brain Res Bull. 2002 Apr; 57(6):759-64. PMID: 12031272.
      View in: PubMed
    56. Moldoveanu T, Hosfield CM, Lim D, Elce JS, Jia Z, Davies PL. A Ca(2+) switch aligns the active site of calpain. Cell. 2002 Mar 08; 108(5):649-60. PMID: 11893336.
      View in: PubMed
    57. Gritti A, Bonfanti L, Doetsch F, Caille I, Alvarez-Buylla A, Lim D, Galli R, Verdugo JM, Herrera DG, Vescovi AL. Multipotent neural stem cells reside into the rostral extension and olfactory bulb of adult rodents. J Neurosci. 2002 Jan 15; 22(2):437-45. PMID: 11784788.
      View in: PubMed
    58. Lim D, Tramontin AD, Trevejo JM, Herrera DG, García-Verdugo JM, Alvarez-Buylla A. Noggin antagonizes BMP signaling to create a niche for adult neurogenesis. Neuron. 2000 Dec; 28(3):713-26. PMID: 11163261.
      View in: PubMed
    59. Li XC, Jarvis ED, Alvarez-Borda B, Lim D, Nottebohm F. A relationship between behavior, neurotrophin expression, and new neuron survival. Proc Natl Acad Sci U S A. 2000 Jul 18; 97(15):8584-9. PMID: 10890902; PMCID: PMC26991.
    60. Lim D, Alvarez-Buylla A. Interaction between astrocytes and adult subventricular zone precursors stimulates neurogenesis. Proc Natl Acad Sci U S A. 1999 Jun 22; 96(13):7526-31. PMID: 10377448; PMCID: PMC22119.
    61. Doetsch F, Caillé I, Lim D, García-Verdugo JM, Alvarez-Buylla A. Subventricular zone astrocytes are neural stem cells in the adult mammalian brain. Cell. 1999 Jun 11; 97(6):703-16. PMID: 10380923.
      View in: PubMed
    62. García-Verdugo JM, Doetsch F, Wichterle H, Lim D, Alvarez-Buylla A. Architecture and cell types of the adult subventricular zone: in search of the stem cells. J Neurobiol. 1998 Aug; 36(2):234-48. PMID: 9712307.
      View in: PubMed
    63. Lim D, Gossen M, Lehman CW, Botchan MR. Competition for DNA binding sites between the short and long forms of E2 dimers underlies repression in bovine papillomavirus type 1 DNA replication control. J Virol. 1998 Mar; 72(3):1931-40. PMID: 9499046; PMCID: PMC109485.
    64. Lim D, Fishell GJ, Alvarez-Buylla A. Postnatal mouse subventricular zone neuronal precursors can migrate and differentiate within multiple levels of the developing neuraxis. Proc Natl Acad Sci U S A. 1997 Dec 23; 94(26):14832-6. PMID: 9405699; PMCID: PMC25123.
    65. Thorner LK, Lim D, Botchan MR. DNA-binding domain of bovine papillomavirus type 1 E1 helicase: structural and functional aspects. J Virol. 1993 Oct; 67(10):6000-14. PMID: 8396665; PMCID: PMC238021.
    66. Yang L, Mohr I, Fouts E, Lim D, Nohaile M, Botchan M. The E1 protein of bovine papilloma virus 1 is an ATP-dependent DNA helicase. Proc Natl Acad Sci U S A. 1993 Jun 01; 90(11):5086-90. PMID: 8389467; PMCID: PMC46659.
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