Zechen Chong

Zechen Chong
Assistant Professor

Scientist (C), Informatics Institute , School of Medicine
Associate Scientist (C), Minority Health & Research Center , General Clinical Research Center
Associate Scientist (C), Center for Clinical and Translational Science (CCTS) , General Clinical Research Center
Assistant Professor (P), Genetics , Academic Joint Departments

Selected Publications

Academic Article

Year	Title	Altmetric
2023	Gene Fusion Detection and Characterization in Long-Read Cancer Transcriptome Sequencing Data with FusionSeeker. Cancer Research. 83:28-33. 2023
2022	B-assembler: a circular bacterial genome assembler. BMC Genomics. 23. 2022
2022	Selective suppression of melanoma lacking IFN-γ pathway by JAK inhibition depends on T cells and host TNF signaling. Nature Communications. 13. 2022
2022	Protein arginine methyltransferase 1 in the generation of immune megakaryocytes: A perspective review. Journal of Biological Chemistry. 298. 2022
2022	Reduced sister chromatid cohesion acts as a tumor penetrance modifier. PLoS Genetics. 18. 2022
2022	DeBreak: Deciphering the exact breakpoints of structural variations using long sequencing reads 2022
2022	Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants 2022
2021	Accurate long-read de novo assembly evaluation with Inspector. Genome Biology. 22. 2021
2021	RNF2 ablation reprograms the tumor-immune microenvironment and stimulates durable NK and CD4⁺ T-cell-dependent antitumor immunity 2021
2021	Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 372. 2021
2021	ClipSV: Improving structural variation detection by read extension, spliced alignment and tree-based decision rules. NAR Genomics and Bioinformatics. 3. 2021
2021	Scalable de Novo Genome Assembly Using a Pregel-Like Graph-Parallel System. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 18:731-744. 2021
2020	Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (Nature Communications, (2020), 11, 1, (4748), 10.1038/s41467-020-18151-y). Nature Communications. 11. 2020
2020	Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications. 11. 2020
2020	Sex differences in oncogenic mutational processes. Nature Communications. 11. 2020
2020	Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics. 52:306-319. 2020
2020	Pan-cancer analysis of whole genomes. Nature. 578:82-93. 2020
2020	De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. 2020
2020	The effects of common structural variants on 3D chromatin structure. BMC Genomics. 21. 2020
2020	MRLR: Unraveling high-resolution meiotic recombination by linked reads. Bioinformatics. 36:10-16. 2020
2020	Ozone and Particulate Matter Exposure and Alzheimer's Disease: A Review of Human and Animal Studies. Journal of Alzheimer's Disease. 76:807-824. 2020
2019	Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10. 2019
2019	Human-specific tandem repeat expansion and differential gene expression during primate evolution. 2019
2019	Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell. 176:1310-1324.e10. 2019
2018	In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer. Nature Communications. 9. 2018
2018	Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biology. 19. 2018
2018	Identification of meiotic recombination through gamete genome reconstruction using whole genome linked-reads 2018
2018	Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Human Mutation. 39:939-946. 2018
2018	Regenerative potential of neonatal porcine hearts. Circulation. 138:2809-2816. 2018
2018	Structural variant breakpoint detection with novoBreak. Methods in Molecular Biology. 1833:129-141. 2018
2017	A murine preclinical syngeneic transplantation model for breast cancer precision medicine. Science Advances. 3. 2017
2017	Integrated genomic and molecular characterization of cervical cancer. Nature. 543:378-384. 2017
2017	An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell. 168:830-842.e7. 2017
2017	A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Systems. 5:485-497.e3. 2017
2016	NovoBreak: Local assembly for breakpoint detection in cancer genomes. Nature Methods. 14:65-67. 2016
2016	Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types. BMC Genomics. 17. 2016
2016	Functional annotation of rare gene aberration drivers of pancreatic cancer. Nature Communications. 7. 2016
2016	Single-cell isolation by a modular single-cell pipette for RNA-sequencing 2016
2015	Identification of variant-specific functions of PIK3CA by rapid phenotyping of rare mutations. Cancer Research. 75:5341-5354. 2015
2015	TransVar: A multilevel variant annotator for precision genomics. Nature Methods. 12:1002-1003. 2015
2015	A global reference for human genetic variation. Nature. 526:68-74. 2015
2015	An integrated map of structural variation in 2,504 human genomes. Nature. 526:75-81. 2015
2015	ClinSeK: A targeted variant characterization framework for clinical sequencing 2015
2015	Clinical actionability enhanced through deep targeted sequencing of solid tumors 2015
2015	A global reference for human genetic variation. Nature. 526:68-74. 2015
2015	Genome-wide 5-hydroxymethylcytosine modification pattern is a novel epigenetic feature of globozoospermia. Oncotarget. 6:6535-6543. 2015
2014	Towards accurate characterization of clonal heterogeneity based on structural variation. BMC Bioinformatics. 15. 2014
2014	Trrap-dependent histone acetylation specifically regulates cell-cycle gene transcription to control neural progenitor fate decisions. Cell Stem Cell. 14:632-643. 2014
2014	Redox-Active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism. Nucleic Acids Research. 42:1593-1605. 2014
2014	Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination. Cell Research. 24:532-541. 2014
2013	The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster. Molecular Biology and Evolution. 30:2699-2708. 2013
2013	Pseudo-Sanger sequencing: Massively parallel production of long and near error-free reads using NGS technology. BMC Genomics. 14. 2013
2013	Ascorbic acid enhances tet-mediated 5-methylcytosine oxidation and promotes DNA demethylation in mammals. Journal of the American Chemical Society. 135:10396-10403. 2013
2013	Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism. Nucleic Acids Research. gkt1090-gkt1090. 2013
2012	Rainbow: An integrated tool for efficient clustering and assembling RAD-seq reads. Bioinformatics. 28:2732-2737. 2012
2011	Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data 2011