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Jingfa Xiao
Jingfa Xiao

Professor

Administration

Email: xiaojf (AT) big.ac.cn

Tel: +86 108409-7443

PROFESSIONAL EXPERIENCE

  • Professor, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, China, 2019−Present

  • Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2012−2019

  • Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2007−2012

  • Postdoctoral Associate, Department of Chistry, Utah University, United States of America, 2005−2007

  •  Postdoctoral Associate, Institute of Materia Medica, Chinese Academy of Medical Sciences, 2003−2005


EDUCATION

  • PhD in Computational Chemistry and Biology, Jilin University, China, 1998−2003

  • BS in Department of Biology, Sichuan University, China, 1991−1995


RESEARCH INTERESTS

  • Integrated analysis of cancer single-cell transcriptome data and resource construction

  • Construction of a knowledge graph for multi-omics association studies

  • Establish the microbial pan-genome annotation and data analysis platform


PROJECTS & RESOURCES

  • PGAP2: a comprehensive toolkit for prokaryotic pan-genome analysis. https://github.com/bucongfan/PGAP2

  • PlantPan: a comprehensive multi-species plant pan-genome database. https://ngdc.cncb.ac.cn/plantpan

  • scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies. https://ngdc.cncb.ac.cn/sctwas

  • CVD Atlas: a multi-omics database of cardiovascular disease. https://ngdc.cncb.ac.cn/cvd

  • CCLHunter: an efficient toolkit for cancer cell line authentication. https://ngdc.cncb.ac.cn/cclhunter/home

  • ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics. https://ngdc.cncb.ac.cn/propan

  • TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies. https://ngdc.cncb.ac.cn/twas

  • TSomVar: a tumor-only somatic and germline variant identification method with random forest. https://ngdc.cncb.ac.cn/biocode/tools/BT007299.

  • CancerSCEM: a database of single-cell expression maps across various human cancers. https://ngdc.cncb.ac.cn/cancerscem

  • RefRGim: an intelligent reference panel reconstruction method for genotype imputation. https://github.com/shishuo16/RefRGim

  • PADS Arsenal: a database of prokaryotic defense systems related genes. https://bigd.big.ac.cn/padsarsenal

  • NucMap: a database of genome-wide nucleosome positioning map across species. https://bigd.big.ac.cn/nucmap

  • VCGDB: a dynamic genome database of the Chinese population. http://vcg.cbi.ac.cn/index.html

  • MTD: a mammalian transcriptomic database to explore gene expression regulation. http://mtd.cbi.ac.cn/

  • WikiCell: a unified resource platform for human transcriptomics research. http://wikicell.big.ac.cn/index.php/Human

  • PGAP: pan-genomes analysis pipeline. https://sourceforge.net/projects/pgap/files/

  • PanGP: a tool for quickly analyzing bacterial pan-genome profiles. https://pangp.zhaopage.com/faq.html

  • GAAP: genome-organization-framework-assisted assembly pipeline for the prokaryotic genome. http://gaap.big.ac.cn/

  • PGAP-X: extension on pan-genome analysis pipeline. https://pgapx.zhaopage.com/

  • PGAweb: a web server for bacterial pan-genome analysis. http://pgaweb.vlcc.cn/


ACADEMIC ACTIVITIES

  • Academic Editor: Genomics, Proteomics & Bioinformatics 2012 -

  • Academic Editor: Frontiers of Data & Computing 2019 -

  • Academic Editor: MDPI Biology 2021 –

  • Academic Editor: Genomics 2024 -

  • Academic Editor: China Science & Technology Resources Review 2018-

  • Associate Editor: Frontiers in Plant Science 2016 - 2018

  • Academic Editor: PLoS ONE 2013 - 2018

  • Review Editor: Peer J 2013 - 2018

  • Journal Reviewer: National Science Review, Advanced Science, Alzheimer's & Dementia: The Journal of the Alzheimer's Association, Archives of Virology, Briefings in Bioinformatics, Bioinformatics, BMC Genomics, BMC Plant Biology, BMC Bioinformatics, BMC Systems Biology, Biophysics Reports, Biosafety and Health, Cell Genomics, Cell Reports Methods, Chinese Bulletin of Life Sciences, Chinese Medical Journal, Chinese Medical Sciences Journal. Communications Biology, Computers in Biology and Medicine, Database, Evolutionary Bioinformatics, European Urology, Frontiers in Genetics, Frontiers in Pharmacology, Frontiers in Microbiology, Genomics Proteomics & Bioinformatics, Genome Biology, Genomics, Gene, GigaScience, Infection Genetics and Evolution, Innovation Life, International Journal of Biomathematics, iScience, Journal of Chemical Information and Modeling, Journal of Genetics and Genomics, Journal of Medicinal Chemistry, Journal of Translational Medicine, Molecular Therapy Nucleic Acids, Microbiology Spectrum, Molecular Genetics and Genomics, National Science Review, Nature Communications, Nucleic Acids Research, Patterns, PLoS Computational Biology, PLoS ONE, Scientific Reports, Scientific Data, Science Bulletin

  • Grant Referee: NSFC, CPSF, BSNF, Austrian Science Fund

  • Membership: Genetics Society of China, Computational Systems Biology Society of ORSC, Technical Committee on Biometric and Quality Control, Beijing Bioinformatics Research Society


PUBLICATIONS

  1. Gao H#, Bu C#, Zheng S#, Mai J#, Wang J, Tang R, Fan Z, Zeng J*, Li J*, Xiao J*, TWAS Atlas 2.0: an updated data resource for transcriptome-wide association studies. Nucleic Acids Research. 2026, 54:D1321-D1330.

  2. Ji X#, Qian Q#, Zhang H#, Cai Q#, Zhang K, Xiao J*, Jiang X*, Li M*, ResMicroDb: A comprehensive database and analysis platform for the human respiratory microbiome. Nucleic Acids Research. 2026, 54: D858-D870.

  3. Lei W#, Li C#, Zhou H#, Nie Z#, Wang A#, Pan Li P, Fan Z, Zhu R, Cheng H, Guo Y, Yue L, Jiang X, Gao R, Sheng Y, Niu H, Bahetibieke T, Zhang W, Zhao W, Xiao J*, Chen F*, TEDD: A Comprehensive Resource for Translation Efficiency Dynamics. Nucleic Acids Research. 2026, 54: D511-D521.

  4. Bao Y*, Zhang Z*, Zhao W*, Xiao J*, Song S*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2026. Nucleic Acids Research. 2026, 54:D28-D47.

  5. Meng X#, Nie Z#, Wang Q, Hu Y, Deng Y, Ai N, Huang Z, Li Y, Yuan Y, Xiao J, Zeng J*, Li G*, Jiang L*, TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution. Nucleic Acids Research. 2026, 54: D1658-D1671.

  6. Bu C#, Zhang H#, Zhang F#, Liang W, Gao H, Zhao J, Lv F, Xue R, Liu Q, Zhang Z, Jin Z*, Xiao J*, PGAP2: A Comprehensive Toolkit for Prokaryotic Pan-Genome Analysis Based on Fine-grained Feature Networks. Nature Communications. 2025,16:9865.

  7. Shang Y#, Zeng J#,*, Mai J, Xiao J*, Metabolic reprogramming landscape of pan-cancer by single-cell transcriptome data integration. Science Bulletin. 2025, 70:852-855.

  8. Zeng J#, Nie Z#, Shang Y#, Mai J#, Zhang Y, Yang Y, Xu C, Zhao J, Fan Z, Xiao J*, CancerSCEM 2.0: an updated data resource of single-cell expression map across various human cancers. Nucleic Acids Research. 2025, 53:D1278-D1286.

  9.  Mai J#, Qian Q#, Gao H#, Fan Z, Zeng J*, Xiao J*, scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies. Nucleic Acids Research. 2025, 53:D1195-D1204.

  10. Qian Q#, Xue R#, Xu C, Wang F, Zeng J, Xiao J*, CVD Atlas: a multi-omics database of cardiovascular disease. Nucleic Acids Research. 2025, 53:D1348-D1355.

  11. Luo J#, Zeng J#, Wang H#, Qian Q#, Li H, Chen Y, Xiu J, Fang R, Feng Z, Li Y*, Xiao J*, Wei W*, Characterization of Early Metastatic Subpopulations in Uveal Melanoma: Single-Cell Insights into SPP1+ Cells and their Interactions with Macrophages. Investigative Ophthalmology & Visual Science. 2025, 66(14):37.

  12. Xia Z#, Du Z#, Zhou X#, Jiang S#, Zhu T, Wang L, Chen F, Carvalho L, Zou M, Lo´pez-Lavalle L, Zhang X, Xu L, Wang Z, Chen M, Wang S, Li M, Li Y, Wang H, Liu S, Bao Y, Zhao L, Zhang C, Xiao J, Guo F, Shen X, Li H, Lu C, Qiao F, Ceballos H, Yan H, Qin X, Ma L, Zhang H, He S, Zhao W, Wan Y, Chen Y, Huang D, Li K, Liu B, Peng M, Zhang W, Muller B, Chen C*, Luo M, Xiao J*, Wang W*, Pan-genome and Haplotype Map of Cassava (Manihot esculenta Crantz) Provide Insights into Evolution of Its Photosynthesis, Storage Root Formation, and Cyanogenic Glycoside Metabolism. Molecular Plant. 2025,18:1047-1071.

  13. Jiang M#, Qian Q#, Lu M, Chen M, Fan Z, Shang Y, Bu C, Du Z, Song S, Zeng J*, Xiao J*, PlantPan: A comprehensive multi-species plant pan-genome database. The Plant Journal. 2025,122, e70144.

  14. Duan G, Zhang S, Tang B, Xiao J, Zhang Z, Cui P*, Yu J*, Zhao W*, Lineage-associated Human Divergently-Paired Genes (DPGs) Exhibit Regulatory Characteristics and Evolutionary Trends. Genomics, Proteomics & Bioinformatics. 2025, 23(4), qzaf058.

  15. Zhang S#, Chen X#, Jin E#, Wang A#, Chen T#, Zhang X, Zhu J, Dong L, Sun Y, Yu C, Zhou Y, Fan J, Chen H, Zhai S, Sun Y, Che Q, Xiao J, Song S, Zhang Z, Bao Y, Wang Y*, Zhao W*, The GSA Family in 2024: A Broadened Sharing Platform for Multi-Omics and Multimodal Data. Genomics, Proteomics & Bioinformatics. 2025, 23(4), qzaf072.

  16. Tang B, Wang Y, Zhang S, Zhang M, Kang H, Wang Y, Chen M, Tian D, Xu T, Li R, Hao L, Xiao J, Song S, Zhang Z, Bao Y, Zhao W*, National Genomics Data Center: Multi−omics data resources to support biodiversity conservation. Science & Technology Review. 2025, 43(13):52-62.

  17. Ma Y#, Zhao X#, Jia Y#, Han Z#, Yu C, Fan Z, Zhang Z, Xiao J, Zhao W, Bao Y*, Chen M*, The Updated Genome Warehouse: Enhancing Data Value, Security, and Usability to Address Data Expansion. Genomics, Proteomics & Bioinformatics. 2025, 23(1), qzaf010.

  18. Wang C#, Di Wei D#, Wei Z#, Yang D, Xing J, Wang Y, Wang X, Wang P, Ma G, Zhang X, Li H, Tang C, Hou P, Wang J, Gao R, Xie G, Li C, Ju Y, Wang P, Yue L, Zhao Y, Sheng Y, Xiao J, Niu H, Xu S, Yang H, Liu D, Duan B*, Bu D*, Tan G*, Chen F*, Cost-Effective DNA Storage System with DNA Movable Type. Advanced Science. 2025, 12:2411354.

  19. Bao Y*, Zhang Z*, Zhao W*, Xiao J*, Song S*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025. Nucleic Acids Research. 2025, 53:D30-D44.

  20. Nie Z#, Zhao Y#, Yu S#, Mai J, Gao H, Fan Z, Bao Y*, Li R*, Xiao J*, NucMap 2.0: an updated database of genome-wide nucleosome positioning map across species. Journal of Molecular Biology. 2024, 436:168655.

  21. Liu Y#, Liu J#, Zhang S, Wang J, Sun Z, Sun H, Yang Y, Zheng G, Huang Y, Li M, Zhang Z, Xiao J, Zeng C, Sun C*, Qu H*, Fang X*, A panel sequencing dataset of peripheral blood gene variations in Pan-cancer. Scientific Data. 2024, 11:805.

  22. Ji A#, Sui Y#, Xue X#, Ji X#, Shi W#, Shi Y#, Terkeltaub R, Dalbeth N, Takei R, Yan F, Sun M, Li M, Lu J, Cui L, Liu Z, Wang C, Li X, Han L, Fang Z, Sun W, Liang Y, He Y, Zheng G, Wang X, Wang J, Zhang H, Pang L, Qi H, Li Y, Cheng Z, Li Z, Xiao J, Zeng C, Merriman T*, Qu H*, Fang X*, Li C*, Novel genetic loci in early-onset gout derived from whole genome sequencing of an adolescent gout cohort. Arthritis & Rheumatology. 2025, 77(1):107-115.

  23. Bu C#, Zheng X#, Zhao X#, Xu T#, Bai X#, Jia Y, Chen M, Hao L, Xiao J, Zhang Z, Zhao W, Tang B*, Bao Y*, GenBase: A Nucleotide Sequence Database. Genomics, Proteomics & Bioinformatics. 2024, 22(3):qzae047.

  24. Tian D#, Xu T#, Kang H#, Luo H, Wang Y, Chen M, Li R, Ma L, Wang Z, Hao L, Tang B, Zou D, Xiao J, Zhao W, Bao Y, Zhang Z*, Song S*, Plant genomic resources at National Genomics Data Center assisting in data-driven breeding application. aBIOTECH. 2024, 5:94-106.

  25. Zhang H#, Shao C#, Wang J, Chu Y, Xiao J, Kang Y*, Zhang Z*, Combined study of gene expression and chromosome three-dimensional structure in Escherichia coli during growth process. Current Microbiology. 2024, 81:122.

  26. Jiang M, Chen M, Zeng J, Du Z*, Xiao J*, A comprehensive evaluation of three plant pan-genome construction strategies. Frontiers in Plant Science. 2024, 15:fpls.2024.1371222.

  27. Bao Y*, Zhang Z*, Zhao W*, Xiao J*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Research. 2024, 52:D18-D32.

  28. Li C#, Qian Q#, Yan C#, Lu M#, Li L#, Li P, Fan Z, Lei W, Shang K, Wang P, Wang J, Lu T, Huang Y, Yang H, Wei H, Han J, Xiao J*, Chen F*, HervD Atlas: A Curated Knowledgebase of Associations Between Human Endogenous Retroviruses and Diseases. Nucleic Acids Research. 2024, 52:D1315-D1326.

  29. Kang H#, Huang T#, Duan G#, Meng Y, Chen X, He S, Xia Z, Zhou X, Cao J, Tang B, Wang Z, Zhu J, Du Z, Sun Y, Zhang S, Xiao J, Tian W, Wang W*, Zhao W*, TCOD: an integrated resource for tropical crops. Nucleic Acids Research. 2024, 52:D1651-D1660.

  30. Xiao J, Yu J*, T2T-YAO, T2T-SHUN and more. Genomics, Proteomics & Bioinformatics. 2023, 21:1081-1082.

  31. Ma L#,*, Zou D#, Liu L#, Shireen H, Abbasi A, Bateman A, Xiao J, Zhao W, Bao Y, Zhang Z*, Database Commons: A Catalog of Worldwide Biological Databases. Genomics, Proteomics & Bioinformatics. 2023, 21:1054-1058.

  32. Meng Q#, Zhou Q#, Shi S#, Xiao J, Ma Q, Yu Y, Chen J, Kang Y*, VTwins: inferring causative microbial features from metagenomic data of limited samples. Science Bulletin. 2023, 68:2806-2816.

  33. Bu C#, Zheng X#, Mai J, Nie Z, Zeng J, Qian Q, Xu T, Sun Y, Bao Y*, Xiao J*, CCLHunter: an efficient toolkit for cancer cell line authentication. Computational and Structural Biotechnology Journal. 2023, 21:4675-4682.

  34. Mai J#, Lu M#, Gao Q, Zeng J*, Xiao J*, Transcriptome-wide association studies: recent advances in methods, applications and available databases. Communications Biology. 2023, 6:899.

  35. Wu Z#, Lu M#, Liu D#, Shi Y#, Ren J#, Wang S#, Jing Y, Yu Z, Liu Z, Yang Y, Xiao J, Belmonte J, Qu J*, Zhang W*, Ci W*, Liu G*, m6A-epitranscriptomic regulation of tissue homeostasis during primate aging. Nature Aging. 2023, 3:705–721.

  36. Lu M#, Zhang Y#, Yang F#, Mai J#, Gao Q, Shang Y, Qian Q, Jiang M, Zhang H, Liu J, Wang J, Zhang Z, Zhang Z, Zeng J*, Li J*, Xiao J*, TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies. Nucleic Acids Research. 2023, 51:D1179-D1187.

  37. Zhang Y#, Zhang H#, Zhang Z, Qian Q, Zhang Z*, Xiao J*, ProPan: A comprehensive database for profiling prokaryotic pan-genome dynamics. Nucleic Acids Research. 2023, 51:D767-D776.

  38. Jiang S#, Qian Q#, Zhu T#, Zong W, Shang Y, Jin T, Zhang Y, Chen M, Wu Z, Chu Y, Zhang R, Luo S, Jing W, Zou D, Bao Y, Xiao J*, Zhang Z*, Cell Taxonomy: a curated repository of cell types with multi-faceted characterization. Nucleic Acids Research. 2023, 51:D853-D860.

  39. Xue Y*, Bao Y*, Zhang Z*, Zhao W*, Xiao J*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023. Nucleic Acids Research. 2023, 51:D18-D28.

  40. Li Z#, Liu L#, Feng C#, Qin Y, Xiao J, Zhang Z*, Ma L*, LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. Nucleic Acids Research. 2023, 51:D186-D191.

  41. Duan G#, Wu G#, Chen X, Tian D, Li Z, Sun Y, Du Z, Hao L, Song S, Gao Y, Xiao J, Zhang Z, Bao Y, Tang B*, Zhao W*, HGD: an integrated homologous gene database across multiple species. Nucleic Acids Research. 2023, 51:D994-D1002.

  42. Shi S#, Wang Q#, Shang Y#, Bu C, Lu M, Jiang M, Zhang H, Yu S, Zeng J, Zhang Z, Du Z*, Xiao J*, TSomVar: a tumor-only somatic and germline variant identification method with random forest. Briefings in Bioinformatics. 2022, 23(5): bbac381.

  43. He L, Liu Q, Zhang B, Xiao J*, Jin Z*, Biomedical Applications Community Based on China High-Performance Computing Environment. CCF Transactions on High Performance Computing. 2022, 4:75-85.

  44. Zheng X#, Zong W#, Li Z#, Ma Y, Sun Y, Xiong Z, Wu S, Bu C, Du Z, Xiao J*, Bao Y*, CCAS: One-stop and comprehensive interpretation server for somatic cancer genome. Frontiers in Genetics. 2022, 13:956781.

  45. Wu C#, Zhang Z#, Kang C, Zhang Q, Zhu W, Zhang Y, Zhang H, Xiao J*, Jin M*, The C-terminal repeat units of SpaA mediate adhesion of Erysipelothrix rhusiopathiae to host cells and regulate its virulence. MDPI Biology. 2022, 11:1010.

  46. Zeng J#, Zhang Y#, Shang Y#, Mai J, Shi S, Lu M, Bu C, Zhang Z, Zhang Z, Li Y, Du Z, Xiao J*, CancerSCEM: A database of single-cell expression map across various human cancers. Nucleic Acids Research. 2022, 50: D1147-D1155.

  47. Xue Y*, Bao Y*, Zhang Z*, Zhao W*, Xiao J*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research. 2022, 50: D27-D38.

  48. Zhang Y#, Zou D#, Zhu T#, Xu T#, Chen M#, Niu G, Zong W, Pan R, Jing W, Sang J, Liu C, Xiong Y, Sun Y, Zhai S, Chen H, Zhao W, Xiao J, Bao Y, Hao L*, Zhang Z*, Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. Nucleic Acids Research. 2022, 50: D1016-D1024.

  49. Li R, Zhang X, Song S, Zou D, Xiao J, Zhao W, Zhang Z, Bao Y, Safety Management and Application of Genomics Data. Big Data Research. 2022, 8(1): 37-45.

  50. Shi S, Qian Q, Yu S, Wang Q, Wang J, Zeng J, Du Z*, Xiao J*, RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks. Briefings in Bioinformatics. 2021, 22(6):bbab326.

  51. Kang Y#, Yuan L#, Shi X#, Chu Y#, He Z#, Jia X, Lin Q, Ma Q, Wang J, Xiao J, Hu S, Gao Z*, Chen F*, Yu J*, A Fine-scale Map of Genome-wide Recombination in Population Divergence of Escherichia coli. Briefings in Bioinformatics. 2021, 22(4):bbaa335.

  52. Jiang M#, Bu C#, Zeng J, Du Z*, Xiao J*, Applications and challenges of high performance computing in genomics. CCF Transactions on High Performance Computing. 2021, 3:344-352.

  53. Teng X#, Li Q#, Li Z#, Zhang Y#, Niu G, Xiao J, Yu J*, Zhang Z*, Song S*, Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. Genomics, Proteomics & Bioinformatics. 2021,18:648-663.

  54. Zhang S#, Chen X#, Chen T#, Zhu J, Tang B, Wang A, Dong L, Zhang Z, Sun Y, Yu C, Zhai S, Sun Y, Chen H, Du Z, Xiao J, Zhang Z, Bao Y, Wang Y*, Zhao W*, Genome Sequence Archive for Human. Hereditas (Beijing). 2021, 43(10):988-993.

  55. Song S#, Ma L#, Zou D#, Tian D#, Li C#, Zhu J#, Chen M, Wang A, Ma Y, Li M, Teng X, Cui Y, Duan G, Zhang M, Jin T, Shi C, Du Z, Zhang Y, Liu C, Li R, Zeng J, Hao L, Jiang S, Chen H, Han D, Xiao J, Zhang Z*, Zhao W*, Xue Y*, Bao Y*, The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR. Genomics, Proteomics & Bioinformatics. 2021, 18:749-959.

  56. Xue Y*, Bao Y*, Zhang Z*, Zhao W*, Xiao J*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Research. 2021, 49: D18-D28.

  57. Li Z#, Liu L#, Jiang S, Li Q, Feng C, Du Q, Zou D, Xiao J, Zhang Z*, Ma L*, LncExpDB: an expression database of human long non-coding RNAs. Nucleic Acids Research. 2021, 49: D962-D968.

  58. Lyu W#, Meng Q#, Xiao J, Li J, Wang J, Qiu Z, Song X, Zhu H, Shao C, Chu Y, Zhou Q, Li T, Pierre R, Yu J, Han Y*, Kang Y*, Gut lactate-producing Bacteria Promote CD4 T Cell Recovery on Anti-retroviral Therapy in HIV-infected Patients, Computational and Structural Biotechnology Journal. 2021, 19:2928-2937.

  59. Gong Z, Zhu J, Li C, Jiang S, Ma L, Tang B, Zou D, Chen M, Sun Y, Song S, Zhang Z, Xiao J, Xue Y, Bao Y, Du Z*, Zhao W*, An online coronavirus analysis platform from the National Genomics Data Center, Zoological Research. 2020, 41(6): 705-708.

  60. Zhang Z*, Song S, Yu J, Zhao W, Xiao J, Bao Y, The Elements of Data Sharing. Genomics, Proteomics & Bioinformatics. 2020, 18:1-4.

  61. Zhang Z*, Zhao W*, Xiao J*, Bao Y*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in National Genomics Data Center Members and Partners, Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research. 2020, 48: D24-D33.

  62. Zhang Y, Zhang Z*, Zhang H, Zhao Y, Zhang Z, Xiao J*, PADS Arsenal: a database of prokaryotic defense systems related genes. Nucleic Acids Research. 2020, 48: D590-D598.

  63. Guan Y, Chen M, Ma Y, Du Z, Yuan N, Li Y, Xiao J*, Zhang Y*, Genome and Dual-RNA-Seq Data Analyses Reveal the Inter-action between Ilyonectria destructans CD-56 and Ginseng. Scientific Reports. 2020, 10:1586.

  64. Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang Z, Zhao W, Bao Y, Zhang Z, Wu J, Asmann Y*, Li R*, Xiao J*, NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Research. 2019, 47: D163-D169.

  65. Du Z, Ma L, Qu H, Chen W, Zhang B, Lu X, Weibo W, Sheng X, Sun Y, Li W, Lei M, Qi Q, Yuan N, Shi S, Zeng J, Wang J, Yang Y, Liu Q, Hong Y, Dong L, Zhang Z, Zou D, Wang Y, Song S, Liu F, Fang X, Chen H, Liu X, Xiao J*, Zeng C*, Whole genome analyses of Chinese population and the de novo assembly of a northern Han genome. Genomics, Proteomics & Bioinformatics. 2019, 17:229-247.

  66. Zhang Z*, Zhao W*, Xiao J*, Bao Y*, in BIG Data Center Members, Database Resources of the BIG Data Center in 2019. Nucleic Acids Research. 2019, 47: D8-D14.

  67. Tang B, Zhou Q, Dong L, Li W, Zhang X, Lan L, Zhai S, Xiao J, Zhang Z, Bao Y, Zhang Y, Wang G*, Zhao W*, iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Research. 2019, 47: D793-D800. 

  68. Chen X, Zhang Y, Zhang Z, Zhao Y, Sun C, Yang M, Wang J, Liu Q, Zhang B, Chen M, Yu J, Wu J, Jin Z*, Xiao J*, PGAweb: a web server for bacterial pan-genome analysis. Frontiers in Microbiology. 2018, 9:fmicb.2018.01910.

  69. Zhao Y, Sun C, Zhao D, Zhang Y, You Y, Jia X, Yang J, Wang L, Wang J, Fu H, Kang Y, Chen F, Yu J*, Wu J, Xiao J*, PGAP-X: Extension on pan-genome analysis pipeline. BMC Genomics. 2018, 19 Suppl 1:36.

  70. Shi S, Yuan N, Yang M, Du Z, Wang J, Sheng X, Wu J*, Xiao J*, Comprehensive assessment of genotype imputation performance. Human Heredity, 2017/2018, 83:107-116.

  71. Song S, Teng X, Xiao J*, Database resources of the reference genome and genetic variation maps for the Chinese population. Hereditas. 2018, 4011:1048-1054.

  72. Li R, Liang F, Li W, Zou D, Sun S, Zhao Y, Zhao W, Bao Y, Xiao J, Zhang Z, MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Research. 2018, 46: D288-D295.

  73. Song S, Tian D, Li C, Tang B, Dong L, Xiao J, Bao Y, Zhao W, He H, Zhang Z, Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids Research. 2018, 46: D121-D126.  

  74. Zhang Z*, Zhao W*, Xiao J*, Bao Y*, in BIG Data Center Members, Database Resources of the BIG Data Center in 2018. Nucleic Acids Research. 2018, 46: D14-D20.

  75. Sang J, Wang Z, Li M, Cao J, Niu G, Xia L, Zou D, Wang F, Xu X, Han X, Fan J, Yang Y, Zuo W, Zhang Y, Zhao W, Bao Y, Xiao J, Hu S, Hao L, Zhang Z, ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Research. 2018, 46: D121-D126.

  76. Sheng X, Wu J, Sun Q, Xian F, Li X, Sun M, Fang W, Chen M, Yu J*, Xiao J*, MTD: A mammalian transcriptomic database to explore gene expression regulation. Briefings in Bioinformatics. 2017, 18:28-36.

  77. Su W, Li X, Chen M, Dai W, Sun S, Wang S, Sheng X, Sun S, Gao C, Hou A, Zhou Y, Sun B, Gao F, Xiao J, Zhang Z, Jiang C, Synonymous Codon Usage Analysis of Hand, Foot and Mouth Disease Viruses: a Comparative Study on Coxsackievirus A6, A10, A16, and Enterovirus 71 from 2008 to 2015. Infection, Genetics and Evolution. 2017, 53: 212-217.

  78. Zhang Z*, Zhao W*, Xiao J*, et al, The BIG Data Center: from deposition to integration to translation. Nucleic Acids Research. 2017, 45: D18-D24.

  79. Wang Y, Song F, Zhu J, Zhang S, Yang Y, Chen T, Tang B, Dong L, Ding N, Zhang Q, Bai Z, Dong X, Chen H, Sun M, Zhai S, Sun Y, Yu L, Lan L, Xiao J, Fang X*, Lei H*, Zhang Z*, Zhao W*, GSA: Genome Sequence Archive. Genomics, Proteomics & Bioinformatics. 2017, 15:14-18.

  80. Yuan L, Yu Y, Zhu Y, Li Y, Li C, Li R, Ma Q, Siu G, Yu Y, Xiao J*, Kang Y*, GAAP: Genome-organization-framework-Assisted Assembly Pipeline for the Prokaryotic Genome. BMC Genomics. 2017, 18Suppl 1:952.

  81. Jin J, Li R, Jiang C, Zhang R, Ge X, Liang F, Sheng X, Dai W, Chen M, Wu J, Xiao J*, Su W*, Transcriptome Analysis Reveals Dynamic Changes in Coxsackievirus A16 Infected HEK 293T Cells. BMC Genomics. 2017, 18Suppl 1:933.

  82. Liang F, Wang J, Shi S, Xiao J*, Li R*, BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data. Comput Biol Chem. 2016, 65:173-177.

  83. Xue Y, Lameijer E, Ye K, Zhang K, Chang S, Wang X, Wu J, Gao G, Zhao F, Li J, Han C, Xu S, Xiao J, Yang X, Ying X, Zhang X, Chen W, Liu Y, Zhang Z, Huang K, Yu J, Precision Medicine: What Challenges Are We Facing? Genomics, Proteomics & Bioinformatics. 2016, 14:253-261.

  84. Sun S, Xiao J, Zhang H, Zhang Z, Pangenome evidence for higher codon usage bias and stronger translational selection in core genes. Frontiers in Microbiology. 2016, 7: fmicb.2016.01180.

  85. Tian X, Zhang Z, Yang T, Chen M, Li J, Chen F, Yang J, Li W, Zhang B, Zhang Z, Wu J, Zhang C, Long L*, Xiao J*, Comparative genomics analysis of Streptomyces species reveals their adaptation to the marine environment and their diversity at the genomic level. Frontiers in Microbiology. 2016 7: fmicb.2016.00998.

  86. Zhu L, Zhong J, Jia X, Liu G, Kang Y, Dong M, Zhang X, Li Q, Yue L, Li C, Xie J, Zhang B, Lei M, Xiao J, Yan J, Chen S, Lv L, Zhu B, Huang H, Chen F, Precision methylome characterization of Mycobacterium tuberculosis complex MTBC using PacBio Single-Molecule Real-Time SMRT Technology. Nucleic Acids Research. 2016, 44:730-743.

  87. The IC4R Project Consortium*, Information Commons for Rice IC4R. Nucleic Acids Research. 2016, 44: D1172-D1180.

  88. Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J*, Wei F*, Wu J*, Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome. Scientific Reports. 2015, 5:18019.

  89. Wang X, Chen M, Xiao J, Hao L, Crowley D, Zhang Z, Yu J, Huang N, Wu J, Naphthenic Acid Degradation and Metal Resistance in Cupriavidus gilardii CR3. PLoS ONE. 2015, 108: e0132881.

  90. Xiao J*, Zhang Z, Wu J and Yu J, A Brief Review of Online Software Packages for Pangenomics. Genomics, Proteomics & Bioinformatics. 2015, 13:73-76.

  91. Jia X, Yu J, Wu J, Xiao J*, A Systematic Bioinformatics Research of Small Proteins in Plants. Plant Omics Journal. 2015, 82:112-121.

  92. Zhao Y, Yin J, Guo H, Zhang Y, Xiao W, Sun C, Wu J, Qu X, Yu J, Wang X*, Xiao J*, The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Frontiers in Plant Science. 2015, 5:696.

  93. Kang Y, Gu C, Yuan L, Wang Y, Zhu Y, Li X, Luo Q, Xiao J, Jiang D, Qian M, Khan A, Chen F, Zhang Z, Yu J, Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks. mBio. 2014, 5:e01867-14.

  94. Xu P, Zhang X, Wang X, et al., Xiao J, Wu J, Zhang Z, Yu J, Sun X, Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics. 2014, 46:1212-1221.

  95. Wang W#, Feng B#, Xiao J#, Xia Z, et al, Peng M, Cassava Genome from a Wild Ancestor to Cultivated Varieties. Nature Communications. 2014, DOI:10.1038/ncomms6110.

  96. Wu J, Xiao J, Zhang Z, Wang X, Hu S, Yu J, Ribogenomics: the Science and Knowledge of RNA. Genomics, Proteomics & Bioinformatics. 2014, 12:57-63.

  97. Zhao Y, Jia X, Yang J, Ling Y, Zhang Z, Yu J, Wu J, Xiao J*, PanGP: A tool for quick analyzing bacterial pan-genome profile. Bioinformatics. 2014, 30: 1297-1299.

  98. Zhang Z, Jin Z, Zhao Y, Zhang Z, Li R, Xiao J, Wu J, A systematic study on GPCR prototypes: did they really evolve from prokaryotic genes? IET System Biology. 2014, 84:154-161.

  99. Ling Y, Jin Z, Su M, Zhong J, Zhao Y, Yu J*, Wu J*, Xiao J*, VCGDB: a dynamic genome database of Chinese population. BMC Genomics. 2014, 15:265.

  100. Wang X, Zhang Z, Hao Q, Wu J, Xiao J*, Jing H*, Complete Genome Sequence of Acinetobacter baumannii ZW85-1. Genome Announcement. 2014, 2:e01083-13.

  101. Zhou Y, Gong W, Xiao J, Wu J, Pan L, Li X, Wang X, Wang W, Hu S, Yu J, Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle. Sci China Life Sci. 2014, 573:340-355.

  102. Sun J, Wang L, Wu S, Wang X, Xiao J, Chi S, Liu C, Ren L, Zhao Y, Liu T, Yu J, Transcriptome-wide evolutionary analysis on essential brown algae (Phaeophyceae) in China. Acta Oceanologica Sinica. 2014, 332:13-19.

  103. Choo S, Wee W, Ngeow Y, Mitchell W, Tan J, Wong G, Zhao Y, Xiao J, Genomic reconnaissance of multiple, clinically derived isolates of the emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential. Scientific Reports. 2014, 4:4061.

  104. Wang F, Zhong J, Zhao Y, Xiao J, Liu J, Dai M, Zheng G, Zhang L, Yu J, Wu J, Duan B, Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. BMC Genomics. 2014, 15 Suppl 1, S11.

  105. Zhang Z, Sang J, Ma L, Wu G, Wu H, Huang D, Zou D, Liu S, Li A, Hao L, Tian M, Xu C, Wang X, Wu J, Xiao J, Dai L, Chen L, Hu S, Yu J, RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Research, 2014, 42: D1222-D1228.

  106. Su M, Ling Y, Yu J, Wu J, Xiao J*, Small proteins: untapped area of potential biological importance. Frontiers in Genetics, 2013, 4:286.

  107. Wu J#, Xiao J#, Wang L, Zhong J, Yin H, Wu S, Yu J, Systematic Analysis of Intron Length and Size Parameters in Different Taxa. Sci China Life Sci, 2013, 56:1-7.

  108. Zhang R, Hao L, Wang L, Chen M, Wen Li, Li R, Yu J, Xiao J*, Wu J*, Gene expression analysis of induced pluripotent stem cells from aneuploidy chromosomal syndromes. BMC Genomics. 2013, Suppl 6, S8.

  109. Chen M#, Xiao J#, Zhang Z, Liu J, Wu J, Yu J, Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis. PLoS ONE. 2013, 8:e54082.

  110. Dai L, Tian M, Wu J, Xiao J, Wang X, Cheung K, Townsend J, Zhang Z, Increasing participation in biological knowledge wikis through contribution quantification and explicit authorship. Bioinformatics. 2013, 29:1837-1839.

  111. Dai L, Xu C, Tian M, Shang J, Zou D, Ang Li, Liu G, Chen F, Wu J, Xiao J, Wang X, Yu J, Zhang Z, Community intelligence in knowledge curation: an application to managing scientific nomenclature. PLoS ONE. 2013, 8: e56961.

  112. Zhang Z, Wu J, Yu J, Xiao J*, A mini-review on the evolution of GPCR: conservation and diversification. Open Journal of Genetics. 2012, 2:11-17.

  113. Dai L, Gao X, Marchand B, Guo Y, Xiao J, Zhang Z, Bioinformatics clouds for big data manipulation. Biology Direct. 2012, 7:143.

  114. Yang L, Liu W, Tang Z, Xiao J, Hu S, Deng H, Feng Q, Evolutional and Functional analysis of Chymotrysin protease in Spodoptera litura. Archives of Insect Biochemistry and Physiology. 2012, 81:121-135.

  115. Liang W, Zhao Y, Chen C, Cui X, Yu J, Xiao J*, Kan B*, Pan-genome provides insights into genome variation and evolution in Salmonella Paratyphi A. PLoS ONE. 2012, 7:e45346.

  116. Wu J#, Xiao J#, Yu J, Latest notable achievements in genomics. Sci China Life Sci, 2012, 55:645-648.

  117. Zhao D, Wu J, Zhou Y, Gong W, Xiao J*, Yu J*, WikiCell: a unified resource platform for human transcriptomics research. OMICS: A Journal of Integrative Biology. 2012, 166:357-362.

  118. Ge Y, Wu J, Xia Y, Yang M, Xiao J*, Yu J*, Molecular Dynamics Simulation of the Complex PBP-2x with Drug Cefuroxime to Explore the Drug Resistance Mechanism of Streptococcus suis R61. PLoS ONE. 2012, 7: e35941.

  119. Zhao Q, Xiao J*, Yu J*, An Integrated Analysis of Lineage-specific Small Proteins across Eight Eukaryotes Reveals Functional and Evolutionary Significance. Progress in Biochemistry and Biophysics. 2012, 39:359-367.

  120. Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Lin Dai, ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochemical and Biophysical Research Communications. 2012, 419:779-781.

  121. Zhao Y, Wu J, Yang J, Sun S, Xiao J*, Yu J*, PGAP: Pan-genomes Analysis Pipeline. Bioinformatics. 2012, 28:416-418.

  122. Chen C, Zhang Z, Ding A, Wu J, Xiao J, Sun Y, Bar-Coded Pyrosequencing Reveals the Bacterial Community during Microcystis Water Bloom in Guanting Reservoir, Beijing. Procedia Engineering. 2011, 18:341-346.

  123. Zhang A, Yang M, Hu P, Wu J, Chen B, Hua Y, Yu J, Chen H, Xiao J*, Jin M*, genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. BMC Genomics. 2011, 12:523.

  124. Hu P, Yang M, Zhang A, Wu J, Chen B, Hua Y, Yu J, Chen H, Xiao J*, Jin M*, Comparative genomics study of multi-drug-resistance mechanisms in the antibiotic-resistant Streptococcus suis R61 strain. PLoS ONE. 2011, 6:e24988.

  125. Yan Ge, Wu J, Xiao J*, Yu J*, Exploration of the binding mode of α/β-type small acid soluble proteins SASPs with DNA, J. Mol. Model. 2011, 17: 3183-3193.

  126. Du Z, Zhang Z, Miao T, Wu J, Lü G, Yu J, Xiao J*, Chen G*, Draft Genome Sequence of a Novel Agar-Digesting Marine Bacterium HQM9. Journal of Bacteriology. 2011, 193:4557-4558.

  127. Hu P, Yang M, Zhang A, Wu J, Chen B, Hua Y, Yu J, Chen H, Xiao J*, Jin M*, Complete Genome Sequence of Streptococcus suis Serotype 3 Strain ST3. Journal of Bacteriology. 2011, 193:3428-3429.

  128. Yang M, Ge Y, Wu J, Xiao J*, Yu J*, study of mitochondria respiratory chain proteins: Toward the understanding of protein-protein interaction. Journal of Genetics and Genomics. 2011, 38:201-207.

  129. Hu P, Yang M, Zhang A, Wu J, Chen B, Hua Y, Yu J, Xiao J*, Jin M*, Complete Genome Sequence of Streptococcus suis serotype 14 Strain JS14. Journal of Bacteriology. 2011, 193: 2375-2376.

  130. Wu J, Xiao J, Zhang R, Yu J, DNA sequencing leads to genomics progress in China. Science in China Series C, 2011, 54:290-292.

  131. Zhao Y, Xiao J*, Homology Modeling and Molecular Dynamics Simulation Studies of Human Type 1 3-Hydroxysteroid Dehydrogenase: Toward the Understanding of Cofactor Specificity. J. Comp. Chem. 2011, 32:33-42.

  132. Zhu J, He F, Wang D, Liu K, Huang D, Xiao J, Wu J, Hu S, Yu J, A Novel Role for Minimal Introns: Routing mRNAs to the Cytosol. PLoS ONE. 2010, 5:e10144.

  133. Xiao J, Yu J, On the Genetic Code and Its Origin. Science in China Series C, 2009, 39:717-726.

  134. Wang F, Xiao J*, Pan L, Yang M, Zhang G, Yun Yu*, A Systematic Study of Mini-proteins in Bacteria and Archaea. PLoS ONE. 2008, 3:e4027.

  135. Xiao J, Yu J. A Scenario on the Stepwise Evolution of the Genetic Code. Genomics, Proteomics & Bioinformatics. 2007, 5:143-151.

  136. Xiao J, Guo Z, Guo Y, et al, Computational Study of Human Phosphomannose Isomerase: Insights from Homology Modeling and Molecular Dynamics Simulation of Enzyme Bound Substrate. J. Mol. Graph. Model. 2006, 25:289-295.

  137. Xiao J, Guo Z, Guo Y, et al, Inhibitory mode of pyrazolo[1,5-b]pyridazin series derivatives against GSK-3: molecular docking and 3D-QSAR analyses. Protein. Eng. Des. Sel. 2006, 19:47-54.

  138. Guo C, Guo Y, Guo Z, Xiao J, Chu F, Design, Synthesis and in vitro Evaluation of Thiazole Derivatives of Naproxen as Cyclooxygenase-2 Inhibitors. Acta Chimica Sinica. 2006, 64:1559-1564.

  139. Xiao J, Guo Z, Guo Y, Chu F, Sun P, Quantitative Structure-Activity Relationship of Dipeptidyl Peptidase IV Inhibitors. Acta Chimica Sinica. 2005, 63:757-763.

  140. Zhang Y, Li Z, Xiao J, Sun M, Li T, Sun C, On the homology modeling and docking studies for hepatitis B surface antigen fragment. Chemical Journal of Chinese University. 2005, 26:102-105.

  141. Guo Y, Xiao J, Guo Z, et al, Exploration of a binding mode of indole amide analogues as potent histone deacetylase inhibitors and 3D-QSAR analyses. Bioorganic. Med. Chem. 2005, 13:524-534.

  142. Zhen Q, Li Z, Xiao J, et al, Homology modeling and PAPS ligand cofactor binding study of bovine phenol sulfotransferase. J. Mol. Model. 2005, 11: 97-104.

  143. Xiao J, Li Z, Sun M, et al, Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase. Comp. Bio. Chem. 2004, 3:179-188.

  144. Xiao J, Li Z, Sun C, Homology modeling and molecular dynamics studies of a novel C3-like ADP-ribosyltransferase. Bioorganic. Med. Chem. 2004, 12:2035-2041.