Publications

Journal papers

  1. Maozhen Han1, Kun Yang 1, Pengshuo Yang, Chaofang Zhong , Chaoyun Chen ,Song Wang* , Qunwei Lu* ,Kang Ning* .Stratification of Athletes' Gut Microbiota: The Multifaceted Hubs associated with Dietary Factors, Physical Characteristics and Performance.Gut Microbes,2020,accepted. (SCI impact factor 7.740)
  2. Lixiao Wang1, Maozhen Han1, Xi Li, Bingbing Yu, Huading Wang, Amjed Ginawi, Kang Ning*, Yunjun Yan*.Mechanisms of niche-neutrality balancing can drive the assembling of microbial community.Molecular Ecology,2020,accepted. (SCI impact factor 5.163)
  3. Chaofang Zhong, Lusheng Wang*, Kang Ning*. Pan-genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption.Environmental Microbiology,2020,accepted. (SCI impact factor 4.933)
  4. Wanglin Liu1, Mingyue Cheng1, Jinman Li1, Peng Zhang, Hang Fan, Qinghe Hu, Maozhen Han, Longxiang Su, Huaiwu He, Yigang Tong*, Kang Ning*, Yun Long*.Accurate classification of the gut microbiota of patients in intensive care units during the development of sepsis and septic shock.Genomics, Proteomics & Bioinformatics,2020,accepted. (SCI impact factor 7.051)
  5. Pengshuo Yang, Chongyang Tan, Maozhen Han, Lin Cheng, Xuefeng Cui, Kang Ning*.Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology.NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa042, https://doi.org/10.1093/nargab/lqaa042.
  6. Xue Zhu, Xi Li, Wenjie Wang, Kang Ning*.Bacterial contamination screening and interpretation for biological laboratory environments.Medicine in Microecology, 2020;5:100021.
  7. Runzhi Zhang1, Gao Xi1, Hong Bai *, Kang Ning*.Traditional Chinese Medicine and gut microbiome: Their respective and concert effects on healthcare.Frontiers in Pharmacology. 2020;11:538. Published 2020 Apr 22. doi:10.3389/fphar.2020.00538(SCI impact factor 4.225)
  8. Zhi Wang*, Maozhen Han, Enhua Li, Xi Liu, Huimin Wei, Chao Yang, Shaoyong Lu*, Kang Ning* .Distribution of antibiotic resistance genes in an agriculturally disturbed lake in China: their links with microbial communities, antibiotics, and water quality.Journal of Harzardous Material. 2020;393:122426.(SCI impact factor 7.650)
  9. 韩毛振1, 朱雪1, 宁康*. “水土不服”和肠道菌群:永远在旅行的小家伙们. 科学(上海), 2020,72(4):33-35.
  10. Mo Zhu1, Kai Kang1, Kang Ning* .Meta-Prism: Ultra-fast and highly accurate microbial community structure search utilizing dual-indexing and parallel computation.Briefings in Bioinformatics,2020 Feb 7;bbaa009. doi: 10.1093/bib/bbaa009. (SCI impact factor 8.990)
  11. Wei Miao, Lirong Song, Sang Ba, Longxian Zhang, Guiquan Guan, Zhang Zhang, Kang Ning .The Protist 10,000 Genomes (P10K) Project.Genomics, Proteomics & Bioinformatics,2020,accepted. (SCI impact factor 7.051)
  1. Runzhi Zhang, Xue Zhu, Hong Bai*,Kang Ning* .Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment.Frontiers in Pharmacology,2019 Feb 21;10:123. doi: 10.3389/fphar.2019.00123. eCollection 2019.(SCI impact factor 3.845)
  2. Chaofang Zhong, Maozhen Han, Pengshuo Yang, Chaoyun Chen, Hui Yu, Lusheng Wang*,Kang Ning* .Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas: viewed from both single isolated species and microbial community.mSystems, 2019 Oct 22;4(5). pii: e00252-19. doi: 10.1128/mSystems.00252-19. (SCI impact factor 6.519)
  3. Sicheng Wu1, Chuqing Sun1, Yanze Li, Teng Wang, Longhao Jia, Senying Lai, Yaling Yang, Pengyu Luo, Die Dai, Yong-Qing Yang, Qibin Luo, Na L Gao, Kang Ning, Li-jie He*, Xing-Ming Zhao*, Wei-Hua Chen*. GMrepo: a database of curated and consistently annotated human gut metagenomes.Nucleic Acids Research,2019.10.1093/nar/gkz764. (SCI impact factor 11.147)
  4. Lixiao Wang1, Maozhen Han1, Li Xi, Amjed Ginawi, Kang Ning*, Yunjun Yan*. Niche and neutrality work differently in microbial communities in fluidic and non-fluidic ecosystems.Microbial Ecology,2019 Sep 11. doi: 10.1007/s00248-019-01439-y.(SCI impact factor 3.611)
  5. Yan Wang1, Qiang Shi1, Pengshuo Yang1, Chengxin Zhang1, Golam Mortuza, Zhidong Xue*, Kang Ning*, Yang Zhang*.Fueling ab initio folding with marine microbiome enables structure and function predictions of new protein families.Genome Biology ,2019,Nov 1;20(1):229. doi: 10.1186/s13059-019-1823-z.(SCI impact factor 14.028)
  6. Han Zhao, Shaliu Fu, Yifei Yu, Zhanbing Zhang, Ping Li, Qin Ma, Wei Jia, Kang Ning, Shen Qu, Qi Liu*. MetaMed:Linking microbiota functions with medicine therapeutics. mSystems,2019 Oct 8;4(5). pii: e00413-19. doi: 10.1128/mSystems.00413-19.(SCI impact factor 6.519)
  7. Mingyue Cheng, Le Cao, Kang Ning*. Microbiome big-data mining and applications using single-cell technologies and metagenomics approaches towards precision medicine. Frontiers in Genetics,2019 Oct 9;10:972. doi: 10.3389/fgene.2019.00972. eCollection 2019.(SCI impact factor 3.517)
  8. Chaoyun Chen, Zhangyu Cheng, Ruiqiao He, Maozhen Han, Yuguo Zha, Pengshuo Yang, Qi Yao, Hao Zhou, Chaofang Zhong, Kang Ning*. The seasonal dynamics and the influence of human activities on campus outdoor microbial communities. Frontiers in Microbiology,2019 Jul 10;10:1579. doi: 10.3389/fmicb.2019.01579. (SCI impact factor 4.259)
  9. Wang Xi1, Yan Gao1, Zhangyu Cheng, Chaoyun Chen, Maozhen Han, Pengshuo Yang, Guangzhou Xiong, Kang Ning*. Using QC-Blind for quality control and contamination screening of bacteria DNA sequencing data without reference genome. Frontiers in Microbiology,2019 Jul 9;10:1560. doi: 10.3389/fmicb.2019.01560. (SCI impact factor 4.259)
  10. Yigang Tong*,Kang Ning*. The Fast Track for Microbiome Research. Genomics, Proteomics & Bioinformatics 2019 Feb;17(1):1-3. doi: 10.1016/j.gpb.2019.04.001. (SCI impact factor 6.597)
  11. Hong Bai, Xianhong Li, Hongjun Li, Jialiang Yang, Kang Ning*. Biological ingredient complement chemical ingredient in the assessment of the quality of TCM preparations. Scientific Reports 2019 Apr 10;9(1):5853. doi: 10.1038/s41598-019-42341-4. (SCI impact factor 4.011)
  12. Chaoyun Chen1, Andreas Harst1, Wuxin You, Jian Xu, Kang Ning*,Ansgar Poetsch*. Proteomic study uncovers molecular principles of single-cell level phenotypic heterogeneity in lipid storage of Nannochloropsis oceanica. Biotechnology for Biofuels 2019 Feb 4;12:21. doi: 10.1186/s13068-019-1361-7. (SCI impact factor 5.452)
  13. Pengshuo Yang, Shaojun Yu, Lin Cheng, Kang Ning*. Meta-Network: Optimized species-species network analysis for microbial communities. BMC Genomics 2019, Apr 4;20(Suppl 2):187. doi: 10.1186/s12864-019-5471-1.(SCI impact factor 3.501)
  14. Mingyue Cheng, Kang Ning*. Stereotype About Enterotype: the Old and New Ideas. Genomics, Proteomics & Bioinformatics 2019, Feb;17(1):4-12. doi: 10.1016/j.gpb.2018.02.004. Epub 2019 Apr 23. (SCI impact factor 6.597)
  15. Maozhen Han1, Melissa Dsouza1, Chunyu Zhou1, Hongjun Li, Junqian Zhang, Chaoyun Chen, Qi Yao, Chaofang Zhong, Hao Zhou, Jack A Gilbert*,Zhi Wang* ,Kang Ning*. Agricultural Risks Factors Influence Microbial Ecology in Honghu Lake. Genomics, Proteomics & Bioinformatics 2019, Feb;17(1):76-90. doi: 10.1016/j.gpb.2018.04.008. (SCI impact factor 6.597)
  1. Maozhen Han, Pengshuo Yang, Chaofang Zhong, Kang Ning*. The Human Gut Virome in Hypertension. Frontiers in Microbiology, 2018,Dec 19;9:3150. doi: 10.3389/fmicb.2018.03150. (SCI impact factor 4.259)
  2. Hong Liu1, Maozhen Han1, Shuai Cheng Li1, Guangming Tan, Shiwei Sun, Zhiqiang Hu, Pengshuo Yang, Rui Wang, Yawen Liu, Feng Chen, Jianjun Peng, Hong Peng, Hongxing Song, Yang Xia, Liqun Chu, Quan Zhou, Feng Guan, Jing Wu*, Dongbo Bu*, Kang Ning*. Resilience of Human Gut Microbial Communities for the Long Stay with Multiple Dietary Shifts. Gut, 2018,DOI: 10.1136/gutjnl-2018-317298.(SCI impact factor 17.943)
  3. Chongyang Tan1, Wei Cui1, Xinping Cui*, Kang Ning*. Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling . Bioinformatics, 2018,35(10):1789-1791.(SCI impact factor 4.531)
  4. Qian Zhou, Xiaoqun Su, Gongchao Jing, Songlin Chen*, Kang Ning*. RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data. BMC Genomics, 2018 Feb 14;19(1):144. doi: 10.1186/s12864-018-4503-6.(SCI impact factor 3.501)
  5. 曹乐, 宁康. 昆虫肠道的宏基因组学:微生物大数据的新疆界. 微生物学报, 2018 DOI: 10.13343/j.cnki.wsxb.20170353.
  6. Chaofang Zhong, Maozhen Han, Shaojun Yu, Pengshuo Yang, Hongjun Li ,Kang Ning*.Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway. Biotechnology for Biofuels 2018 Jul 17;11:193. doi: 10.1186/s13068-018-1201-1. (SCI impact factor 5.452)
  1. Chaofang Zhong, Shaojun Yu, Maozhen Han, Jiahuan Chen, Kang Ning*. Heterogeneous circRNA expression profiles and regulatory functions among HEK293T single cells Scientific reports, 2017 Oct 31;7(1):14393. doi: 10.1038/s41598-017-14807-w. (SCI impact factor 4.011)
  2. Run-zhi Zhang, Shao-jun Yu, Hong Bai*, Kang Ning*. TCM-Mesh: The database and analytical system for network pharmacology analysis for TCM preparations. Scientific reports, 2017 Jun 6;7(1):2821. doi: 10.1038/s41598-017-03039-7. (SCI impact factor 4.011)
  3. Dan Wang, Shuaicheng Li, Fei Guo, Kang Ning and Lusheng Wang. Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats. BMC Genomics 2017 18:268. (SCI impact factor 3.501)
  4. 张国庆, 宁康, 职晓阳, 刘婉, 徐萍, 周豪魁, 胡黔楠, 赵国屏. 建设微生物组大数据中心 发挥长期科学影响. 中国科学院院刊, 2017,32 (3) :280-289.
  5. Yin-Ying Wang, Hong Bai, Runzhi Zhang, Kang Ning, Xing-Ming Zhao*. Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as case studies. oncotarget, 2017, Nov 7; 8(55): 93957–93968.(SCI impact factor 5.168)
  6. Kang Ning*,Xinming Zhao,Ansgar Poetsch,WeiHua Chen,and Jialiang Yang.Computational Molecular Networks and Network Pharmacology. BioMed research international,2017. Nov 7; 8(55): 93957–93968.(SCI impact factor 2.197)
  7. Jifang Yan, Guohui Chuai,Tao Qi,Fangyang Shao,Chi Zhou,Chenyu Zhu, Kang Ning,Yuan He and Qi Liu. MetaTopics: an integration tool to analyze microbial community profile by topic model. BMC Genomics, 2017, 18 (1), 962. (SCI impact factor 3.501)
  8. Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, and Xiaoquan Su. Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities. Scientific reports, 2017, 10.1038/srep40371. (SCI impact factor 4.011)
  1. Jiahuan Chen, Qian Zhou, Yangfan Wang and Kang Ning*. Single-cell SNP analyses and interpretations based on RNA-Seq data for colon cancer research. Scientific reports, 2016, 10.1038/srep34420. (SCI impact factor 4.011)
  2. LiJuan Su, LeLe Yang, Shi Huang, XiaoQuan Su, Yan Li, FengQin Wang, EnTao Wang, Jian Xu, AnDong Song and Kang Ning*. Comparative Gut Microbiomes of Four Species Representing the Higher and the Lower Termites.Journal of Insect Science, 2016, 16(1):97. (SCI impact factor 1.446)
  3. Gabriel Murillo, Na You, Xiaoquan Su, Wei Cui, Kang Ning and Xinping Cui*. MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data. Bioinformatics, 2016, 10.1093/bioinformatics/btv753. (SCI impact factor 4.531)
  4. Maozhen Han1, Yanhai Gong1, Chunyu Zhou1, Junqian Zhang, Zhi Wang and Kang Ning*. Comparison and Interpretation of Taxonomical Structure of Bacterial Communities in Two Types of Lakes on Yun-Gui plateau of China. Scientific reports, 2016,Jul 27;6:30616. doi: 10.1038/srep30616. (SCI impact factor 4.011)
  5. Shuyan Tang1, Wang Xi1, Zhangyu Cheng1, Lei Yin, Ruihao Li, Guozhao Wu, Wangjie Liu, Junjie Xu, Shuaiying Xiang, Yanxiao Zheng, Qian Ge, Kang Ning*, Yunjun Yan* and Yi Zhan*. A Living Eukaryotic Autocementation Kit from Surface Display of Silica Binding Peptides on Yarrowia lipolytica. ACS synthetic biology 2016, 10.1021/acssynbio.6b00085 (SCI impact factor 5.571)
  1. Houjin Zhang* and Kang Ning*. The Tara Oceans Project: New opportunities and greater challenges ahead. Genomics, Proteomics & Bioinformatics, 2015, 13 (5): 275-277.(SCI impact factor 6.597)
  2. Jianhua Fan, Kang Ning, Xiaowei Zeng, Yuanchan Luo, Dongmei Wang, Jianqiang Hu, Jing Li, Hui Xu, Jianke Huang, Minxi Wan, Weiliang Wang, Daojing Zhang, Guomin Shen, Conglin Run, Junjie Liao, Lei Fang, Shi Huang, Xiaoyan Jing, Xiaoquan Su, Anhui Wang, Lili Bai, Zanmin Hu, Jian Xu and Yuanguang Li. Genomic foundation of starch-to-lipid switch in oleaginous Chlorella spp. Plant Physiology, 2015, 169 (4):2444-2461. (SCI impact factor 6.305)
  3. Shiwei Sun, Xuetao Wang, Xing Gao, Lihui Ren, Xiaoquan Su, Dongbo Bu and Kang Ning*. Condensing Raman spectrum for single-cell phenotype analysis. BMC Bioinformatics, 2015, 16 (S18): S15. (SCI impact factor 3.501)
  4. Chao Wang, Haicang Zhang, Wei-Mou Zheng, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li and Dongbo Bu*. FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. Bioinformatics, 2015, 32 (3): 462-464. (SCI impact factor 4.531)
  5. Dongdong Meng, Yu Ying, Xiaohua Chen, Ming Lv, Kang Ning, Lushan Wang and Fuli 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, 81 (6): 2006-2014. (SCI impact factor 4.077)
  6. Xiaojun Wang, Xiaoquan Su, Xinping Cui and Kang Ning*. MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data. PeerJ 2015, 3: e993. (SCI impact factor 2.353)
  7. 宁康, 陈挺. 生物医学大数据的现状与展望. 科学通报, 2015, 60 (5/6): 534-546.
  8. 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, 2015, 3: 272-277.
  9. 陈嘉焕, 孙政, 王晓君, 苏晓泉, 宁康. 元基因组学及其在转化医学中的应用. 遗传, 2015, 7: 645-654.
  1. Qian Zhou, Xiaoquan Su and Kang Ning*. Assessment of quality control approaches for metagenomic data analysis. Scientific Reports, 2014, 4: 6957. (SCI impact factor 4.011)
  2. 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, 2: e436. (SCI impact factor 2.353)
  3. Qian Zhou1, Z.Lewis Liu1, Kang Ning1, Anhui Wang, Xiaowei Zeng and Jian Xu. Genomic and transcriptome analyses reveal that MAPK- and phosphatidylinositol-signaling pathways mediate tolerance to 5-hydroxymethyl-2-furaldehyde for industrial yeast Saccharomyces cerevisiae. Scientific Reports, 2014, 4: 6556. (SCI impact factor 4.011)
  4. 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, 2014, 4: 6393. (SCI impact factor 4.011, *Corresponding author)
  5. Peng Yang, Xiaoquan Su, Le Ouyang, Honnian Chua, Xiaoli Li and Kang Ning*. Microbial community pattern detection in human body habitats via ensemble clustering framework. BMC Systems Biology, 2014, 8 (Suppl 4): S7. (SCI impact factor 2.048, *Corresponding author)
  6. Jianqiang Hu, Dongmei Wang, Jing Li, Kang Ning* and Jian Xu*. Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis, Scientific Reports, 2014, 4: 5454. (SCI impact factor 4.011, *Corresponding author)
  7. Xinwei Cheng, Xiaoquan Su, Xiaohua Chen, Huanxin Zhao, Cuipei Bo, Jian Xu, Hong Bai* and Kang Ning*. Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan, Scientific Reports, 2014, 4: 5147. (SCI impact factor 4.011,*Corresponding author)
  8. 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, 2014, 9 (3): e89323.. (SCI impact factor 2.776, *Corresponding author)
  9. Xiaoquan Su, Xuetao Wang, Gongchao Jing and Kang Ning*. GPU-Meta-Storms: Computing the structure similarities among massive amount of microbial community samples using GPU. Bioinformatics 2014, 30 (7): 1031-1033. (SCI impact factor 4.531, *Corresponding author)
  10. Fang Yang1, Kang Ning1, 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 and Jian Xu. Saliva microbiota carry caries-specific functional gene signatures, PLoS ONE, 2014, 9 (2): e76458. (SCI impact factor 2.776, 1First author)
  11. Jing Li1, Danxiang Han1, Dongmei Wang1, Kang Ning1, Jia Jing, Wei Li, Jing Xiaoyan, Huang Shi, Chen Jie, Li Yantao, Qiang Hu and Jian Xu. Choreography of transcriptomes and lipidomes of nannochloropsis reveals the mechanisms of oil synthesis in Microalgae. Plant Cell, 2014, 26 (4), 1645-1665. (SCI impact factor 8.631, 1First author)
  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 Genetics, 2014, 10 (1): e1004094. (SCI impact factor 5.224, 1First author)
  13. Qian Zhou, Xiaoquan Su, Gongchao Jing and Kang Ning*. Meta-QC-Chain: Comprehensive and Fast Quality Control Method for Metagenomic Data. Genomics. Proteomics & Bioinformatics, 2014, 12 (1): 52-56.(SCI impact factor 6.597)
  14. Xinwei Cheng, Xiaohua Chen, Xiaoquan Su, Huanxin Zhao, Maozhen Han, Cunpei Bo, Jian Xu, Hong Bai and Kang Ning*. DNA extraction protocol for biological ingredient analysis of Liuwei Dihuang Wan. Genomics. Proteomics & Bioinformatics, 2014, 12 (3): 137-143.(SCI impact factor 6.597)
  15. 苏晓泉, 宋宝兴, 王雪涛, 马新乐, 徐健, 宁康. Meta-Mesh——元基因组数据分析系统. 生物工程学报, 2014, 30 (1): 6-17.
  1. 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, 2013, 8 (4): e60234. (SCI impact factor 3.776 )
  2. 程新玮, 赵焕新, 宁康, 白虹. DNA条形码技术在中药质量评价中的研究进展. 食品与药品, 2013, 4: 295-299.
  1. Baoxing Song, Xiaoquan Su and Kang Ning*. MetaSee: An interactive and extendable visualization toolbox for metagenomic sample analysis and comparison. PLoS ONE, 2012, 7 (11): e48998. (SCI impact factor 2.776, *Corresponding author)
  2. Yun Wang, Yin Chen, Qian Zhou, Shi Huang, Kang Ning, Jian Xu, Robert M. Kalin, Stephen Rolfe and Wei E. Huang*. A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS ONE, 2012, 7 (10): e47530. (SCI impact factor 2.776)
  3. Xiaoquan Su, Jian Xu and Kang Ning*. Meta-storms: efficient search for similar microbial communities based on a novel indexing scheme and Ssimilarity score for metagenomic data. Bioinformatics, 2012, 28 (19): 2493-2501. (SCI impact factor 4.531, *Corresponding author)
  4. 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 data. Journal of. Proteome Research, 2012, 11 (4): 2261-2271. (SCI impact factor 3.780)
  5. 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 high-throughput sequencing data. Bioinformatics, 2012, 28 (5): 643-650. (SCI impact factor 4.531)
  1. Xiaoquan Su, Jian Xu and Kang Ning*. Parallel-META: efficient metagenomic data analysis based on high-performance computation. BMC Systems Biology, 2011, 6 (S1): S16. (SCI impact factor 2.048)
  2. Fang Yang, Xiaowei Zeng, Kang Ning, Kuanliang Liu, Chienchi Lo,Wei Wang, Jie Chen, Dongmei Wang, Ranran Huang, Xingzhi Chang, Patrick S Chain, Gary Xie, Junqi Ling and Jian Xu. Saliva microbiomes distinguish caries-active from healthy human populations. ISME Journal, 2011, 6 (1): 1-10. (SCI impact factor 9.493)
  3. 凌均棨, 杨芳, 曾晓维, 宁康, 陈劼, Chien-Chi Lo, Patrick S.Chain, Gary Xie,徐健. 龋活跃人群和健康人群的唾液微生物菌群的宏基因组研究. 中华口腔医学会牙体牙髓病学专业委员会. 全国第八次牙体牙髓病学学术会议论文汇编.中华口腔医学会牙体牙髓病学专业委员会, 2011: 3.
  4. Kang Ning, Damian Fermin and Alexey I. Nesvizhskii*. Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. Proteomics, 2010, 10 (14): 2712 - 2718. (SCI impact factor 3.106, 8 citations)
  5. Kang Ning* and Damian Fermin. SAW: A method to identify splicing eents from RNA-Seq data based on splicing fingerprints. PLoS ONE, 2010, 5 (8): e12047. (SCI impact factor 2.776)
  6. Kang Ning, Hoong Kee Ng, Sriganesh Srihari, Hon Wai Leong 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. (SCI impact factor 2.511)
  7. Sriganesh Srihari, Kang Ning* and Hon Wai Leong*. MCL-CAw: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. BMC Bioinformatics, 2010, 11: 504. (SCI impact factor 2.511, *Corresponding author)
  8. 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 (S11): S14. (SCI impact factor 2.511)
  9. Kang Ning. Deposition and Extension Approach to find longest common subsequence for thousands of long sequences. Computational Biology and Chemistry, 2010, 34 (3): 149-157. (SCI impact factor 1.581)
  10. Kang Ning and Hon Wai Leong*. The multiple sequence sets: problem and heuristic algorithms. Journal of Combinatorial Optimization. 2010, 22 (4): 778-796. (SCI impact factor 0.816, premium in Combinatorics)
  11. 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, 2011, 5 (6): 611-625. (SCI impact factor 0.789)
  12. Hoong Kee Ng1, Kang Ning1 and Hon Wai Leong. Two-phase filtering strategy for efficient peptide identification from mass spectrometry. J Proteomics Bioinformatics, 2010, 3: 121-129.. (1Co-first authors)
  13. Hon Nian Chua1, Kang Ning1, Wing-Kin Sung, Hon Wai Leong and Limsoon Wong. Using indirect protein-protein interactions for protein complex prediction. Journal of Bioinformatics and Computational Biology, 2008, 6 (3): 435-466. (1Co-first authors, 25 citations)(SCI impact factor 0.816)
  14. Kang Ning1, Nan Ye1 and Hon Wai Leong. On preprocessing and antisymmetry in de novo peptide sequencing: improving efficiency and accuracy. Journal of Bioinformatics and Computational Biology, 2008, 6 (3): 467-492. (1Co-first authors, 2 citations)(SCI impact factor 0.816)
  15. 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, 2006, 4 (6): 1329-1352. (4 citations)(SCI impact factor 0.816)
  16. Kang Ning and Hon Wai Leong. Towards a better solution to the shortest common supersequence problem: The deposition and reduction algorithm. BMC Bioinformatics, 2006, 7 (Suppl 4): S12. (SCI impact factor 2.511, 5 citations)
  17. 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, 2005, 33 (17): e144. (SCI impact factor 11.147, 10 citations)

 

Book Chapters

 

  1. 丁明跃、刘笔锋、赵元弟、宁康、刘欣、薛宇、肖鹏、尉迟明、马军、陈威等.生物医学工程与信息技术概论, in press.
  2. 宁康、常俊丽、白虹、计磊等.生物统计学:生物大数据的概率统计模型与机器学习方法, in press.
  3. 宁康、常俊丽、白虹、钟朝芳等.生物统计学习题集, in press.
  4. Maozhen Han, Pengshuo Yang, Hao Zhou, Hongjun Li and Kang Ning*. Metagenomics and Single-Cell Omics Data Analysis for Human Microbiome Research. Translational Biomedical Informatics: A Precision Medicine Perspective, 117-137, 2016. Springer.
  5. Kang Ning and Jian Xu. Bioinformatics in microbial metagenomics: Status and prospects. Industrial Biotechnology 2011. Science Press (China).

 

Peer reviewed conference papers

 

  1. Xiaoquan Su, Gongchao Jing, Shi Huang, Jian Xu and Kang Ning*. Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats. IEEE ISB, 2014.
  2. 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.
  3. Fang, Wei, Xingzhi Chang, Xiaoquan Su, Jian Xu, Zhang Deli and Kang Ning*. A machine learning framework of functional biomarker discovery for different microbial communities based on metagenomic data. Systems Biology (ISB), 2012 IEEE 6th International Conference on Systems Biology. IEEE, 2012, 106-112.
  4. Xiaoquan Su, Jian Xu and Kang Ning*. An Open-source collaboration environment for metagenomics research. 2011 IEEE 7th International Conference on e-Science. IEEE , 2011, 7-14.
  5. Xiaoquan Su, Jian Xu and Kang Ning*. Parallel-META: A high-performance computational pipeline for metagenomic data analysis. 2011 IEEE 5th International Conference on Systems Biology. 2011, 173-178.
  6. 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. GIW 2010, 2010.
  7. Sriganesh Srihari, Kang Ning1 and Hon Wai Leong. Refining markov clustering for protein complex prediction by core-attachment. GIW 2009, 2009. Genome Informatics Series Vol. 23, page 159-168. (1Corresponding author, 1 citation)
  8. Sriganesh Srihari, Hoong Kee Ng, Kang Ning and Hon Wai Leong. Detecting hubs and quasi cliques in scale-free networks. ICPR 2008, 2008. IEEE Catalog Number: CFP08182; ISBN: 978-1-4244-2175-6; ISSN: 1051-4651. (EI indexed)
  9. Kang Ning, Hoong Kee Ng and Hon Wai Leong. An accurate and efficient algorithm for peptide and PTM identification by tandem mass spectrometry. GIW 2007, 2007. Genome Informatics Series, 19: 119-130.
  10. Kang Ning and Hon Wai Leong. Algorithm for peptide sequencing by tandem mass spectrometry based on better preprocess and anti-symmetric computational model. CSB 2007, 2007. Computational Systems Bioinformatics: CSB 2007 Conference Proceedings, 6: 19-30. (2 citations)
  11. Hon Nian Chua1, Kang Ning1, Wing-Kin Sung, Hon Wai Leong and Limsoon Wong. A novel algorithm for protein complex prediction based on PPI networks. CSB 2007, 2007. Computational Systems Bioinformatics: CSB 2007 Conference Proceedings, page 97-110. (1Co-first authors)
  12. Hoong Kee Ng, Kang Ning and Hon Wai Leong. A new approach for similarity queries of biological sequences in databases. PAKDD 2007, 2007. Lecture Notes in Computer Science, Vol. 4426, page 728-736. (EI indexed, 1 citation)
  13. Kang Ning, Ket Fah Chong and Hon Wai Leong. De Novo peptide sequencing for mass spectra based on multi-charge strong Tags. APBC 2007, 2007. Series on Advances in Bioinformatics and Computational Biology, Vol. 5, page 287-296. (3 citations)
  14. Kang Ning and Hon Wai Leong. The distribution and deposition algorithm for the multiple oligo nucleotide arrays. GIW 2006, 2006. Genome Informatics. 17 (2): 89-99. (1 citation)
  15. Kang Ning, Hoong Kee Ng and Hon Wai Leong. PepSOM: An algorithm for peptide identification by tandem mass spectrometry based on SOM. GIW 2006, 2006. Genome Informatics 17 (2): 194-205. (3 citations)
  16. Kang Ning, Hoong Kee Ng and Hon Wai Leong. Finding patterns in biological sequences by longest common subsequences and shortest common supersequences. BIBE 2006, 2006. Sixth IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2006), ISBN 0-7695-2727-2, page 53-60. (EI indexed, 2 citations)
  17. Kang Ning and Hon Wai Leong. Towards a better solution to the shortest common supersequence problem: A post processing approach. Proceeding of the First International Multi-symposiums on Computer and Computational Sciences (IMSCCS|06), IEEE Computer Society Press, ISBN 0-7695-2581-4, Vol. 1, page 84-90. (EI indexed, 4 citations)
  18. Kang Ning and Hon Nian Chua. Automated identification of protein classification and detection of annotation errors in protein databases using statistical approaches. KDLL 2006, 2006. Lecture Notes in Computer Science, Vol. 3886, page 123-138.
  19. Kang Ning, Ket Fah Chong and Hon Wai Leong. A database search algorithm for identification of peptides with multiple charges using tandem mass spectrometry. BioDM 2006, 2006. Lecture Notes in Computer Science, Vol. 3916, page 2-13. (EI indexed, 3 citations)
  20. Ket Fah Chong, Kang Ning, Hon Wai Leong and Pavel Pevzner. Characterization of multi-charge mass spectra for peptide sequencing. APBC 2006, 2006. Proceedings of 4th Asia-Pacific Bioinformatics Conference, page 109-119. (2 citations)

 

Patent Of Invention

 

  1. 宁康、杨朋硕、余少俊、韩毛振.微生物群中物种的关联性挖掘方法, CN201910342119.X.
  2. 宁康、白虹、姚奇、朱雪.中药复方制剂的生物成分分析方法,CN201910334789.7.
  3. 宁康、白虹、李洪军.基于ITS2鉴定植物物种的方法及设备,CN201910335741.8.
  4. 宁康、陈超云、何睿乔、成章昱、韩毛振、查毓国、杨朋硕、姚奇、周豪、钟朝芳. 确定环境因素与菌群结构和功能相关性的方法及设备,201910334811.8.
  5. 宁康、韩毛振、杨朋硕、钟朝芳.一种肠道病毒组的高通量检测方法及应用,201811130676.7.
  6. 宁康、奚望、高岩、成章昱、陈超云、韩毛振.一种高通量测序的微生物数据处理方法,201811130694.5 .
  7. 宁康、李锐豪、陈超云、朱雪. 酵母DNA的保真存储方法,201811249175.0 .
  8. 宁康、李希、朱雪、王雯婕. 一种实验室的微生物污染鉴别方法,201811130690.7.
  9. 宁康、谭重阳、杨鹏硕、韩毛振. 确定肠道细菌亚种的方法及设备,201811249167.6.
  10. 宁康、曹乐、周纯羽、朱雪. 海洋珊瑚菌群结构分析、基因挖掘方法及设备,201811252030.6.
  11. 宁康、钱晓波、陈超云、杨朋硕. 一种高通量测序的RNA数据处理方法,201811130687.5.
  12. 宁康、白虹、李洪军、张润之、朱雪. 中药及中药制剂的网络药理分析方法以及系统,201811249212.8.
  13. 宁康、白虹、张润之、余少俊.中药制剂非处方物种化学成分致病的分析方法及设备 , 201710820809.2.
  14. 周茜、宁康、苏晓泉、徐健. 基于多核CPU硬件的高通量转录组测序数据质量控制方法,201410205571.9.
  15. 宁康、王静. 活体单细胞拉曼分析平台数字控制系统和方法, 201510026994.9
  16. 任立辉、宁康、苏晓泉、徐健、肖航. 一种中药制剂非处方物种化学成分的网络药理分析方法,201410579147.0
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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

 

  1. 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.
  2. 任立辉、宁康、苏晓泉、徐健. 单细胞拉曼光谱模拟系统软件, 2013SR079944.
  3. 任立辉、宁康、苏晓泉、徐健. 单细胞拉曼光谱系统控制软件. 2013SR015642.
  4. 苏晓泉、宁康、徐健. 元基因组数据库索引与搜索系统, 2013SR000258.
  5. 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.