Publications

Complete Lists

 
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2026
  1. Zhu I, Chien J, Rech GE, Mirchia K, Pan S, Miller K, Pak J, Wustrack R, Monga V, Braunstein SE, Adams MD, Jacques L, Pekmezci M, Liu SJ, Vasudevan HN. IFN signaling is associated with radiotherapy response in malignant peripheral nerve sheath tumors. J Clin Invest. 2026 Mar 2;136(5). doi: 10.1172/JCI195652. PMID: 41766654; PMCID: PMC12948414.
  2. Dougherty MC, Syed HS, Xu L, Liu SJ, Raleigh DR, Rauckhorst AJ, Taylor EB, Hansen MR. Metabolomic profiling and stable isotope tracing of human schwannomas: A novel perspective on tumor biology and radiation response. Neurooncol Adv. 2026 Jan-Dec;8(1):vdaf223. doi: 10.1093/noajnl/vdaf223. PMID: 41635804; PMCID: PMC12863081.
2025
  1. Casey-Clyde T, Liu SJ, Pelonero A, Serrano JAC, Teng C, Jang YG, Vasudevan HN, Padmanabhan A, Bush JO, Raleigh DR. Eed controls craniofacial osteoblast differentiation and mesenchymal proliferation from the neural crest. Elife. 2025 Dec 2;13. doi: 10.7554/eLife.100159. PMID: 41329158; PMCID: PMC12671911.
  2. Pan S, Mirchia K, Payne E, Liu SJ, Al-Adli N, Peeran Z, Shukla P, Young JS, Gupta R, Wu J, Pak J, Ozawa T, Na B, Reddy AT, Braunstein SE, Phillips JJ, Chang S, Solomon DA, Perry A, Raleigh DR, Berger MS, Abate AR, Vasudevan HN. Tumor heterogeneity underlies clinical outcome and MEK inhibitor response in somatic NF1-mutant glioblastoma. JCI Insight. 2025 Sep 23;10(18). doi: 10.1172/jci.insight.192658. PMID: 40985888; PMCID: PMC12487855.
  3. Lin K, Zou C, Hubbard A, Sengelmann S, Goudy L, Wang IC, Sharma R, Pak J, Foster K, Ozawa T, de Groot JF, Phillips J, Vasudevan HN, Raleigh DR, Marson A, Murthy N, Gilbert LA, Berger MS, Liu SJ. Multiplexed epigenetic memory editing using CRISPRoff sensitizes glioblastoma to chemotherapy. Neuro Oncol. 2025 Jul 30;27(6):1443-1457. doi: 10.1093/neuonc/noaf055. PMID: 39998382; PMCID: PMC12309708.
  4. Casey-Clyde T, Liu SJ, Pelonero A, Serrano JAC, Teng C, Jang YG, Vasudevan HN, Padmanabhan A, Bush JO, Raleigh DR. Eed controls craniofacial osteoblast differentiation and mesenchymal proliferation from the neural crest. bioRxiv. 2025 Jul 21. doi: 10.1101/2024.03.13.584903. PMID: 38558995; PMCID: PMC10979956.
2024
  1. Liu SJ, Zou C, Pak J, Morse A, Pang D, Casey-Clyde T, Borah AA, Wu D, Seo K, O'Loughlin T, Lim DA, Ozawa T, Berger MS, Kamber RA, Weiss WA, Raleigh DR, Gilbert LA. In vivo perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma. Genome Biol. 2024 Oct 7;25(1):256. doi: 10.1186/s13059-024-03404-6. PMID: 39375777; PMCID: PMC11457336.
  2. Eaton CD, Avalos L, Liu SJ, Chen Z, Zakimi N, Casey-Clyde T, Bisignano P, Lucas CG, Stevenson E, Choudhury A, Vasudevan HN, Magill ST, Young JS, Krogan NJ, Villanueva-Meyer JE, Swaney DL, Raleigh DR. Merlin(S13) phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features. Nat Commun. 2024 Sep 9;15(1):7873. doi: 10.1038/s41467-024-52284-8. PMID: 39251601; PMCID: PMC11383945.
  3. Liu SJ, Raleigh DR, de Groot JF. Proteasome inhibition for glioblastoma: Lessons learned and new opportunities. Neuro Oncol. 2024 Sep 5;26(9):1683-1684. doi: 10.1093/neuonc/noae118. PMID: 38934653; PMCID: PMC11376452.
  4. Halasz H, Malekos E, Covarrubias S, Yitiz S, Montano C, Sudek L, Katzman S, Liu SJ, Horlbeck MA, Namvar L, Weissman JS, Carpenter S. CRISPRi screens identify the lncRNA, LOUP, as a multifunctional locus regulating macrophage differentiation and inflammatory signaling. Proc Natl Acad Sci U S A. 2024 May 28;121(22):e2322524121. doi: 10.1073/pnas.2322524121. PMID: 38781216; PMCID: PMC11145268.
  5. Lucas CG, Mirchia K, Seo K, Najem H, Chen WC, Zakimi N, Foster K, Eaton CD, Cady MA, Choudhury A, Liu SJ, Phillips JJ, Magill ST, Horbinski CM, Solomon DA, Perry A, Vasudevan HN, Heimberger AB, Raleigh DR. Spatial genomic, biochemical and cellular mechanisms underlying meningioma heterogeneity and evolution. Nat Genet. 2024 Jun;56(6):1121-1133. doi: 10.1038/s41588-024-01747-1. PMID: 38760638; PMCID: PMC11239374.
  6. Ramesh P, Ruan D, Liu SJ, Seo Y, Braunstein S, Sheng K. Hypoxia-informed RBE-weighted beam orientation optimization for intensity modulated proton therapy. Med Phys. 2024 Mar;51(3):2320-2333. doi: 10.1002/mp.16978. PMID: 38345134; PMCID: PMC10940223.
  7. Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez KJ, Stevenson E, Chen KH, Lien BV, Wu D, Braunstein SE, Sneed PK, Magill ST, Lim D, McDermott MW, Berger MS, Perry A, Krogan NJ, Hansen MR, Spitzer MH, Gilbert L, Theodosopoulos PV, Raleigh DR. Epigenetic reprogramming shapes the cellular landscape of schwannoma. Nat Commun. 2024 Jan 12;15(1):476. doi: 10.1038/s41467-023-40408-5. PMID: 38216587; PMCID: PMC10786948.
2023
  1. Lucas CH, Mirchia K, Seo K, Najem H, Chen W, Zakimi N, Choudhury A, Liu SJ, Phillips J, Magill S, Horbinski C, Solomon D, Perry A, Vasudevan H, Heimberger A, Raleigh D. Spatial genomic, biochemical, and cellular mechanisms drive meningioma heterogeneity and evolution. Res Sq. 2023 May 15. doi: 10.21203/rs.3.rs-2921804/v1. PMID: 37292686; PMCID: PMC10246120.
  2. Eaton C, Avalos L, Liu SJ, Casey-Clyde T, Bisignano P, Lucas CH, Stevenson E, Choudhury A, Vasudevan H, Magill S, Krogan N, Villanueva-Meyer J, Swaney D, Raleigh D. Merlin(S13) phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features. Res Sq. 2023 Mar 14. doi: 10.21203/rs.3.rs-2577844/v1. PMID: 36993679; PMCID: PMC10055685.
2022
  1. 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 Genom. 2022 Nov 9;2(11). doi: 10.1016/j.xgen.2022.100177. PMID: 36381608; PMCID: PMC9648144.
  2. Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW, Qiu Z, Martin MV, Susko MS, Braunstein SE, Bush NAO, Schulte JD, Butowski N, Sneed PK, Berger MS, Krogan NJ, Perry A, Phillips JJ, Solomon DA, Costello JF, McDermott MW, Rich JN, Raleigh DR. Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Nat Genet. 2022 May;54(5):649-659. doi: 10.1038/s41588-022-01061-8. PMID: 35534562; PMCID: PMC9374001.
  3. Chen WC, Lafreniere M, Phuong C, Liu SJ, Baal JD, Lometti M, Morin O, Ziemer B, Vasudevan HN, Lucas CG, Hervey-Jumper SL, Theodosopoulos PV, Magill ST, Fogh S, Nakamura JL, Boreta L, Sneed PK, McDermott MW, Raleigh DR, Braunstein SE. Resection with intraoperative cesium-131 brachytherapy as salvage therapy for recurrent brain tumors. J Neurosurg. 2022 Oct 1;137(4):924-930. doi: 10.3171/2021.10.JNS211886. PMID: 35061986.
2021
  1. Liu SJ, Horlbeck MA, Weissman JS, Lim DA. 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. PMID: 33326085; PMCID: PMC7917014.
  2. Liu SJ, Dang HX, Lim DA, Feng FY, Maher CA. Long noncoding RNAs in cancer metastasis. Nat Rev Cancer. 2021 Jul;21(7):446-460. doi: 10.1038/s41568-021-00353-1. Review. PMID: 33953369; PMCID: PMC8288800.
  3. 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. miRNA-independent function of long noncoding pri-miRNA loci. Proc Natl Acad Sci U S A. 2021 Mar 30;118(13). doi: 10.1073/pnas.2017562118. PMID: 33758101; PMCID: PMC8020771.
2020
  1. Liu SJ, Malatesta M, Lien BV, Saha P, Thombare SS, Hong SJ, Pedraza L, Koontz M, Seo K, Horlbeck MA, He D, Birk HS, Jain M, Olsen HE, Akeson M, Weissman JS, Monje M, Gupta N, Raleigh DR, Ullian EM, Lim DA. CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma. Genome Biol. 2020 Mar 31;21(1):83. doi: 10.1186/s13059-020-01995-4. PMID: 32234056; PMCID: PMC7110660.
  2. Horlbeck MA, Liu SJ, Chang HY, Lim DA, Weissman JS. Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes. Nat Biotechnol. 2020 May;38(5):573-576. doi: 10.1038/s41587-020-0428-0. PMID: 32094656; PMCID: PMC8128075.
  3. Liu SJ, Magill ST, Vasudevan HN, Hilz S, Villanueva-Meyer JE, Lastella S, Daggubati V, Spatz J, Choudhury A, Orr BA, Demaree B, Seo K, Ferris SP, Abate AR, Oberheim Bush NA, Bollen AW, McDermott MW, Costello JF, Raleigh DR. Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma. Cell Rep. 2020 Feb 4;30(5):1300-1309.e5. doi: 10.1016/j.celrep.2020.01.018. PMID: 32023450; PMCID: PMC7313374.
  4. 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. doi: 10.1016/j.stem.2019.11.015. PMID: 31901251; PMCID: PMC7029801.
2019
  1. Burke JE, Longhurst AD, Natarajan P, Rao B, Liu J, Sales-Lee J, Mortensen Y, Moresco JJ, Diedrich JK, Yates JR 3rd, Madhani HD. A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast Cryptococcus neoformans. G3 (Bethesda). 2019 Jul 9;9(7):2235-2244. doi: 10.1534/g3.119.400330. PMID: 31092606; PMCID: PMC6643885.
  2. 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. PMID: 31112699; PMCID: PMC6556063.
2018
  1. Liu SJ, Lim DA. Modulating the expression of long non-coding RNAs for functional studies. EMBO Rep. 2018 Dec;19(12). doi: 10.15252/embr.201846955. Review. PMID: 30467236; PMCID: PMC6280642.
  2. Kline C, Liu SJ, Duriseti S, Banerjee A, Nicolaides T, Raber S, Gupta N, Haas-Kogan D, Braunstein S, Mueller S. Reirradiation and PD-1 inhibition with nivolumab for the treatment of recurrent diffuse intrinsic pontine glioma: a single-institution experience. J Neurooncol. 2018 Dec;140(3):629-638. doi: 10.1007/s11060-018-2991-5. PMID: 30206764.
  3. 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. doi: 10.1016/j.cell.2018.03.068. PMID: 29731168; PMCID: PMC5984165.
2017
  1. 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. PMID: 29262845; PMCID: PMC5738907.
  2. 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. PMID: 29217575; PMCID: PMC5991609.
  3. 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 DA. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science. 2017 Jan 6;355(6320). doi: 10.1126/science.aah7111. PMID: 27980086; PMCID: PMC5394926.
2016
  1. 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 Nov 25;12(11):889. doi: 10.15252/msb.20166969. PMID: 27888226; PMCID: PMC5147052.
  2. 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 Jul 15;32(14):2219-20. doi: 10.1093/bioinformatics/btw201. PMID: 27153637; PMCID: PMC4937196.
  3. 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 Apr 14;17:67. doi: 10.1186/s13059-016-0932-1. PMID: 27081004; PMCID: PMC4831157.
2015
  1. 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. doi: 10.1016/j.cell.2015.09.004. PMID: 26406371; PMCID: PMC4583716.
  2. Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, 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 Apr 2;16(4):439-447. doi: 10.1016/j.stem.2015.02.007. PMID: 25800779; PMCID: PMC4388801.
2014 and earlier
  1. 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. doi: 10.1016/j.celrep.2014.07.060. PMID: 25176653; PMCID: PMC4201382.
  2. Thomson M, Liu SJ, Zou LN, Smith Z, Meissner A, Ramanathan S. Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell. 2011 Jun 10;145(6):875-89. doi: 10.1016/j.cell.2011.05.017. PMID: 21663792; PMCID: PMC5603300.
  3. Xie Z, Liu SJ, Bleris L, Benenson Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 2010 May;38(8):2692-701. doi: 10.1093/nar/gkq117. PMID: 20194121; PMCID: PMC2860122.