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Our Team

John Liu

John Liu, MD, PhD

Education

Education
  • Radiation Oncology Residency, University of California, San Francisco (2020-2024)
  • Kaiser Permanente San Francisco Medical Center, Internship, 07/19-06/20, Internal Medicine
  • University of California, San Francisco, M.D., 07/11-06/19, Medicine
  • University of California, San Francisco, Ph.D., 07/11-03/17, Biomedical Sciences
  • Harvard University, Cambridge, M.A., A.B., 09/07-05/11, Chemical and Physical Biology

Awards & Honors
  • 2022, UCSF Catalyst Award
  • 2022, ASCO Conquer Cancer – The Sontag Foundation Young Investigator Award
  • 2021, UCSF Brain Tumor Center SPORE Career Enhancement Program
  • 2015-2017, Ruth L. Kirschstein National Research Service Award (NIH F30)
  • 2011-2019, Medical Scientist Training Program (NIH)
  • 2011, A.B. awarded magna cum laude with Highest Honors, Harvard University
  • 2011, Lawrence J. Henderson Prize for most meritorious thesis in department, Harvard University
  • 2011, Phi Beta Kappa National Honor Society
  • 2007-2010, Harvard College Research Program
  • 2009, John Harvard Scholar
  • 2007, Intel Science Talent Search Finalist
  • 2007, Siemens Math, Science, Technology Competition Semifinalist

Selected Publications and Abstracts
  • Liu SJ, Chen WC, Zhang Y, Young JS, Morshed RA, Villanueva-Meyer J, Phillips J, Oberheim-Bush NA, Aghi MK, Sneed PK, Braunstein SE, Berger MS, Molinaro AM, Hervey-Jumper S, Raleigh D. Timing of Adjuvant Radiotherapy and Survival Analysis for Molecularly Defined Low Grade Glioma. IJROBP 2022; 144(3):e75. https://doi.org/10.1016/j.ijrobp.2022.07.838
  • 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; 2(11) https://doi.org/10.1016/j.xgen.2022.100177.
  • 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.
  • 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 Jan 21:1-7. doi: 10.3171/2021.10.JNS211886
  • He D, Wu D, Muller S, Wang L, Saha P, Hamid S, Liu SJ, Cui M, Hong SJ, Jain M, Olson HE, Akeson M, Costello J, 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):e2017562118. doi: 10.1073/pnas.2017562118.
  • 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.
  • Liu SJ, Dang H, Lim D, Feng F, Maher CA. Long non-coding RNAs in metastasis. Nature Rev. Cancer. 2021 Jul;21(7):446-460. doi: 10.1038/s41568-021-00353-1.
  • 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 21, 83 (2020). https://doi.org/10.1186/s13059-020-01995-4 *Equal Contribution
  • Horlbeck MA, Liu SJ, Chang HY, Lim DA, Weissman JS. Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes. Nature Biotech. 2020 Feb 24;1-4 doi 10.1038/s41587-020-0428-0
  • 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, Bush NAO, Bollen AW, McDermott M, Costello JF, Raleigh DR. Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma. Cell Reports. 2020 Feb 4;1300-1309. e5. doi 10.1016/j.celrep.2020.01.018. *Equal Contribution
  • Bhaduri A, Di Lullo E, Jung D, Müller S, Crouch EE, Sandoval Espinosa C, 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; 48-63. e6. doi 10.1016/j.stem.2019.11.015
  • 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.
  • Liu SJ, Lim DA. Modulating the expression of long non‐coding RNAs for functional studies. EMBO Reports. 2018;e46955; doi 10.15252/embr.201846955
  • Kline CN*, 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 Neuro-Oncol. 2018;86:1064-10  *Equal Contribution
  • 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; doi.org/10.1016/j.cell.2018.03.068
  • 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; bty316
  • Nowakowski TJ, Bhaduri A, Pollen AA, Alvarado B, Mostajo-Radji MA, Di Lullo E, Haeussler M, Sandoval-Espinosa C, Liu SJ, Velmeshev S, 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;358:1318-1323
  • 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 Biology 2017;18:234
  • 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;355 aah7111  *Equal Contribution
  • 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) PMID 27888226 *Equal Contribution
  • 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 PMID 27081004
  • Diaz AA, Liu SJ, Sandoval C, Pollen AA, Nowakowski TJ, Lim DA, Kriegstein AR. SCell: integrated analysis of single-cell RNA-seq data Bioinformatics. 2016; doi:10.1093/bioinformatics/btw201
  • 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;163(1):55-67. PMID 26406371
  • 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. PMID 25800779
  • 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;8(5):1290-9. PMID 25176653
  • Thomson M, Liu SJ, Zou L-N, Smith Z, Meissner A, Ramanathan S. Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell. 2011;145:875–889. PMID 21663792
  • Bax DV, Liu SJ, McKenzie DR, Bilek MMM, Weiss AS. Tropoelastin switch and modulated endothelial cell binding to PTFE. BioNanoScience. 2011;1(4):123-127. doi: 10.1007/s12668-011-0018-1
  • Xie Z, Liu SJ, Bleris L, Benenson Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 2010;38:2692–2701. PMID 20194121
  • Liu SJ, Malatesta M, Seo K, Lien BV, Hong S, Koontz M, Raleigh DR, Ullian E, Lim D. GENE-39. CRISPRi-BASED RADIATION MODIFIER SCREEN IDENTIFIES LONG NON-CODING RNA THERAPEUTIC TARGETS IN GLIOMA. Neuro-Oncology. 2019 November;21 Supplement_6.
  • Liu SJ, Vasudevan H, Breshears JD, Pekmezci M, Villanueva-Meyer J, Lang U, Chen WC, Choudhury A, Magill S, Braunstein SE, Gopinath C, Nakamura JL, Tward A, Sneed PK, Perry A, McDermott MW, Theodosopoulos PV, Raleigh DRR. Multiplatform Molecular Profiling of Vestibular Schwannoma Reveals Immune Enrichment after Radiosurgery and a Methylation-Based Predictor of Recurrence. Int J Radiat Oncol Biol Phys. 2019 Sept 1;105, E67
  • Liu SJ, Magill S, Vasudevan H, Hilz S, Daggubati V, Villanueva-Meyer J, Choudhury A, Ferris S, Orr B, Bush NAO, Bollen A, McDermott M, Costello J, Raleigh DR. EPEN-02. MULTIPLATFORM MOLECULAR PROFILING REVEALS INTRATUMOR HETEROGENEITY IN EPENDYMOMA. Neuro-Oncology. 2019 April 23;ii77-ii78
  • Vasudevan HN, Demaree B, Lucas CG, Liu SJ, Choudhury A, Magill ST, Gopinath C, Delley C, Nakamura J, Braunstein SE, Jacques L, Perry A, Pekmezci M, Butte AJ, Abate AR, Raleigh DR. Clinical outcomes and epigenomic profiling of malignant peripheral nerve sheath tumors (MPNSTs). 2019 Children’s Tumor Foundation – Neurofibromatosis Conference. San Francisco, CA.
  • Liu SJ, Vasudevan HN, Breshears JD, Pekmezci M, Villanueva-Meyer JE, Lang U, Chen WC, Choudhury A, Magill ST, Braunstein SE, Nakamura JL, Tward A, Sneed PK, Perry A, McDermott MW, Theodosopoulos PV, Raleigh DR. Multiplatform molecular profiling of vestibular schwannoma reveals immune enrichment after radiosurgery and a methylation-based predictor of recurrence. 2019 ASTRO Annual Meeting. Chicago, IL.
  • Vasudevan HN, Lucas CG, Liu SJ, Choudhury A, Magill ST, Nakamura J, Braunstein SE, Perry A, Pekmezci M, Raleigh DR. Postoperative radiation therapy improves progression free survival in malignant peripheral nerve sheath tumors. 2019 ASTRO Annual Meeting. Chicago, IL.
  • Liu SJ, Vasudevan HN, Pekmezci M, Choudhury A, Lien BV, Breshears JD, Swaney D, Magill ST, Lang U, Chen WC, Gopinath C, Castro MRH, Villanueva-Meyer JE, Braunstein SE, Sneed PK, Lim DA, Perry A, Krogan NJ, McDermott MW, Berger MS, Theodosopoulos PV, Raleigh DR. Vestibular schwannoma is comprised of neural crest and immune subgroups. 2019 Society of Neuro-Oncology Annual Meeting. Phoneix, AZ.
  • 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. Genome-scale CRISPRi-based screening of lncRNAs reveals radiation sensitizers for glioma therapy. Keystone Non-Coding RNAs. 2017
  • Mueller S, Liu S, Malatesta M, Aghi M, Kriegstein A, Kohanbash G, Lim D, Diaz A. Single-cell profiling of glioblastoma biopsies identifies a family of activating PDGF-receptor deletions. Society for Neuro-Oncology. 2016
  • Muller S, Kohanbash G, Liu S, Carrera D, Aghi M, Lim D, Okada H, Diaz A. Distinct molecular signatures of microglia and bone-marrow macrophages in the glioma perivascular niche. Society for Neuro-Oncology. 2016
  • Liu SJ*, Horlbeck MA*, Cho SW, Birk HS, Malatesta M, He D, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Conklin BR, Chang HY, Weissman JS, Lim DA. Systematic identification of essential long non-coding RNA genes in human cells. CSHL Regulatory and Non-coding RNA. 2016 *Equal Contribution
  • Liu SJ, Di Lullo E, Malatesta M, Kohanbash G, Castro B, Okada H, Kriegstein A, Aghi MK, Lim DA, Diaz AA. GENO-14 SINGLE-CELL TRANSCIPTOMICS AND GENOMICS REVEALS A DIVERSITY OF TUMOR AND IMMUNE CELL POLARIZATION SIGNALS IN GBM. Neuro-Oncology. 2015;17(suppl 5):v94-v94. doi: 10.1093/neuonc/nov215.14
  • Attenello F, Liu SJ, Malatesta M, Zarabi H, Andersen R, Ramos A, Lim DA. GENO-04 REGULATION OF GLIOBLASTOMA BY NOVEL LONG NONCODING RNA (lncRNA). Neuro-Oncology. 2015;17(suppl 5):v91-v92. doi: 10.1093/neuonc/nov215.04
  • Salinas R, Liu SJ, Delgado R, Park KY, Price J, Ramos R, Phillips J, Lim DA. EG-14 EPIGENETIC DYSREGULATION OF THE HoxA LOCUS AND OTHER HOMEOBOX GENES DRIVEN BY Ink4a/arf DEFICIENCY AND EGFRviii. Neuro-Oncology. 2014;16(Suppl 5):v78. doi:10.1093/neuonc/nou254.14
  • All abstracts above were also presented as posters.

 

 

Redefining Possible