Publications

2020

1. X. Su*, G. Jing, Z. Sun, L. Liu, Z. Xu, D. McDonald, Z. Wang, H. Wang, A. Gonzalez, Y. Zhang, S. Huang, G. Huttley, R. Knight*, J. Xu*. Multiple-Disease Detection and Classification across Cohorts via Microbiome Search. mSystems. doi:10.1128/mSystems.00150-20.Pubmed

2019

1. G. Jing¹, Y. Zhang¹, M. Yang, L. Liu, J. Xu, X. Su*. Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level. Bioinformatics. doi:10.1093/bioinformatics/btz910.Pubmed
2. X. Su*, G. Jing, D. McDonald, H. Wang, Z. Wang, A. Gonzalez, Z. Sun, S. Huang, J. Navas, R. Knight* and J. Xu*. Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”. mBio. doi:10.1128/mBio.01234-19.Pubmed
3. Z. Sun, S. Huang, P. Zhu, F. Yue, H. Zhao, M. Yang, Y. Niu, G. Jing, X. Su, H. Li, C. Callewaert, R. Knight, J. Liu, E. Smith, K. Wei, J. Xu*. A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children. mSystems. doi:10.1128/mSystems.00293-19.Pubmed

2018

1. X. Su*, G. Jing, D. McDonald, H. Wang, Z. Wang, A. Gonzalez, Z. Sun, S. Huang, J. Navas, R. Knight* and J. Xu*. Identifying and predicting novelty in microbiome studies. mBio. doi:10.1128/mBio.02099-18.Pubmed
2. Zhou Q, Su X, Jing G, Chen S, Ning K. RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data. BMC Genomics. 19(1):144. doi: 10.1186/s12864-018-4503-6.Pubmed
3. Xiaoyan Jing,Honglei Gou,Yanhai Gong,Xiaolu Su,La Xu,Yuetong Ji,Yizhi Song,Ian P. Thompson,Jian Xu & Wei E.Huang. Raman‐activated cell sorting and metagenomic sequencing revealing carbon‐fixing bacteria in the ocean. Environmental microbiology. doi:10.1111/1462-2920.14268. Pubmed
4. Mark H.J.Sturme,Yanhai Gong,Josué MiguelHeinrich,Anne J.Klok,GerritEggink,Dongmei Wang,Jian Xu & Rene H.Wijffels. Transcriptome analysis reveals the genetic foundation for the dynamics of starch and lipid production in Ettlia oleoabundans.Algal Research. doi:10.1111/1462-2920.14268. Pubmed
5. Chen Ma, Zheng Sun, Benhua Zeng, Shi Huang, Jie Zhao, Yong Zhang, Xiaoquan Su, Jian Xu, Hong Wei & Heping Zhang.Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis. Microbiome. doi:10.1186/s40168-018-0578-1. Pubmed

2017

1. Qiang Zhang, Tingting Wang, Qian Zhou, Peng Zhang, Yanhai Gong, Honglei Gou, Jian Xu, Bo Ma. Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms. Scientific Reports 7:41192. doi: 10.1038/srep41192.Pubmed
2. Jing, G., Sun, Z., Wang, H., Gong, Y., Huang, S., Ning, K, Xu, J., & Su, X. Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities. Scientific Reports 7:40371. doi: 10.1038/srep40371. Pubmed

2016

1. Teng, L., Wang, X., Gou, H., Ren L., Wang, T., et al.Label-free, rapid and quantitative phenotyping of stress response in E. coli via ramanome. Scientific Reports 6:34359.doi: 10.1038/srep34359. Pubmed
2. Han, M.*, Gong, Y.*, Zhou, C.*, Zhang, J., Wang, Z., & Ning, K.Comparison and interpretation of taxonomical structure of bacterial communities in two types of lakes on yun-gui plateau of china. Scientific Reports 6:30616. doi: 10.1038/srep30616. Pubmed

2015

1. Zhang P, Ren L, Zhang X, Shan Y, Wang Y, Ji Y, Yin H, Huang WE, Xu J, Ma B. Raman-activated cell sorting based on dielectrophoretic single-cell trap and release.Analytical Chemistry 87(4): 2282-2289. Pubmed
2. Sun, S., Wang, X., Gao, X., Ren, L., Su, X., Bu, D. Condensing Raman spectrum for single-cell phenotype analysis. Bmc Bioinformatics, 16, 1471-2105.Pubmed

2014

1. 宁康, 陈挺. 生物医学大数据的现状与展望. 科学通报, 2015, 60: 1–13.
2. Dong-Dong Meng, Yu Ying, Xiao-Hua Chen, Ming Lu, Kang Ning, Lu-Shan Wang, Fu-Li Li*. Distinct Roles for Carbohydrate-Binding Modules of Glycoside Hydrolase 10 (GH10) and GH11 Xylanases from Caldicellulosiruptor sp. Strain F32 in Thermostability and Catalytic Efficiency. Applied and Environmental Microbiology 2015.
3. Lihui Ren, Xiaoquan Su, Yun Wang, Jian Xu and Kang Ning*. QSpec: online control and data analysis system for single-cell Raman spectroscopy. PeerJ. 2014. Jun 26;2:e436. doi: 10.7717/peerj.436. eCollection 2014.Pubmed
4. Qian Zhou, Xiaoquan Su, Kang Ning*. Assessment of quality control approaches for metagenomic data analysis. Scientific Reports, 2014 Nov 7;4:6957. doi: 10.1038/srep06957.Pubmed
5. Xiaoquan Su, Gongchao Jing, Shi Huang, Jian Xu, Kang Ning*. Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats. IEEE ISB, 2014.
6. 白虹,宁康*,王长云*. 运用基于高通量测序和大数据挖掘的元基因组学方法分析中药制剂的物种成分. 药学学报, 2014.
7. Qian Zhou^1*,Z.Lewis Liu^2*,Kang Ning^1*,Anhui Wang³,Xiaowei Zeng¹ & Jian Xu¹. Genome and transcriptome analyses reveal that MAPK-and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae, Scientific Reports 4:6556, DOI: 10.1038/srep06556, 2014.Pubmed
8. Xiaoquan Su, Jianqiang Hu, Shi Huang, and Kang Ning*. Rapid comparison and correlation analysis among massive number of microbial community samples based on MDV data model, Scientific Reports 4:6393, DOI: 10.1038/srep0639, 2014.Pubmed
9. Peng Yang, Xiaoquan Su, Le Ouyang, Hon-Nian Chua, Xiaoli Li and Kang Ning*. Microbial community pattern detection in human body habitats via ensemble clustering framework, BMC System Biology Volume 8 Suppl 3, S 12.In press
10. Xinwei Cheng¹, Xiaoquan Su¹, Xiaohua Chen, Huanxin Zhao, Cuipei Bo, Jian Xu, Hong Bai, Kang Ning. Biological ingredient analysis otraditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei DihuangWan, Scientific Reports 4:5147, doi:10.1038/srep05147. Pubmed
11. Xiaoquan Su, Weihua Pan, Baoxing Song, Jian Xu and Kang Ning*. Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization, PLoS ONE 9(3): e89323. doi:10.1371/journal.pone.0089323, 2014. Pubmed
12. Dongmei Wang¹, Kang Ning¹, Jing Li¹, Jianqiang Hu, Danxiang Han, Hui Wang, Xiaowei Zeng, Xiaoyan Jing, Qian Zhou, Xiaoquan Su, Xingzhi Chang, Anhui Wang, Wei Wang, Jing Jia, Li Wei, Yi Xin, Yinghe Qiao, Ranran Huang, Jie Chen, Bo Han, Russell T. Hill, Yonathan Zohar, Feng Chen, Qiang Hu, and Jian Xu. Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits, PLoS Genet 10(1): e1004094. doi:10.1371/journal.pgen.1004094. Pubmed
13. Xinwei Cheng, Xiaohua Chen, Xiaoquan Su, Huanxin Zhao, Maozhen Han, Cunpei Bo, Jian Xu, Hong Bai, Kang Ning. DNA Extraction Protocol for Biological Ingredient Analysis of LiuWei DiHuang Wan, Proteomics & Bioinformatics 2014 Jun;12(3):137-43. doi: 10.1016/j.gpb. Pubmed
14. Jing Li¹, Danxiang Han¹, Dongmei Wang¹, Kang Ning¹, Jing Jia, Li Wei, Xiaoyan Jing, Shi Huang, Jie Chen, Yantao Li, Qiang Hu, Jian Xu. Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oil Synthesis in Microalgae, The Plant Cell April 2014 vol. 26 no. 4 1645-1665. Pubmed
15. Qian Zhou, Xiaoquan Su, Gongchao Jing, Kang Ning. Meta-QC-Chain: Comprehensive and Fast Quality Control Method for Metagenomic Data, Genomics, proteomics & bioinformatics 12 (1), 52-56 2014. Pubmed
16. Fang Yang, Kang Ning, Xingzhi Chang, Xiao Yuan, Qichao Tu, Tong Yuan, Ye Deng, Christopher L Hemme, Joy Van Nostrand, Xinping Cui, Zhili He, Zhenggang Chen, Dawei Guo, Jiangbo Yu, Yue Zhang, Jizhong Zhou, Jian Xu, Saliva Microbiota Carry Caries-Specific Functional Gene Signatures, PLoS ONE 9(2): e76458. doi:10.1371/journal.pone.0076458. Pubmed
17. Xiaoquan Su, Baoxing Song, X Wang, X Ma, Jian Xu, Kang Ning. Meta-Mesh: metagenomic data analysis system,Sheng wu Gong Cheng xue bao = Chinese Journal of Biotechnology [2014, 30(1):6-17]. Pubmed
18. 苏晓泉, 宋宝兴, 王雪涛等.Meta-Mesh—元基因组数据分析系统, 生物工程学报，2014, 30(1): 1−12. Pubmed
19. Jianqiang Hu^1,2, Dongmei Wang¹, Li Jing^1,2, Kang Ning^1,*, Jian Xu^1,*. Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis, Scientific Reports.2014 Jun 26;4:5454. doi: 10.1038/srep05454. Pubmed

2013

20. Xiaoquan Su¹, Xuetao Wang¹, Gongchao Jing and Kang Ning*. GPU-Meta-Storms: Computing the structure similarities among massive amount of microbial community samples using GPU, Bioinformatics 30(7):1031-3.doi: 10.1093, 2013. Pubmed
21. Xiaoquan Su, Xuetao Wang, Jian Xu and Kang Ning*. GPU-Meta-Storms: Computing the similarities among massive microbial communities using GPU,IEEE Systems Biology doi:10.1109/ISB, 2013.IEEE
22. Qian Zhou, Xiaoquan Su, Anhui Wang, Jian Xu and Kang Ning*. QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data,PLOS ONE 8(4): e60234.doi: 10.1371/ journal.pone.0060234, 2013.Pubmed

2012

23. Baoxing Song, Xiaoquan Su and Kang Ning*. MetaSee: An interactive and extendable visualization toolbox for metagenomic sample analysis and comparison, PLOS ONE 7(11): e48998.doi:10.1371/ journal.pone.0048998,2012. Pubmed
24. Xiaoquan Su, Jian Xu, Kang Ning*. Meta-Storms: Efficient Search for Similar Microbial Communities Based on a Novel Indexing Scheme and Similarity Score for Metagenomic Data ,Bioinformatics 28 (19): 2493-2501.doi: 10.1093,2012 . Pubmed
25. Kang Ning, Damian Fermin and Alexey I. Nesvizhskii. Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression dataJ. Proteome Res 11 (4),pp 2261–2271 DOI: 10.1021/pr201052x, 2012. Pubmed
26. Xiaoquan Su, Jian Xu and Kang Ning*. Parallel-META: A High-Performance Computational Pipeline for Metagenomic Data Analysis. BMC Systems Biology, 2012. Pubmed
27. Na You, Gabriel Murillo, Xiaoquan Su, Xiaowei Zheng, Jian Xu, Kang Ning, Shoudong Zhang, Jiankang Zhu and Xinping Cui*. SNP calling using genotype model selection on next generation sequencing data.Bioinformatics(2012)28(5):643-650. doi: 10.1093, 2012. Pubmed

2011

28. Xiaoquan Su, Jian Xu and Kang Ning*. An Open-source Collaboration Environment for Metagenomics Research. IEEE e-Science doi:10.1109/eScience.2011.10, 2011. IEEE
29. Kang Ning and Jian Xu. Bioinformatics in Microbial Metagenomics: Status and Prospects. Annual Advances (2011) of Industrial Biotechnology. Science Press (China).
30. Yang F, Zeng XW, Ning K, Liu KL, Lo CC, Wang W, Chen J, Wang DM, Huang RR, Chang XZ, Chain PS, Xie G, Ling JQ, Xu J. Saliva microbiomes distinguish caries-active from healthy human-populations, The ISME Journal (2012) 6, 1–10; doi:10.1038/ismej.2011.71,2012 Pubmed

2010 and Before

31. Kang Ning and Alexey I. Nesvizhskii. Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. BMC Bioinformatics, 2010, 11:505. Pubmed
32. Kang Ning and Alexey I. Nesvizhskii. The Utility of Mass Spectrometry-based Proteomic Data for Validation of Novel Alternative Splice Forms Reconstructed from RNA-Seq Data: A Preliminary Assessment. BMC Bioinformatics, 2010, 11:S14. Pubmed
33. Kang Ning and Damian Fermin. SAW: A Method to Identify Splicing Events from RNA-Seq Data based on Splicing Fingerprints. PLoS ONE 5(8): e12047 (2010). Pubmed
34. Kang Ning, Damian Fermin and Alexey I. Nesvizhskii. Computational Analysis of Unassigned High Quality MS/MS Spectra in Large-scale Proteomic Datasets. Proteomics, Vol. 10, Issue 14, Pages 2712 - 2718 (2010). Pubmed
35. Kang Ning. Deposition and Extension Approach to Find Longest Common Subsequence for Thousands of Long Sequences. Computational Biology and Chemistry 34(3):149-157.Pubmed
36. Kang Ning and Hon Wai Leong. The multiple sequence sets: problem and heuristic algorithms. Journal of Combinatorial Optimization. doi: 10.1007/s10878-010-9329-3. SpringerLink
37. Kang Ning, Hoong Kee Ng and Hon Wai Leong. Analysis of the Relationships among Longest Common Subsequences, Shortest Common Supersequences and Patterns and its application on Pattern Discovery in Biological Sequences. International Journal of Data Mining and Bioinformatics. Pubmed
38. Hoong Kee Ng, Kang Ning and Hon Wai Leong. Two-phase Filtering Strategy for Efficient Peptide Identification from Mass Spectrometry. Journal of Proteomics & Bioinformatics 3: 121-129. Pubmed
39. Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong and Limsoon Wong. Using Indirect Protein-Protein Interactions for Protein Complex Prediction. Journal of Bioinformatics and Computational Biology, Vol. 6, No. 3 (2008) page 435-466. Pubmed
40. Kang Ning, Nan Ye and Hon Wai Leong. On preprocessing and anti-symmetry in de novo peptide sequencing: Improving efficiency and accuracy. Journal of Bioinformatics and Computational Biology, Vol. 6, No. 3 (2008) page 467-492. Pubmed
41. Ket Fah Chong, Kang Ning, Hon Wai Leong and Pavel Pevzner. Modeling and Characterization of Multi-Charge Mass Spectra for Peptide Sequencing. Journal of Bioinformatics and Computational Biology, Vol. 4, No. 6 (2006) page 1329-1352. Pubmed
42. Kang Ning and Hon Wai Leong. Towards a Better Solution to the Shortest Common Supersequence Problem: The Deposition and Reduction Algorithm. BMC Bioinformatics, 7 (Suppl 4): S12 (2006). Pubmed
43. Kang Ning, Kwok Pui Choi, Hon Wai Leong and Louxin Zhang. A Post Processing Method for Optimizing Synthesis Strategy for Oligonucleotide Microarrays. Nucleic Acids Research, Vol. 33, No 17 (2005): e144. Pubmed

Patent Of Invention

宁康、胡建强、苏晓泉、徐健. 一种利用DNA进行信息存储的编码方法和解码方法, 201410163020.0.
任立辉、宁康、籍月彤、王允、徐健、黄巍. 单细胞表现型数据库系统和搜索引擎, 201310105207.0.
宁康、白虹、苏晓泉、程新玮、赵焕新、徐健、陈晓华. 一种基于高通量测序技术的中药制剂生物成分分析方法, 201310612193.1.
任立辉、宁康、马波、徐健、黄巍. 活体单细胞分选电子控制系统, 201210567603.0.
宁康、苏晓泉、徐健. 基于GPGPU和多核CPU硬件的高性能元基因组数据分析系统, 201210055384.8.
周茜、宁康、苏晓泉、徐健. 基于多核CPU和GPGPU硬件的高通量测序数据质量控制系统, 201210478392.3

Software Copyright

任立辉、马波、徐健.基于微流控芯片的快速活菌计数软件系统 ,2015SR219580.
任立辉、苏晓泉、徐健.基于单细胞图像数据库的图像分析处理系统.2015SR219902
任立辉、苏晓泉、徐健.基于单细胞拉曼光谱的分析处理软件系统.2015SR078469.
任立辉、马波、徐健.基于智能手机的活菌检测分析软件系统.2016R11L482793 .
苏晓泉、周茜、宁康、徐健. 并行化高通量测序数据质量控制软件 1.0, 2013SR080803.
任立辉、宁康、苏晓泉、徐健. 单细胞拉曼光谱模拟系统软件, 2013SR079944.
任立辉、宁康、苏晓泉、徐健. 单细胞拉曼光谱系统控制软件. 2013SR015642.
苏晓泉、宁康、徐健. 元基因组数据库索引与搜索系统, 2013SR000258.
宁康、苏晓泉、徐健. 基于GPGPU 和多核心CPU 硬件的元基因组数据分析软件 2.0, 2012SR055051.

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