Publications
Full list of publications can be found at Google Scholar
*: First Authors; #: Corresponding Authors
Selected

Identifying predictors of glioma evolution from longitudinal sequencing
Science Translational Medicine
·
04 Oct 2023
·
doi:10.1126/scitranslmed.adh4181
We portrayed the evolution landscape of three subtypes of adult diffuse gliomas, and identified early predictors of glioma evolution, including MYC activation that promoted hypermutation after temozolomide treatment.

Mutational Landscape of Secondary Glioblastoma Guides MET-Targeted Trial in Brain Tumor
Cell
·
29 Nov 2018
·
https://doi.org/10.1016/j.cell.2018.09.038
We discovered MET exon 14 skipping enriched in secondary glioblastomas, which activated MET signaling and brought vulnerability to MET-targeted therapy as demonstrated in pre-clinical models and a clinical trial.

MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas
Nature Communications
·
04 Aug 2020
·
https://doi.org/10.1038/s41467-020-17717-0
We identified multiple novel MGMT fusions in temozolomide-treated recurrent gliomas, and demonstrated that they contribute to temozolomide resistance.
All
2025

Proteogenomic Profiling Reveals Small ORFs and Functional Microproteins in Activated T Cells
Molecular & Cellular Proteomics
·
04 Feb 2025
·
doi:10.1016/j.mcpro.2025.100914
2024

Genetic and microenvironmental evolution of colorectal liver metastases under chemotherapy
Cell Reports Medicine
·
04 Dec 2024
·
doi:10.1016/j.xcrm.2024.101838
2023

Adaptive DNA amplification of synthetic gene circuit opens a way to overcome cancer chemoresistance
Proceedings of the National Academy of Sciences
·
05 Dec 2023
·
https://doi.org/10.1073/pnas.2303114120
We found DNA amplification as a driver of drug resistance, and proposed targeting the amplified DNA via triplex forming oligonucleotides (TFOs).

Identifying predictors of glioma evolution from longitudinal sequencing
Science Translational Medicine
·
04 Oct 2023
·
doi:10.1126/scitranslmed.adh4181
We portrayed the evolution landscape of three subtypes of adult diffuse gliomas, and identified early predictors of glioma evolution, including MYC activation that promoted hypermutation after temozolomide treatment.

Genomic profiling and prognostic factors of H3 K27M-mutant spinal cord diffuse glioma
Brain Pathology
·
01 Jul 2023
·
https://doi.org/10.1111/bpa.13153

Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma
Genome Medicine
·
13 Mar 2023
·
https://doi.org/10.1186/s13073-023-01165-8

scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors
Science Advances
·
06 Jan 2023
·
https://doi.org/10.1126/sciadv.abp8901
2022
MET fusions and splicing variants convergently define a subgroup of glioma sensitive to MET inhibitors
Holistic Integrative Oncology
·
20 Nov 2022
·
https://doi.org/10.1007/s44178-022-00014-9
2021

Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors
Nature Communications
·
18 Nov 2021
·
https://doi.org/10.1038/s41467-021-27017-w

CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression
IEEE/ACM Transactions on Computational Biology and Bioinformatics
·
01 Jan 2021
·
doi:10.1109/TCBB.2019.2944827
We developed a computational method to infer copy number alterations from transcriptomic data of human cancers.
2020

CELLO: a longitudinal data analysis toolbox untangling cancer evolution
Quantitative Biology
·
01 Sep 2020
·
https://doi.org/10.1007/s40484-020-0218-1

MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas
Nature Communications
·
04 Aug 2020
·
https://doi.org/10.1038/s41467-020-17717-0
We identified multiple novel MGMT fusions in temozolomide-treated recurrent gliomas, and demonstrated that they contribute to temozolomide resistance.

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure
Environmental Science & Technology
·
07 Apr 2020
·
https://doi.org/10.1021/acs.est.9b04116
We found that when the water microbiome was exposed to an ionic liquid, [BMIm][PF6], the resistome was enriched within 24 hours, long before the community strucutre was altered.
2019

Deciphering Brain Complexity Using Single-cell Sequencing
Genomics, Proteomics & Bioinformatics
·
01 Aug 2019
·
https://doi.org/10.1016/j.gpb.2018.07.007
We summarized the technologies and computational methods to analyze single cell sequencing data, as well as their application in studying brain diseases.
2018

Mutational Landscape of Secondary Glioblastoma Guides MET-Targeted Trial in Brain Tumor
Cell
·
29 Nov 2018
·
https://doi.org/10.1016/j.cell.2018.09.038
We discovered MET exon 14 skipping enriched in secondary glioblastomas, which activated MET signaling and brought vulnerability to MET-targeted therapy as demonstrated in pre-clinical models and a clinical trial.
2017

RNA Exosome Complex-Mediated Control of Redox Status in Pluripotent Stem Cells
Stem Cell Reports
·
10 Oct 2017
·
http://dx.doi.org/10.1016/j.stemcr.2017.08.024
2015

Prevalence and proliferation of antibiotic resistance genes in two municipal wastewater treatment plants
Water Research
·
15 Nov 2015
·
https://doi.org/10.1016/j.watres.2015.09.010

Fate and proliferation of typical antibiotic resistance genes in five full-scale pharmaceutical wastewater treatment plants
Science of the Total Environment
·
01 Sep 2015
·
https://doi.org/10.1016/j.scitotenv.2015.05.046

Enhanced Horizontal Transfer of Antibiotic Resistance Genes in Freshwater Microcosms Induced by an Ionic Liquid
PLOS ONE
·
07 May 2015
·
https://doi.org/10.1371/journal.pone.0126784
Occurrence of sulfonamide-, tetracycline-, plasmid-mediated quinolone- and macrolide-resistance genes in livestock feedlots in Northern China
Environmental Science and Pollution Research
·
01 May 2015
·
https://doi.org/10.1007/s11356-014-3905-5
Occurrence and distribution of sulfonamides, tetracyclines, quinolones, macrolides, and nitrofurans in livestock manure and amended soils of Northern China
Environmental Science and Pollution Research
·
01 Mar 2015
·
https://doi.org/10.1007/s11356-014-3632-y
2014

An Ionic Liquid Facilitates the Proliferation of Antibiotic Resistance Genes Mediated by Class I Integrons
Environmental Science & Technology Letters
·
13 May 2014
·
https://doi.org/10.1021/ez500103v

Persistence of Extracellular DNA in River Sediment Facilitates Antibiotic Resistance Gene Propagation
Environmental Science & Technology
·
07 Jan 2014
·
https://doi.org/10.1021/es404280v