Publications
Full list of publications can be found at Google Scholar
*: First Authors; #: Corresponding Authors
Selected
![Identifying predictors of glioma evolution from longitudinal sequencing](https://www.science.org/cms/asset/9a45e350-fd65-4c7f-a78b-0c9c7764e6eb/stm.2023.15.issue-716.largecover.jpg)
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](https://ars.els-cdn.com/content/image/1-s2.0-S0092867417X00251-cov200h.gif)
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](https://upload.wikimedia.org/wikipedia/en/b/bf/Nature_Communications_-_Journal_Cover.jpg)
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
2023
![Adaptive DNA amplification of synthetic gene circuit opens a way to overcome cancer chemoresistance](https://www.pnas.org/cms/asset/dc351847-695d-465d-8347-32e00fe78d43/pnas.2023.120.issue-49.largecover.png)
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](https://www.science.org/cms/asset/9a45e350-fd65-4c7f-a78b-0c9c7764e6eb/stm.2023.15.issue-716.largecover.jpg)
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](https://onlinelibrary.wiley.com/cms/asset/26681dff-d0cd-4649-bfd2-06cb96cb08a6/bpa.v33.4.cover.gif)
Genomic profiling and prognostic factors of H3 K27M-mutant spinal cord diffuse glioma
Brain Pathology
·
01 Jul 2023
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https://doi.org/10.1111/bpa.13153
![Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma](https://media.springernature.com/w184/springer-static/cover/journal/13073.jpg)
Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma
Genome Medicine
·
13 Mar 2023
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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](https://www.science.org/cms/asset/1528b7c2-51c2-4c18-ae72-12c2743055c9/sciadv.2023.9.issue-1.largecover.jpg)
scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors
Science Advances
·
06 Jan 2023
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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
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20 Nov 2022
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https://doi.org/10.1007/s44178-022-00014-9
2021
![Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors](https://upload.wikimedia.org/wikipedia/en/b/bf/Nature_Communications_-_Journal_Cover.jpg)
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
![Long-Term Succession Shows Interspecies Competition of <i>Geobacter</i> in Exoelectrogenic Biofilms](https://pubs.acs.org/cms/10.1021/esthag.2021.55.issue-21/asset/183f9f04-7018-f9f0-3701-3f9f04370183/esthag.2021.55.issue-21.largecover.jpg)
Long-Term Succession Shows Interspecies Competition of Geobacter in Exoelectrogenic Biofilms
Environmental Science & Technology
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02 Nov 2021
·
https://doi.org/10.1021/acs.est.1c03010
![Metagenomic and bioanalytical insights into quorum sensing of methanogens in anaerobic digestion systems with or without the addition of conductive filter](https://ars.els-cdn.com/content/image/1-s2.0-S0048969720X00556-cov150h.gif)
Metagenomic and bioanalytical insights into quorum sensing of methanogens in anaerobic digestion systems with or without the addition of conductive filter
Science of The Total Environment
·
01 Apr 2021
·
https://doi.org/10.1016/j.scitotenv.2020.144509
![CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression](https://csdl-images.ieeecomputer.org/website/default-covers/trans/tb.jpg)
CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression
IEEE/ACM Transactions on Computational Biology and Bioinformatics
·
01 Jan 2021
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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](https://onlinelibrary.wiley.com/cms/asset/56dca4bf-7720-49ab-9b17-39bbffd131da/qub2.v8.3.cover.jpg)
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](https://upload.wikimedia.org/wikipedia/en/b/bf/Nature_Communications_-_Journal_Cover.jpg)
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](https://pubs.acs.org/cms/10.1021/esthag.2020.54.issue-7/asset/esthag.2020.54.issue-7.largecover-2.jpg)
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](https://ars.els-cdn.com/content/image/1-s2.0-S1672022919X00078-cov150h.gif)
Deciphering Brain Complexity Using Single-cell Sequencing
Genomics, Proteomics & Bioinformatics
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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](https://ars.els-cdn.com/content/image/1-s2.0-S0092867417X00251-cov200h.gif)
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.
![Real-Time Imaging Revealed That Exoelectrogens from Wastewater Are Selected at the Center of a Gradient Electric Field](https://pubs.acs.org/cms/10.1021/esthag.2018.52.issue-15/asset/17e92854-0a17-9285-50a1-e9285450a17e/esthag.2018.52.issue-15.largecover.jpg)
Real-Time Imaging Revealed That Exoelectrogens from Wastewater Are Selected at the Center of a Gradient Electric Field
Environmental Science & Technology
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07 Aug 2018
·
https://doi.org/10.1021/acs.est.8b01468
2017
![RNA Exosome Complex-Mediated Control of Redox Status in Pluripotent Stem Cells](https://ars.els-cdn.com/content/image/1-s2.0-S2213671116X00112-cov200h.gif)
RNA Exosome Complex-Mediated Control of Redox Status in Pluripotent Stem Cells
Stem Cell Reports
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10 Oct 2017
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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](https://ars.els-cdn.com/content/image/1-s2.0-S0043135415X00169-cov150h.gif)
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](https://ars.els-cdn.com/content/image/1-s2.0-S0048969715X0012X-cov150h.gif)
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](https://upload.wikimedia.org/wikipedia/commons/thumb/e/e7/PLOS_ONE_logo_2012.svg/600px-PLOS_ONE_logo_2012.svg.png)
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
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01 May 2015
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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
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01 Mar 2015
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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](https://pubs.acs.org/cms/10.1021/estlcu.2014.1.issue-5/asset/1460509c-ab14-0509-5ab1-60509c5ab146/estlcu.2014.1.issue-5.largecover.jpg)
An Ionic Liquid Facilitates the Proliferation of Antibiotic Resistance Genes Mediated by Class I Integrons
Environmental Science & Technology Letters
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13 May 2014
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https://doi.org/10.1021/ez500103v
![Persistence of Extracellular DNA in River Sediment Facilitates Antibiotic Resistance Gene Propagation](https://pubs.acs.org/cms/10.1021/esthag.2014.48.issue-1/asset/1458c842-2214-8c84-e221-58c842e22145/esthag.2014.48.issue-1.largecover.jpg)
Persistence of Extracellular DNA in River Sediment Facilitates Antibiotic Resistance Gene Propagation
Environmental Science & Technology
·
07 Jan 2014
·
https://doi.org/10.1021/es404280v