Publications

2017

 

Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta J, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin B, Chang HY, Weissman JS, Lim DA. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science.  2017 Jan 6;355(6320). pii: aah7111.   

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Cohen-Pfeffer JL, Gururangan S, Lester T, Lim DA, Shaywitz AJ, Westphal M, Slavc I. Intracerebroventricular Delivery as a Safe, Long-Term Route of Administration. Pediatric Neurology. 2017, 67:23-35.

2016

Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA, Diaz A.  Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas.  Mol Syst Biol.  2016, 12(11):889. 

 

 

 

 

Delgado RN, Lu C, Lim DA.  Maintenance of neural stem cell regional identity in culture. Neurogenesis.  2016, 3:1, e1187321, DOI: 10.1080/23262133.2016.1187321

 

Diaz A, Liu SJ, Sandoval C, Pollen A, Nowakowski TJ, Lim DA, Kriegstein A.  SCell: integrated analysis of single-cell RNA-seq data.  Bioinformatics. 2016 Apr 19. pii: btw201. [Epub ahead of print].  

 

Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA.  Single-cell analysis of long non-coding RNAs in the developing human neocortex.  Genome Biol.  2016 17:67 DOI: 10.1186/s13059-016-0932-1.

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Lim DA, Alvarez-Buylla A.  The Adult Ventricular-Subventricular Zone (V-SVZ) and Olfactory Bulb (OB) Neurogenesis.  Cold Spring Harb Perspect Biol. 2016 Apr 5. pii: a018820. doi: 10.1101/cshperspect.a018820.  

 

Ramos AD, Attenello FJ, Lim DA. Uncovering the roles of long noncoding RNAs in neural development and glioma progression. Neurosci Lett. 2016, S0304-3940(15)30316-5.

 

Rowland NC, Kalia SK, Kalia LV, Larson PS, Lim DA, 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 Jan 13;3:15051.

 

2015

Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR.  Molecular Identity of Human Outer Radial Glia during Cortical Development. Cell. 2015 Sep 24; 163(1):55-67.  

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Delgado RN, Lim DA.  Embryonic Nkx2.1-expressing neural precursor cells contribute to the regional heterogeneity of adult V-SVZ neural stem cells. Dev Biol. 2015, 407:265-274.  

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Lim DA.  Transcriptional and epigenetic insights from stem cells and developing tissues. Development. 2015. Aug 1;142(15):2549-53.

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Rolston JD, Ramos A, Heath S, Englot DJ, Lim DA. 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 Jul 21.

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Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz CC, Salinas RD, Zarabi H, Kriegstein AR, Lim DA. The long noncoding RNA pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells.  Cell Stem Cell. 2015. 16(4):439-47

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Rowland NC, Starr PA, Larson PS, Ostrem JL, Marks WJ Jr, Lim DA. Combining cell transplants or gene therapy with deep brain stimulation for Parkinson's disease. Mov Disord. 2015 Feb;30(2):190-5.

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2014

Lim DA, Alvarez-Buylla A. Adult neural stem cells stake their ground. Trends Neurosci. 2014 Sep 12.

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Price JD, Park KY, Chen J, Salinas RD, Cho MJ, Kriegstein AR, Lim DA. The ink4a/arf locus is a barrier to direct neuronal transdifferentiation. J Neurosci. 2014 Sep 10; 34(37):12560-7.

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Park DH, Hong SJ, Salinas RD, Liu SJ, Sun SW, Sgualdino J, Testa G, Matzuk MM, Iwamori N, Lim DA. 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.

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Silvestrini MT, Yin D, Martin AJ, Coppes VG, Mann P, Larson PS, Starr PA, Zeng X, Gupta N, Panter SS, Desai TA, Lim DA. Interventional Magnetic Resonance Imaging-guided Cell Transplantation Into the Brain With Radially Branched Deployment. Mol Ther. 2014 Aug 20.

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Andersen RE, Lim DA. An ingredient for the elixir of youth. Cell Res. 2014 Aug 12.

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Benitah SA, Bracken A, Dou Y, Huangfu D, Ivanova N, Koseki H, Laurent L, Lim DA, Meshorer E, Pombo A, Sander M, Xu GL. Stem cell epigenetics: looking forward. Cell Stem Cell. 2014 Jun 5; 14(6):706-9.

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Potts MB, Siu JJ, Price JD, Salinas RD, Cho MJ, Ramos AD, Hahn J, Margeta M, Oldham MC, Lim DA. Analysis of Mll1-deficiency Identifies Neurogenic Transcriptional Modules and Brn4 as a Factor for Direct Astrocyte-to-neuron Reprogramming. Neurosurgery. 2014 May 30.

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Featured article, eLIFE home page

Hwang WW, Salinas RD, Siu JJ, Kelley KW, Delgado RN, Paredes MF, Alvarez-Buylla A, Oldham MC, Lim DA. Distinct and separable roles for EZH2 in neurogenic astroglia. Elife. 2014; 3:e02439.

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Cheng JS, Lim DA, Chang EF, Barbaro NM. A review of percutaneous treatments for trigeminal neuralgia. Neurosurgery. 2014 Mar; 10 Suppl 1:25-33.

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2013

Gonzales-Roybal G, Lim DA. Chromatin-based epigenetics of adult subventricular zone neural stem cells. Front Genet. 2013; 4:194.

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Cheng JS, Lim DA, Chang EF, Barbaro NM. A Review of Percutaneous Treatments for Trigeminal Neuralgia. Neurosurgery. 2013 Sep 23.

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Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell. 2013 May 2; 12(5):616-28.

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Potts MB, Silvestrini MT, Lim DA. Devices for cell transplantation into the central nervous system: Design considerations and emerging technologies. Surg Neurol Int. 2013; 4(Suppl 1):S22-30.

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Silvestrini MT, Yin D, Coppes VG, Mann P, Martin AJ, Larson PS, Starr PA, Gupta N, Panter SS, Desai TA, Lim DA. Radially branched deployment for more efficient cell transplantation at the scale of the human brain. Stereotact Funct Neurosurg. 2013; 91(2):92-103.

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2012

Gupta N, Henry RG, Strober J, Kang SM, Lim DA, 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.

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Potts MB, Lim DA. An old drug for new ideas: metformin promotes adult neurogenesis and spatial memory formation. Cell Stem Cell. 2012 Jul 6; 11(1):5-6.

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Diaz A, Park K, Lim DA, Song JS. Normalization, bias correction, and peak calling for ChIP-seq. Stat Appl Genet Mol Biol. 2012; 11(3):Article 9.

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Crowell AL, Ryapolova-Webb ES, Ostrem JL, Galifianakis NB, Shimamoto S, Lim DA, Starr PA. Oscillations in sensorimotor cortex in movement disorders: an electrocorticography study. Brain. 2012 Feb; 135(Pt 2):615-30.

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2011

Sugiarto S, Persson AI, Munoz EG, Waldhuber M, Lamagna C, Andor N, Hanecker P, Ayers-Ringler J, Phillips J, Siu J, Lim DA, 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.

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2010

Johnston MA, Lim DA. Keeping them quiet: BMPs maintain adult neural stem cell quiescence. Cell Stem Cell. 2010 Jul 2; 7(1):9-10.

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2009

Oh MC, Lim DA. Novel treatment strategies for malignant gliomas using neural stem cells. Neurotherapeutics. 2009 Jul; 6(3):458-64.

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Lim DA, Larson PS. Intraoperative MRI in functional neurosurgery. Preface. Neurosurg Clin N Am. 2009 Apr; 20(2):xi.

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Roskom J, Swistowski A, Zeng X, Lim DA. Future directions: use of interventional MRI for cell-based therapy of Parkinson disease. Neurosurg Clin N Am. 2009 Apr; 20(2):211-8.

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Lim DA, 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.

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Lim DA, 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.

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2008

Silber J, Lim DA, 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; 6:14.

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2007

Lim DA, 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.

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Lim DA, 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.

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Lim DA, 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.

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2006

Lim DA, 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.

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— 2005

Palma V, Lim DA, 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.

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Alvarez-Buylla A, Lim DA. For the long run: maintaining germinal niches in the adult brain. Neuron. 2004 Mar 4; 41(5):683-6.

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Caporaso GL, Lim DA, Alvarez-Buylla A, Chao MV. Telomerase activity in the subventricular zone of adult mice. Mol Cell Neurosci. 2003 Aug; 23(4):693-702.

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Tramontin AD, García-Verdugo JM, Lim DA, 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.

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Naef F, Lim DA, 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.

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Lim DA, 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.

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Gritti A, Bonfanti L, Doetsch F, Caille I, Alvarez-Buylla A, Lim DA, 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.

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Lim DA, 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.

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Li XC, Jarvis ED, Alvarez-Borda B, Lim DA, 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.

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Lim DA, 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.

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Doetsch F, Caillé I, Lim DA, 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.

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García-Verdugo JM, Doetsch F, Wichterle H, Lim DA, 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.

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Lim DA, 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.

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Lim DA, 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.

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Thorner LK, Lim DA, Botchan MR. DNA-binding domain of bovine papillomavirus type 1 E1 helicase: structural and functional aspects. J Virol. 1993 Oct; 67(10):6000-14.

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Yang L, Mohr I, Fouts E, Lim DA, 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 1; 90(11):5086-90.

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