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Sheng Li

Associate Professor of Cancer Biology

Co-leader of the Epigenetic Regulation in Cancer (ERC) Program

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Email sli68423@usc.edu
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Awards

  • Leukemia & Lymphoma Society : Career Development Program Scholar Award, 2024-2029
  • American Association for Cancer Research: NextGen Star, 2020-2021
  • National Institute of General Medical Sciences: Maximizing Investigators’ Research Award, 2019-2024
  • Leukemia Research Foundation: New Investigator Award, 2017-2018

Publications

  • MorPhiC Consortium: towards functional characterization of all human genes Nature. 2025 Feb; 638(8050):351-359. . View in PubMed
  • Quantifying interpretation reproducibility in Vision Transformer models with TAVAC Sci Adv. 2024 Dec 20; 10(51):eabg0264. . View in PubMed
  • Intermittent clearance of p21-highly-expressing cells extends lifespan and confers sustained benefits to health and physical functionCell Metab. 2024 Aug 06; 36(8):1795-1805. e6. . View in PubMed
  • Inferring single-cell spatial gene expression with tissue morphology via explainable deep learning bioRxiv. 2024 Jun 14. . View in PubMed
  • Causal network perturbation analysis identifies known and novel type-2 diabetes driver genes bioRxiv. 2024 May 26. . View in PubMed
  • Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML NPJ Syst Biol Appl. 2024 Apr 09; 10(1):38. . View in PubMed
  • Challenges and opportunities for modeling aging and cancer Cancer Cell. 2023 04 10; 41(4):641-645. . View in PubMed
  • Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns Cancer Treat Res. 2023; 190:375-393. . View in PubMed
  • NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity Genome Biol. 2022 12 27; 23(1):270. . View in PubMed
  • Interchromosomal interaction of homologous Stat92E alleles regulates transcriptional switch during stem-cell differentiation Nat Commun. 2022 07 09; 13(1):3981. . View in PubMed
  • DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation Genome Biol. 2021 10 18; 22(1):295. . View in PubMed
  • Network Topology of Biological Aging and Geroscience-Guided Approaches to COVID-19 Front Aging. 2021 Jul; 2. . View in PubMed
  • epihet for intra-tumoral epigenetic heterogeneity analysis and visualization Sci Rep. 2021 01 11; 11(1):376. . View in PubMed
  • Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development Cell Rep. 2020 12 08; 33(10):108448. . View in PubMed
  • Somatic Mutations Drive Specific, but Reversible, Epigenetic Heterogeneity States in AML Cancer Discov. 2020 12; 10(12):1934-1949. . View in PubMed
  • Lung mesenchymal cells elicit lipid storage in neutrophils that fuel breast cancer lung metastasis Nat Immunol. 2020 11; 21(11):1444-1455. . View in PubMed
  • CUP-AI-Dx: A tool for inferring cancer tissue of origin and molecular subtype using RNA gene-expression data and artificial intelligence EBioMedicine. 2020 Nov; 61:103030. . View in PubMed
  • HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis Genome Biol. 2020 07 13; 21(1):171. . View in PubMed
  • ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization Sci Adv. 2020 07; 6(28):eaay2078. . View in PubMed
  • CRISPR artificial splicing factors Nat Commun. 2020 06 12; 11(1):2973. . View in PubMed
  • TET2 deficiency reprograms the germinal center B cell epigenome and silences genes linked to lymphomagenesis Sci Adv. 2020 06; 6(25):eaay5872. . View in PubMed
  • Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin DysregulationCancer Cell. 2020 04 13; 37(4):584-598. e11. . View in PubMed
  • Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data Nat Commun. 2020 03 03; 11(1):1173. . View in PubMed
  • Molecular Biology and Evolution of Cancer: From Discovery to Action Mol Biol Evol. 2020 02 01; 37(2):320-326. . View in PubMed
  • The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing Nat Cancer. 2020; 1:653-664. . View in PubMed
  • Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways Nat Commun. 2019 Sep 20; 10(1):4296. . View in PubMed
  • Ontogeny and Biology of Human Small Airway Epithelial Club Cells Am J Respir Crit Care Med. 2018 12 01; 198(11):1375-1388. . View in PubMed
  • TET2 Deficiency Causes Germinal Center Hyperplasia, Impairs Plasma Cell Differentiation, and Promotes B-cell Lymphomagenesis Cancer Discov. 2018 12; 8(12):1632-1653. . View in PubMed
  • Extracellular vesicles in DLBCL provide abundant clues to aberrant transcriptional programming and genomic alterations Blood. 2018 08 16; 132(7):e13-e23. . View in PubMed
  • Jak1 Integrates Cytokine Sensing to Regulate Hematopoietic Stem Cell Function and Stress HematopoiesisCell Stem Cell. 2017 10 05; 21(4):489-501. e7. . View in PubMed
  • Genetic and epigenetic heterogeneity and the impact on cancer relapse Exp Hematol. 2017 10; 54:26-30. . View in PubMed
  • Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia Nat Med. 2016 07; 22(7):792-9. . View in PubMed
  • A benchmark for RNA-seq quantification pipelines Genome Biol. 2016 Apr 23; 17:74. . View in PubMed
  • Genetic and epigenetic heterogeneity in acute myeloid leukemia Curr Opin Genet Dev. 2016 02; 36:100-6. . View in PubMed
  • Clinical Genomics: Challenges and Opportunities Crit Rev Eukaryot Gene Expr. 2016; 26(2):97-113. . View in PubMed
  • Correction: Tissue elasticity regulated tumor gene expression: implication for diagnostic biomarkers of primitive neuroectodermal tumor PLoS One. 2015; 10(5):e0128504. . View in PubMed
  • Dynamic evolution of clonal epialleles revealed by methclone Genome Biol. 2014 Sep 27; 15(9):472. . View in PubMed
  • Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures Nat Commun. 2014 Sep 25; 5:5125. . View in PubMed
  • Detecting and correcting systematic variation in large-scale RNA sequencing data Nat Biotechnol. 2014 Sep; 32(9):888-95. . View in PubMed
  • Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study Nat Biotechnol. 2014 Sep; 32(9):915-925. . View in PubMed
  • The pivotal regulatory landscape of RNA modifications Annu Rev Genomics Hum Genet. 2014; 15:127-50. . View in PubMed
  • Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers J Clin Invest. 2013 Nov; 123(11):4935-44. . View in PubMed
  • Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia Nat Genet. 2013 Mar; 45(3):290-4. . View in PubMed
  • Mandarin fish caveolin 1 interaction with major capsid protein of infectious spleen and kidney necrosis virus and its role in early stages of infection J Virol. 2013 Mar; 87(6):3027-38. . View in PubMed
  • An optimized algorithm for detecting and annotating regional differential methylation BMC Bioinformatics. 2013; 14 Suppl 5:S10. . View in PubMed
  • methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles Genome Biol. 2012 Oct 03; 13(10):R87. . View in PubMed
  • Tyrosine phosphorylation modulates store-operated calcium entry in cultured rat epididymal basal cells J Cell Physiol. 2011 Apr; 226(4):1069-73. . View in PubMed
  • Sodium coupled bicarbonate influx regulates intracellular and apical pH in cultured rat caput epididymal epithelium PLoS One. 2011; 6(8):e22283. . View in PubMed
  • Functional studies of acid transporter in cultured rat epididymal cell Fertil Steril. 2010 May 15; 93(8):2744-9. . View in PubMed
  • Stimulating effects of dopamine on chloride transport across the rat caudal epididymal epithelium in culture Biol Reprod. 2009 Jan; 80(1):13-23. . View in PubMed
  • Outreach clinic experiment extends care with paramedics Hospitals. 1977 Jan 01; 51(1):77-80. . View in PubMed
  • Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution Biochem Biophys Res Commun. 1975 Oct 27; 66(4):1173-9. . View in PubMed
  • Digitoxin metabolism by rat liver microsomes Biochem Pharmacol. 1975 Sep 01; 24(17):1639-41. . View in PubMed
  • The amino acid sequence of Neurospora NADP-specific glutamate dehydrogenasePeptic and chymotryptic peptides and the complete sequence. Biochem J. 1975 Sep; 149(3):757-73. . View in PubMed

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