Jingfa Xiao

Head of Precision Medicine Omics Databank

Precision Medicine Resources

Email: xiaojf (AT) big.ac.cn
Tel: +86 (10)8409-7443

PROFESSIONAL EXPERIENCE

EDUCATION

RESEARCH INTERESTS

PROJECTS & RESOURCES

ACADEMIC ACTIVITIES

PUBLICATIONS

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

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

  3. 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. 65:173-177 (2016).

  4. 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. 14:253-261 (2016).

  5. 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 7: fmicb.2016.01180 (2016).

  6. 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 7: fmicb.2016.00998 (2016).

  7. 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) TechnologyNucleic Acids Research. 44, 730-743 (2016).

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

  9. Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J*, Wei F*, Wu J*. Improvement of genome completeness and identification of novel full-length transcripts by RNA-seq in giant pandaScientific Reports. 5:18019 (2015).

  10. 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 CR3PLoS ONE. 10(8): e0132881 (2015).

  11. Xiao J*, Zhang Z, Wu J and Yu J. A Brief Review of Online Software Packages for PangenomicsGenomics, Proteomics & Bioinformatics. 13:73-76 (2015).

  12. Jia X, Yu J, Wu J, Xiao J*. A Systematic Bioinformatics Research of Small Proteins in PlantsPlant Omics Journal. 8(2):112-121 (2015).

  13. 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 ginsengFrontiers in Plant Science. 5:696 (2015).

  14. 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 FrameworksmBio. 5, e01867-14 (2014).

  15. Fu L, Chen M, Wu J, Xiao J, Zhang Z. Comparative analysis of RNA-seq data from polyA RNAs selection and ribosomal RNAs deletion protocol by strand-specific RNA sequencing technology2014 IEEE 8th International Conference on Systems Biology (ISB), Qingdao, China, October 25-27, pp. 71-76 (2014).

  16. 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 carpioNature Genetics. 46, 1212-1221 (2014).

  17. Wang W, Feng B, Xiao J, Xia Z, et al, Peng M. Cassava Genome from a Wild Ancestor to Cultivated VarietiesNature Communications. DOI:10.1038/ncomms6110 (2014).

  18. Wu J, Xiao J, Zhang Z, Wang X, Hu S, Yu J. Ribogenomics: the Science and Knowledge of RNAGenomics, Proteomics & Bioinformatics. 12, 57-63 (2014).

  19. 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 profileBioinformatics. 30, 1297-1299 (2014).

  20. 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. 8(4), 154-161 (2014).

  21. Ling Y, Jin Z, Su M, Zhong J, Zhao Y, Yu J, Wu J, Xiao J*, VCGDB: a dynamic genome database of Chinese populationBMC genomics. 15:265 (2014).

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

  23. 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 cycleSci China Life Sci. 57(3):340-355 (2014).

  24. 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. 33(2):13-19 (2014).

  25. Choo S, Wee W, Ngeow Y, Mitchell W, Tan J, Wong G, Zhao Y, Xiao JGenomic reconnaissance of multiple, clinically derived isolates of the emerging human pathogen Mycobacterium abscessus reveals high evolutionary potentialScientific Report. 4, 4061 (2014).

  26. 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 chrysogenumBMC genomics. 15 Suppl 1, S11 (2014).

  27. 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 genesNucleic Acids Research, 42(D1): D1222-D1228 (2014).

  28. Su M, Ling Y, Yu J, Wu J, Xiao J*, Small proteins: untapped area of potential biological importanceFrontiers in Genetics, 4:286 (2013).

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

  30. 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. Suppl 6, S8 (2013).

  31. 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 Trancsriptomics Data Analysis.PLoS ONE. 8, e54082 (2013).

  32. 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 authorshipBioinformatics. 29, 1837-1839 (2013).

  33. 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 nomenclaturePLoS ONE. 8, e56961 (2013).

  34. Zhang Z, Wu J, Yu J, Xiao J*, A mini-review on the evolution of GPCR: conservation and diversificationOpen Journal of Genetics. 2, 11-17 (2012).

  35. Dai L, Gao X, Marchand B, Guo Y, Xiao J, Zhang Z. Bioinformatics clouds for big data manipulationBiology Direct. 7, 143 (2012).

  36. Yang L, Liu W, Tang Z, Xiao J, Hu S, Deng H, Feng Q. Evolutional and Functional analysis of Chymotrysin protease in Spodoptera lituraArchives of insect Biochemistry and Physiology. 81, 121-135 (2012).

  37. 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 APLoS ONE. 7, e45346 (2012).

  38. Bu J, Wu J, Chen M, Xiao J, Yu J, Chi X, Jin Z. BAsplice: Bi-direction Alignment for detecting splice junctions2012 IEEE 6th International Conference on Systems Biology (ISB), Xian, China, August 18-20, pp. 253-256 (2012).

  39. Wu J, Xiao J, Yu J, Latest notable achievements in genomicsSci China Life Sci, 55, 645-648 (2012).

  40. Zhao D, Wu J, Zhou Y, Gong W, Xiao J*, Yu J*. WikiCell: a unified resource platform for human transcriptomics research. OMICSA Journal of Integrative Biology 16(6), 357-362 (2012).

  41. 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 R61PLoS ONE. 7, e35941 (2012).

  42. Zhao Q, Xiao J*, Yu J*. An Integrated Analysis of Lineage-specific Small Proteins across Eight Eukaryotes Reveals Functional and Evolutionary SignificanceProgress in Biochemistry and Biophysics. 39, 359-367 (2012).

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

  44. Zhao Y, Wu J, Yang J, Sun S, Xiao J*, Yu J*, PGAP: Pan-genomes Analysis PipelineBioinformatics. 28, 416-418 (2012).

  45. 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 18, 341-346 (2011).

  46. Liu Z, Xiao J, Wu J, Yu J. RNADAP—RNA-Seq Data Annotation Pipeline2011 IEEE Conference on Systems Biology (ISB), 84-86 Zhuhai, China, September 2-4, pp. 84-86 (2011).

  47. 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 serotypesBMC Genomics. 12, 523 (2011).

  48. 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 strainPLoS ONE. 6, e24988 (2011).

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

  50. Du Z, Zhang Z, Miao T, Wu J, Lü G, Yu J, Xiao J*, and Chen G, Draft Genome Sequence of a Novel Agar-Digesting Marine Bacterium HQM9Journal of Bacteriology. 193, 4557-4558 (2011).

  51. Pan Hu, 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 ST3Journal of Bacteriology. 193, 3428-3429 (2011).

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

  53. 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. 193, 2375-2376 (2011).

  54. Wu J, Xiao J, Zhang R, Yu J. DNA sequencing leads to genomics progress in ChinaScience in China Series C, 54, 290-292 (2011).

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

  56. 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 CytosolPLoS ONE. 5, e10144 (2010).

  57. Xiao J, Yu J. On the Genetic Code and Its OriginScience in China Series C, 39, 717-726 (2009).

  58. Jiang B, Wang J, Xiao J, Wang Y. Gene Prioritization for Type 2 Diabetes in Tissue-specific Protein Interaction NetworksThe Third International Symposium on Optimization and Systems Biology, Zhangjiajie, China, September 20-22, pp. 319-328 (2009).

  59. Wang F, Xiao J*, Pan L, Yang M, Zhang G, Yun Yu. A Systemic Study of Mini-proteins in Bacterial and ArchaeaPLoS ONE. 3, e4027 (2008).

  60. Xiao J, Yu J. A Scenario on the Stepwise Evolution of the Genetic CodeGenomics, Proteomics & Bioinformatics. 5, 1 (2007).

  61. 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 SubstrateJ. Mol. Graph. Model. 25, 289 (2006).

  62. 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 analysesProtein. Eng. Des. Sel. 19, 47 (2006).

  63. Guo C, Guo Y, Guo Z, Xiao J, Chu F. Design, Synthesis and in vitro Evaluation of Thiazole Derivatives of Naproxen as Cyclooxygenase-2 InhibitorsActa Chimica Sinica. 64, 1559 (2006).

  64. Xiao J, Guo Z, Guo Y, Chu F, Sun P. Quantitative Structure-Activity Relationship of Dipeptidyl Peptidase IV InhibitorsActa Chimica Sinica. 63, 757 (2005).

  65. Zhang Y, Li Z, Xiao J, Sun M, Li T, Sun C. On the homology modeling and docking studies for hepatitis B surface antigen fragmentChemical Journal of Chinese University. 26, 102 (2005).

  66. 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 analysesBioorganic. Med. Chem. 13, 5424 (2005).

  67. Zhen Q, Li Z, Xiao J, et al, Homology modeling and PAPS ligand (cofactor) binding study of bovine phenol sulfotransferaseJ. Mol. Model. 11, 97 (2005).

  68. Xiao J, Li Z, Sun M, et al, Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinaseComp. Bio. Chem. 3, 179 (2004).

  69. Xiao J, Ze-Sheng Li, Sun C. Homology modeling and molecular dynamics studies of a novel C3-like ADP-ribosyltransferaseBioorganic. Med. Chem. 12, 2035 (2004).