0710Z1-基因组学
0710J3-生物信息学
071007-遗传学

医学基因组
测序技术
生物信息学

1999-09--2002-07   北京大学   博士
1991-09--1996-07   北京医科大学   本科

   

2023-05~2024-05,中国科学院北京基因组研究所（国家生物信息中心）, 研究员
2016-01~2023-05,中国科学院北京基因组研究所（国家生物信息中心）, 副研究员
2012-06~2015-12,中国科学院北京基因组研究所, 助理研究员
2010-03~2012-05,中国科学院北京基因组研究所, 博后
2002-08~2010-02,本元正阳基因技术有限责任公司, 经理
1996-09~1999-08,北京大学人民医院, 住院医师

   

（1） Approaching an error-free diploid human genome using a support-based validation framework, The Innovation, 2026, 第 17 作者  通讯作者
（2） A complete diploid human genome benchmark for personalized genomics, Cell, 2026, 第 43 作者
（3） Filling the holes in whole genomes: A vision for personalized genomics from telomere to telomere, Cell, 2026, 第 3 作者
（4） Genotype-driven variations in lncRNA expression underlie predisposition to high-grade serous ovarian cancer, Journal of Advanced Research, 2025, 第 22 作者  通讯作者
（5） T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese, Genomics, Proteomics & Bioinformatics, 2023, 第 33 作者  通讯作者
（6） Enhanced intestinal protein fermentation in schizophrenia, BMC MEDICINE, 2022, 第 10 作者  通讯作者
（7） Intestinal butyrate-metabolizing species contribute to autoantibody production and bone erosion in rheumatoid arthritis., Science Advances, 2022, 第 1 作者
（8） Gut lactate-producing bacteria promote CD4 T cell recovery on Anti-retroviral therapy in HIV-infected patients, COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2021, 第 16 作者  通讯作者
（9） Complete sequences of two new KPC-harbouring plasmids in Klebsiella pneumoniae ST11 strains in China, JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, 2021, 第 8 作者
（10） A fine-scale map of genome-wide recombination in divergent Escherichia coli population, Briefings in Bioinformatics, 2021, 第 1 作者
（11） Genetic factors related to the widespread dissemination of ST11 extensively drug-resistant carbapenemase-producing Klebsiella pneumoniae strains within hospital, Genetic factors related to the widespread dissemination of ST11 extensively drug-resistant carbapenemase-producing Klebsiella pneumoniae strains within hospital, CHINESE MEDICAL JOURNAL, 2020, 第 9 作者
（12） Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients, GENOMICS, PROTEOMICS & BIOINFORMATICS, 2020, 第 6 作者
（13） The bacterial RNA ligase RtcB accelerates the repair process of fragmented rRNA upon releasing the antibiotic stress, The bacterial RNA ligase RtcB accelerates the repair process of fragmented rRNA upon releasing the antibiotic stress, SCIENCE CHINA Life Sciences, 2020, 第 7 作者  通讯作者
（14） Genomic characterization of an emerging Enterobacteriaceae species: the first case of co-infection with a typical pathogen in a human patient, BMC GENOMICS, 2020, 第 12 作者  通讯作者
（15） Genomic characterization of an emerging Enterobacteriaceae species for the first case of human infection in cooperation with a typical pathogen., BMC Genomics, 2020, 第 1 作者  通讯作者
（16） A quasi-paired cohort strategy reveals the impaired detoxifying function of microbes in the gut of autistic children, SCIENCE ADVANCES, 2020, 第 12 作者  通讯作者
（17） Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics, MSYSTEMS, 2019, 第 9 作者  通讯作者
（18） Inflammatory responses relate to distinct bronchoalveolar lavage lipidome in community-acquired pneumonia patients: a pilot study, RESPIRATORY RESEARCH, 2019, 第 9 作者  通讯作者
（19） Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients, Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients, GENOMICS, 2019, 第 6 作者  通讯作者
（20） Spatial coordination in a mutually beneficial bacterial community enhances its antibiotic resistance, COMMUNICATIONS BIOLOGY, 2019, 第 5 作者
（21） Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes, BRIEFINGS IN BIOINFORMATICS, 2018, 第 5 作者
（22） Complete Genomic Analysis of a Kingdom-Crossing Klebsiella variicola Isolate, FRONTIERS IN MICROBIOLOGY, 2018, 第 9 作者  通讯作者
（23） Metabolic profiles in community-acquired pneumonia: developing assessment tools for disease severity, CRITICAL CARE, 2018, 第 5 作者
（24） Comparative Whole-Genomic Analysis of an Ancient L2 Lineage Mycobacterium tuberculosis Reveals a Novel Phylogenetic Clade and Common Genetic Determinants of Hypervirulent Strains, FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 2018, 第 4 作者
（25） Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder, NEUROPSYCHIATRIC DISEASE AND TREATMENT, 2018, 第 13 作者  通讯作者
（26） PGAP-X: extension on pan-genome analysis pipeline, BMC Genomics, 2018, 第 11 作者
（27） Streamline-based purification of bacterial samples from liquefied sputum utilizing microfluidics, LAB ON A CHIP, 2017, 第 6 作者  通讯作者
（28） GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes, BMC GENOMICS, 2017, 第 12 作者  通讯作者
（29） Complete nucleotide sequence of ph11, an inchi2 plasmid conferring multi-antibiotic resistance and multi-heavy metal resistance genes in a clinical klebsiella pneumoniae isolate, PLASMID, 2016, 第 3 作者
（30） A Pilot Study of Quantitative Loop-mediated Isothermal Amplification-guided Target Therapies for Hospital-acquired Pneumonia, A Pilot Study of Quantitative Loop-mediated Isothermal Amplification-guided Target Therapies for Hospital-acquired Pneumonia, 中华医学杂志：英文版, 2016, 第 11 作者
（31） An integrative and applicable phylogenetic footprinting framework for cis -regulatory motifs identification in prokaryotic genomes, BMC GENOMICS, 2016, 第 7 作者
（32） A Pilot Study of Quantitative Loop-mediated Isothermal Amplification-guided Target Therapies for Hospital-acquired Pneumonia, A Pilot Study of Quantitative Loop-mediated Isothermal Amplification-guided Target Therapies for Hospital-acquired Pneumonia, CHINESE MEDICAL JOURNAL, 2016, 第 11 作者
（33） Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology., Nucleic Acids Research, 2016, 第 5 作者
（34） Heteroresistance at the Single-Cell Level: Adapting to Antibiotic Stress through a Population-Based Strategy and Growth-Controlled Interphenotypic Coordination, MBIO, 2014, 第 2 作者
（35） Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections, GENOMICS, 2014, 第 2 作者
（36） Studies of the drug resistance response of sensitive and drug-resistant strains in a microfluidic system, INTEGRATIVE BIOLOGY, 2014, 第 2 作者
（37） Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks, MBIO, 2014, 第 1 作者
（38） Complete genome sequence of methicillin-sensitive Staphylococcus aureus containing a heterogeneic staphylococcal cassette chromosome element, SCIENCE CHINA Life Sciences, 2013, 第 6 作者
（39） 类SCC样甲氧西林敏感性金黄色葡萄球菌的基因组学分析, 中国科学: 生命科学, 2013, 第 6 作者
（40） Prevalence and characterization of plasmid-mediated blaEsBL with their genetic environment in Escherichia coli and Klebsiella pneumoniae in patients with pneumonia, Prevalence and characterization of plasmid-mediated blaEsBL with their genetic environment in Escherichia coli and Klebsiella pneumoniae in patients with pneumonia, 中华医学杂志：英文版, 2012, 第 3 作者
（41） Prevalence and characterization of plasmid-mediated bla_(ESBL) with their genetic environment in Escherichia coli and Klebsiella pneumoniae in patients with pneumonia, CHINESE MEDICAL JOURNAL, 2012, 第 3 作者
（42） Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-Mediated Isothermal Amplification, PLOS ONE, 2012, 第 1 作者
（43） Complete sequences of two new KPC-harboring plasmids in Klebsiella pneumoniae ST11 strains in China, JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, 第 8 作者

（1） 基因组学与精准医学, 上海交通大学出版社, 2017-01, 第 其他 作者

   

（1）AntigenLM: Structure-Aware DNA Language Modeling for Influenza   国际表征学习大会 ICLR 2026   2026-04-23
（2）整合赢未来健康在肠道   中国肠道大会   2021-05-28
（3）微生物基因组研究   2019年用户大会暨技术交流会   2019-10-11

现指导学生

羊阳  博士研究生  0710Z1-基因组学  

刘馨凝  博士研究生  0710J3-生物信息学  

陈雨  硕士研究生  0710J3-生物信息学  

阳益吉  硕士研究生  0710J3-生物信息学  

黄濯  博士研究生  0710J3-生物信息学  

余欣瑶  硕士研究生  0710J3-生物信息学  

段杨彬  硕士研究生  0710J3-生物信息学  

张瑞阳  博士研究生  0710J3-生物信息学  

王辉军  硕士研究生  1001Z1-精准医学  

李兴雷  硕士研究生  0710J3-生物信息学  

罗喻榕  博士研究生  0710J3-生物信息学