Dan Lim Lab at UCSF

 

2022

Wu D, Poddar A, Ninou E, Hwang E, Cole MA, Liu SJ, Horlbeck MA, Chen J, Replogle JM, Carosso GA, Eng NWL, Chang J, Shen Y, Weissman JS, Lim DA.  Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.  Cell Genomics.  2022 Nov 9;2(11):100177.  

Winkler EA, Kim CN, Ross JM, Garcia JH, Gil E, Oh I, Chen LQ, Wu D, Catapano JS, Raygor K, Narsinh K, Kim H, Weinsheimer S, Cooke DL, Walcott BP, Lawton MT, Gupta N, Zlokovic BV, Chang EF, Abla AA*, Lim DA*, Nowakowski TJ*.  A single-cell atlas of the normal and malformed human brain vasculature.  Science. 2022 Mar 4;375(6584):eabi7377. doi: 10.1126/science.abi7377.  *co-corresponding authors.  

Dong C, Zhao C, Chen X, Berry K, Wang J, Zhang F, Liao Y, Han R, Ogurek S, Xu L, Zhang L, Lin Y, Zhou W, Xin M, Lim DA, Campbell K, Nakafuku M, Waclaw RR, Lu QR.  Conserved and Distinct Functions of the Autism-Related Chromatin Remodeler CHD8 in Embryonic and Adult Forebrain Neurogenesis.  J Neurosci. 2022 Nov 2;42(44):8373-8392.

Winkler E, Wu D, Gil E, McCoy D, Narsinh K, Sun Z, Mueller K, Ross J, Kim H, Weinsheimer S, Berger M, Nowakowski T, Lim D, Abla A, Cooke D.  Endoluminal Biopsy for Molecular Profiling of Human Brain Vascular Malformations.  Neurology. 2022 Apr 19;98(16):e1637-e1647.

2021

Cebrian-Silla A, Nascimento MA, Redmond SA, Mansky B, Wu D, Obernier K, Romero Rodriguez R, Gonzalez-Granero S, García-Verdugo JM, Lim DA, Álvarez-Buylla A.  Single-cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenesis.  Elife. 2021 Jul 14;10:e67436. doi: 10.7554/eLife.67436.

He D, Wu D, Muller S, Wang L, Saha P, Ahanger SH, Liu SJ, Cui M, Hong SJ, Jain M, Olson HE, Akeson M, Costello JF, Diaz A, Lim DA (2021). miRNA-independent function of long noncoding pri-miRNA loci. Proc Natl Acad Sci U S A, Mar 30;118(13):e2017562118. doi: 10.1073/pnas.2017562118.

Burke JF, Tanzillo D, Starr PA, Lim DA, Larson PS (2021).  CT and MRI Image Fusion Error: An Analysis of Co-Registration Error Using Commercially Available Deep Brain Stimulation Surgical Planning Software. Stereotact Funct Neurosurg, Feb 3;1-7. doi: 10.1159/000511114.

Liu SJ, Horlbeck MA, Weissman JS, Lim DA (2021).  Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference.  Methods Mol Biol. 2021;2254:323-338. doi: 10.1007/978-1-0716-1158-6_20.

Liu SJ, Dang H, Lim DA, Feng F, and Maher CA (2021).  Long non-coding RNAs in cancer metastasis, Nat Rev Cancer, May 5. doi: 10.1038.  

2020

Delgado RN, Mansky B, Ahanger SH, Lu C, Andersen RE, Dou Y, Alvarez-Buylla A, Lim DA (2020). Maintenance of neural stem cell positional identity by Mixed-lineage leukemia 1.  Science, 2020 03 Apr; 368(6486): 48-53.  

Liu SJ, Malatesta M, Lien B, Saha P, Thombare SS, Hong SJ, Pedraza L, Koontz M, Kyonghee S, Horlbeck MA, He D, Birk D, Jain M, Olsen HE, Akeson M, Weissman JS, Monje M, Gupta N, Raleigh D, Ullian E, Lim DA, (2020). CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma. Genome Biol., 2020 Mar 31; 21(83) doi.org/10.1186/s13059-020-01995-4

Chen W, de Hemptinne C, Miller AM, Leibbrand M, Little SJ, Lim DA, Larson PS, Starr PA.  Prefrontal-Subthalamic Hyperdirect Pathway Modulates Movement Inhibition in Humans.  Neuron. 2020 Feb 26. pii: S0896-6273(20)30135-5.  

Horlbeck MA, Liu SJ, Chang HY, Lim DA, Weissman JS.  Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes.  Nat Biotechnol.  2020 Feb 24. doir.org/10.1038/s41587-020-04428-0. 

Bhaduri A, Di Lullo E, Jung D, Müller S, Crouch EE, Espinosa CS, Ozawa T, Alvarado B, Spatazza J, Cadwell CR, Wilkins G, Velmeshev D, Liu SJ, Malatesta M, Andrews MG, Mostajo-Radji MA, Huang EJ, Nowakowski TJ, Lim DA, Diaz A, Raleigh DR, Kriegstein AR.  Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma.  Cell Stem Cell. 2020 Jan 2;26(1):48-63.e6.

2019

Andersen RE, Hong SJ, Lim JJ, Cui M, Harpur BA, Hwang E, Delgado RN, Ramos AD, Liu SJ, Blencowe BJ, Lim DA.  The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo.  Dev Cell. 2019 May 20;49(4):632-642.e7. doi: 10.1016/j.devcel.2019.04.032.

Gupta N, Henry RG, Kang SM, Strober J, Lim DA, Ryan T, Perry R, Farrell J, Ulman M, Rajalingam R, Gage A, Huhn SL, Barkovich AJ, Rowitch DH.  Long-Term Safety, Immunologic Response, and Imaging Outcomes following Neural Stem Cell Transplantation for Pelizaeus-Merzbacher Disease.  Stem Cell Reports. 2019 Aug 13;13(2):254-261.

2018

Liu SJ, Lim DA.  Modulating the expression of long non-coding RNAs for functional studies.  EMBO Rep. 2018 Dec;19(12). pii: e46955. doi: 10.15252/embr.201846955.

Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY.  Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element.  Cell. 2018 May 31;173(6):1398-1412.e22.  

Müller S, Cho A, Liu SJ, Lim DA, Diaz A.  CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones.  Bioinformatics. 2018 Apr 20. doi: 10.1093/bioinformatics/bty316. [Epub ahead of print]

Slavc I, Cohen-Pfeffer JL, Gururangan S, Krauser J, Lim DA, Maldaun M, Schwering C, Shaywitz AJ, Westphal M.  Best practices for the use of intracerebroventricular drug delivery devices.  Mol Genet Metab. 2018 May 16. pii: S1096-7192(18)30019-2

2017

Müller S, Kohanbash G, Liu SJ, Alvarado B, Carrera D, Bhaduri A, Watchmaker PB, Yagnik G, Di Lullo E, Malatesta M, Amankulor NM, Kriegstein AR, Lim DA, Aghi M, Okada H, Diaz A.  Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment.  Genome Biol. 2017 Dec 20;18(1):234. doi: 10.1186/s13059-017-1362-4.

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 DA, West JA, Leyrat AA, Kent WJ, Kriegstein AR.  Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.  Science. 2017 Dec 8;358(6368):1318-1323. doi: 10.1126/science.aap8809.

Delgado RN, Lim DA.  Maintenance of Positional Identity of Neural Progenitors in the Embryonic and Postnatal Telencephalon.  Front Mol Neurosci. 2017 Nov 13;10:373. doi: 10.3389/fnmol.2017.00373. eCollection 2017.

Andersen RE, Lim DA.  Forging our understanding of lncRNAs in the brain.  Cell Tissue Res. 2018 Jan;371(1):55-71. doi: 10.1007/s00441-017-2711-z. Epub 2017 Oct 27. 

Cebrián-Silla A, Alfaro-Cervelló C, Herranz-Pérez V, Kaneko N, Park DH, Sawamoto K, Alvarez-Buylla A, Lim DA, 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. doi: 10.1016/j.stemcr.2017.05.024. 

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].  

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.  

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.  

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

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.

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.

2014

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

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.

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.

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.

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

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.

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.

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.

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

2013

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

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

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.

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.

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.

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.

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.

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.

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.

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.

2009

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

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

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.

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.

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.

 

-before 2008-

 

papers from postdoctoral and neurosurgery residency years

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

 

papers from my PhD thesis work at Rockefeller University

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.  View in: PubMed

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.  View in: PubMed

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.  View in: PubMed

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.  View in: PubMed

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.  View in: PubMed

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.  View in: PubMed

papers from my undergraduate thesis work at UC Berkeley

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.  View in: PubMed

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.  View in: PubMed

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.  View in: PubMed