John Liu, MD, PhD
Resident
Radiation Oncology
School of Medicine

Awards

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• CRISPR Cures for Cancer Initiative Pilot Award, University of California, San Francisco, 2023-2024
• Catalyst Award, University of California, San Francisco, 2022-2023
• The Sontag Foundation Conquer Cancer Young Investigator Award, University of California, San Francisco, 2022-2023
• BTC SPORE Career Enhancement Award, University of California, San Francisco, 2021-2022
• ABR Holman Pathway, University of California, San Francisco, 2020-2024

Education & Training

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• Internal Medicine Prelim Kaiser Permanente 06/2020
• MD Medicine University of California, San Francisco 06/2019
• PhD Biomedical Sciences University of California, San Francisco 03/2017
• AB Chemical and Physical Biology Harvard University 05/2011
• Radiation Oncology University of California, San Francisco

Grants and Projects

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• Regulation of neurogenesis by the novel long non-coding RNA Pnky, NIH, 2015-2017

Publications (23)

Top publication keywords:
CRISPR-Cas SystemsEpigenomicsGlioblastomaNeocortexClustered Regularly Interspaced Short Palindromic RepeatsEpendymoglial CellsGenetic HeterogeneityLentivirusRNA, Long NoncodingSingle-Cell AnalysisGene Expression ProfilingGenome, HumanGene Knockdown TechniquesEpendymomaNeoplasm Metastasis

• Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.
  Nature genetics 2022 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,…
• Resection with intraoperative cesium-131 brachytherapy as salvage therapy for recurrent brain tumors.
  Journal of neurosurgery 2022 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, …
• Long noncoding RNAs in cancer metastasis.
  Nature reviews. Cancer 2021 Liu SJ, Dang HX, Lim DA, Feng FY, Maher CA
• miRNA-independent function of long noncoding pri-miRNA loci.
  Proceedings of the National Academy of Sciences of the United States of America 2021 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
• Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference.
  Methods in molecular biology (Clifton, N.J.) 2021 Liu SJ, Horlbeck MA, Weissman JS, Lim DA

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• CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma.
  Genome biology 2020 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, …
• Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes.
  Nature biotechnology 2020 Horlbeck MA, Liu SJ, Chang HY, Lim DA, Weissman JS
• Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma.
  Cell reports 2020 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, …
• Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma.
  Cell stem cell 2020 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, …
• The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo.
  Developmental cell 2019 Andersen RE, Hong SJ, Lim JJ, Cui M, Harpur BA, Hwang E, Delgado RN, Ramos AD, Liu SJ, Blencowe BJ, Lim DA
• Modulating the expression of long non-coding RNAs for functional studies.
  EMBO reports 2018 Liu SJ, Lim DA
• Reirradiation and PD-1 inhibition with nivolumab for the treatment of recurrent diffuse intrinsic pontine glioma: a single-institution experience.
  Journal of neuro-oncology 2018 Kline C, Liu SJ, Duriseti S, Banerjee A, Nicolaides T, Raber S, Gupta N, Haas-Kogan D, Braunstein S, Mueller S
• Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element.
  Cell 2018 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
• 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 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
• Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.
  Science (New York, N.Y.) 2017 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…
• CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.
  Science (New York, N.Y.) 2016 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
• Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas.
  Molecular systems biology 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 analysis of long non-coding RNAs in the developing human neocortex.
  Genome biology 2016 Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA
• Molecular identity of human outer radial glia during cortical development.
  Cell 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
• The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells.
  Cell stem cell 2015 Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, Salinas RD, Zarabi H, Kriegstein AR, Lim DA
• Activation of neuronal gene expression by the JMJD3 demethylase is required for postnatal and adult brain neurogenesis.
  Cell reports 2014 Park DH, Hong SJ, Salinas RD, Liu SJ, Sun SW, Sgualdino J, Testa G, Matzuk MM, Iwamori N, Lim DA
• Pluripotency factors in embryonic stem cells regulate differentiation into germ layers.
  Cell 2011 Thomson M, Liu SJ, Zou LN, Smith Z, Meissner A, Ramanathan S
• Logic integration of mRNA signals by an RNAi-based molecular computer.
  Nucleic acids research 2010 Xie Z, Liu SJ, Bleris L, Benenson Y