Kang Ning, PhD - Publications

Affiliations: 
Qingdao Institute 
Area:
Computational Biology, Bioinformatics

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Fan J, Ning K, Zeng X, Luo Y, Wang D, Hu J, Li J, Xu H, Huang J, Wan M, Wang W, Zhang D, Shen G, Run C, Liao J, et al. Genomic Foundation of Starch to Lipid Switch in Oleaginous Chlorella. Plant Physiology. PMID 26486592 DOI: 10.1104/pp.15.01174  1
2015 Wang X, Su X, Cui X, Ning K. MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data. Peerj. 3: e993. PMID 26213658 DOI: 10.7717/peerj.993  1
2015 Bai H, Ning K, Wang CY. [Biological ingredient analysis of traditional Chinese medicines utilizing metagenomic approach based on high-throughput-sequencing and big-data-mining]. Yao Xue Xue Bao = Acta Pharmaceutica Sinica. 50: 272-7. PMID 26118104  1
2014 Yang P, Su X, Ou-Yang L, Chua HN, Li XL, Ning K. Microbial community pattern detection in human body habitats via ensemble clustering framework. Bmc Systems Biology. 8: S7. PMID 25521415 DOI: 10.1186/1752-0509-8-S4-S7  0.44
2014 Zhou Q, Su X, Ning K. Assessment of quality control approaches for metagenomic data analysis. Scientific Reports. 4: 6957. PMID 25376098 DOI: 10.1038/srep06957  1
2014 Zhou Q, Liu ZL, Ning K, Wang A, Zeng X, Xu J. 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. 4: 6556. PMID 25296911 DOI: 10.1038/srep06556  1
2014 Su X, Hu J, Huang S, Ning K. Rapid comparison and correlation analysis among massive number of microbial community samples based on MDV data model. Scientific Reports. 4: 6393. PMID 25227622 DOI: 10.1038/srep06393  1
2014 Ren L, Su X, Wang Y, Xu J, Ning K. QSpec: online control and data analysis system for single-cell Raman spectroscopy. Peerj. 2: e436. PMID 25024908 DOI: 10.7717/peerj.436  1
2014 Hu J, Wang D, Li J, Jing G, Ning K, Xu J. Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis. Scientific Reports. 4: 5454. PMID 24965723 DOI: 10.1038/srep05454  1
2014 Cheng X, Su X, Chen X, Zhao H, Bo C, Xu J, Bai H, Ning K. Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan. Scientific Reports. 4: 5147. PMID 24888649 DOI: 10.1038/srep05147  1
2014 Cheng X, Chen X, Su X, Zhao H, Han M, Bo C, Xu J, Bai H, Ning K. DNA extraction protocol for biological ingredient analysis of Liuwei Dihuang Wan. Genomics, Proteomics & Bioinformatics. 12: 137-43. PMID 24838067 DOI: 10.1016/j.gpb.2014.03.002  1
2014 Su X, Song B, Wang X, Ma X, Xu J, Ning K. [Meta-Mesh: metagenomic data analysis system]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 30: 6-17. PMID 24818475 DOI: 10.13345/j.cjb.130429  1
2014 Li J, Han D, Wang D, Ning K, Jia J, Wei L, Jing X, Huang S, Chen J, Li Y, Hu Q, Xu J. Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oil Synthesis in Microalgae. The Plant Cell. 26: 1645-1665. PMID 24692423 DOI: 10.1105/tpc.113.121418  1
2014 Su X, Pan W, Song B, Xu J, Ning K. Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization. Plos One. 9: e89323. PMID 24595159 DOI: 10.1371/journal.pone.0089323  1
2014 Yang F, Ning K, Chang X, Yuan X, Tu Q, Yuan T, Deng Y, Hemme CL, Van Nostrand J, Cui X, He Z, Chen Z, Guo D, Yu J, Zhang Y, et al. Saliva microbiota carry caries-specific functional gene signatures. Plos One. 9: e76458. PMID 24533043 DOI: 10.1371/journal.pone.0076458  1
2014 Zhou Q, Su X, Jing G, Ning K. Meta-QC-Chain: comprehensive and fast quality control method for metagenomic data. Genomics, Proteomics & Bioinformatics. 12: 52-6. PMID 24508279 DOI: 10.1016/j.gpb.2014.01.002  1
2014 Wang D, Ning K, Li J, Hu J, Han D, Wang H, Zeng X, Jing X, Zhou Q, Su X, Chang X, Wang A, Wang W, Jia J, Wei L, et al. Nannochloropsis genomes reveal evolution of microalgal oleaginous traits. Plos Genetics. 10: e1004094. PMID 24415958 DOI: 10.1371/journal.pgen.1004094  1
2014 Su X, Wang X, Jing G, Ning K. GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU. Bioinformatics (Oxford, England). 30: 1031-3. PMID 24363375 DOI: 10.1093/bioinformatics/btt736  1
2013 Wei L, Xin Y, Wang D, Jing X, Zhou Q, Su X, Jia J, Ning K, Chen F, Hu Q, Xu J. Nannochloropsis plastid and mitochondrial phylogenomes reveal organelle diversification mechanism and intragenus phylotyping strategy in microalgae. Bmc Genomics. 14: 534. PMID 23915326 DOI: 10.1186/1471-2164-14-534  1
2013 Zhou Q, Su X, Wang A, Xu J, Ning K. QC-Chain: fast and holistic quality control method for next-generation sequencing data. Plos One. 8: e60234. PMID 23565205 DOI: 10.1371/journal.pone.0060234  1
2013 Su X, Wang X, Xu J, Ning K. GPU-Meta-Storms: Computing the similarities among massive microbial communities using GPU International Conference On Systems Biology, Isb. 69-74. DOI: 10.1109/ISB.2013.6623796  1
2013 Ma Y, Shi T, Li W, Qian F, Ning K, Cui C, Zhu Y. A scientific collaboration cloud platform and its multidisciplinary applications 2013 Ieee 3rd International Conference On Information Science and Technology, Icist 2013. 466-470. DOI: 10.1109/ICIST.2013.6747590  1
2012 Song B, Su X, Xu J, Ning K. MetaSee: an interactive and extendable visualization toolbox for metagenomic sample analysis and comparison. Plos One. 7: e48998. PMID 23145044 DOI: 10.1371/journal.pone.0048998  1
2012 Wang Y, Chen Y, Zhou Q, Huang S, Ning K, Xu J, Kalin RM, Rolfe S, Huang WE. A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. Plos One. 7: e47530. PMID 23082176 DOI: 10.1371/journal.pone.0047530  1
2012 Su X, Xu J, Ning K. Parallel-META: efficient metagenomic data analysis based on high-performance computation. Bmc Systems Biology. 6: S16. PMID 23046922 DOI: 10.1186/1752-0509-6-S1-S16  1
2012 Su X, Xu J, Ning K. Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data. Bioinformatics (Oxford, England). 28: 2493-501. PMID 22843983 DOI: 10.1093/bioinformatics/bts470  1
2012 Ning K, Fermin D, Nesvizhskii AI. 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. 11: 2261-71. PMID 22329341 DOI: 10.1021/pr201052x  1
2012 You N, Murillo G, Su X, Zeng X, Xu J, Ning K, Zhang S, Zhu J, Cui X. SNP calling using genotype model selection on high-throughput sequencing data. Bioinformatics (Oxford, England). 28: 643-50. PMID 22253293 DOI: 10.1093/bioinformatics/bts001  1
2012 Yang F, Zeng X, Ning K, Liu KL, Lo CC, Wang W, Chen J, Wang D, Huang R, Chang X, Chain PS, Xie G, Ling J, Xu J. Saliva microbiomes distinguish caries-active from healthy human populations. The Isme Journal. 6: 1-10. PMID 21716312 DOI: 10.1038/ismej.2011.71  1
2012 Fang W, Chang X, Su X, Xu J, Zhang D, Ning K. A machine learning framework of functional biomarker discovery for different microbial communities based on metagenomic data 2012 Ieee 6th International Conference On Systems Biology, Isb 2012. 106-112. DOI: 10.1109/ISB.2012.6314121  1
2011 Ning K, Ng HK, Leong HW. 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. 5: 611-25. PMID 22295747 DOI: 10.1504/IJDMB.2011.045413  1
2011 Su X, Xu J, Ning K. Parallel-META: A high-performance computational pipeline for metagenomic data analysis 2011 Ieee International Conference On Systems Biology, Isb 2011. 173-178. DOI: 10.1109/ISB.2011.6033151  1
2011 Su X, Ma Y, Yang H, Chang X, Nan K, Xu J, Ning K. An open-source collaboration environment for metagenomics research Proceedings - 2011 7th Ieee International Conference On Escience, Escience 2011. 7-14. DOI: 10.1109/eScience.2011.10  1
2011 Ning K, Leong HW. The multiple sequence sets: Problem and heuristic algorithms Journal of Combinatorial Optimization. 22: 778-796. DOI: 10.1007/s10878-010-9329-3  1
2010 Ning K, Nesvizhskii AI. 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. 11: S14. PMID 21172049 DOI: 10.1186/1471-2105-11-S11-S14  1
2010 Ning K, Ng HK, Srihari S, Leong HW, Nesvizhskii AI. Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. Bmc Bioinformatics. 11: 505. PMID 20939873 DOI: 10.1186/1471-2105-11-505  1
2010 Srihari S, Ning K, Leong HW. MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. Bmc Bioinformatics. 11: 504. PMID 20939868 DOI: 10.1186/1471-2105-11-504  1
2010 Ng HK, Ning K, Leong HW. Two-phase Filtering Strategy for Efficient Peptide Identification from Mass Spectrometry. Journal of Proteomics & Bioinformatics. 3: 121-129. PMID 20717493 DOI: 10.4172/jpb.1000130  1
2010 Ning K, Fermin D. SAW: a method to identify splicing events from RNA-Seq data based on splicing fingerprints. Plos One. 5: e12047. PMID 20706591 DOI: 10.1371/journal.pone.0012047  1
2010 Ning K. Deposition and extension approach to find longest common subsequence for thousands of long sequences. Computational Biology and Chemistry. 34: 149-57. PMID 20570215 DOI: 10.1016/j.compbiolchem.2010.05.001  1
2010 Ning K, Fermin D, Nesvizhskii AI. Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. Proteomics. 10: 2712-8. PMID 20455209 DOI: 10.1002/pmic.200900473  1
2009 Srihari S, Ning K, Leong HW. Refining Markov Clustering for protein complex prediction by incorporating core-attachment structure. Genome Informatics. International Conference On Genome Informatics. 23: 159-68. PMID 20180271  1
2008 Ning K, Ye N, Leong HW. On preprocessing and antisymmetry in de novo peptide sequencing: improving efficiency and accuracy. Journal of Bioinformatics and Computational Biology. 6: 467-92. PMID 18574859 DOI: 10.1142/S0219720008003503  1
2008 Chua HN, Ning K, Sung WK, Leong HW, Wong L. Using indirect protein-protein interactions for protein complex prediction. Journal of Bioinformatics and Computational Biology. 6: 435-66. PMID 18574858 DOI: 10.1142/S0219720008003497  1
2008 Srihari S, Ng HK, Ning K, Leong HW. Detecting hubs and quasi cliques in scale-free networks Proceedings - International Conference On Pattern Recognition 1
2007 Ning K, Ng HK, Leong HW. An accurate and efficient algorithm for Peptide and ptm identification by tandem mass spectrometry. Genome Informatics. International Conference On Genome Informatics. 19: 119-30. PMID 18546510  1
2007 Chua HN, Ning K, Sung WK, Leong HW, Wong L. Using indirect protein-protein interactions for protein complex predication. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 6: 97-109. PMID 17951816  1
2007 Ning K, Leong HW. Algorithm for peptide sequencing by tandem mass spectrometry based on better preprocessing and anti-symmetric computational model. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 6: 19-30. PMID 17951809  1
2007 Ning K, Chong KF, Leong HW. De novo peptide sequencing for mass spectra based on multi-charge strong tags Series On Advances in Bioinformatics and Computational Biology. 5: 287-296.  1
2007 Ng HK, Ning K, Leong HW. A new approach for similarity queries of biological sequences in databases Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4426: 728-736.  1
2006 Ning K, Ng HK, Leong HW. PepSOM: an algorithm for peptide identification by tandem mass spectrometry based on SOM. Genome Informatics. International Conference On Genome Informatics. 17: 194-205. PMID 17503392  1
2006 Ning K, Leong HW. The distribution and deposition algorithm for multiple oligo nucleotide arrays. Genome Informatics. International Conference On Genome Informatics. 17: 89-99. PMID 17503382  1
2006 Chong KF, Ning K, Leong HW, Pevzner P. Modeling and characterization of multi-charge mass spectra for peptide sequencing. Journal of Bioinformatics and Computational Biology. 4: 1329-52. PMID 17245817 DOI: 10.1142/S021972000600248X  1
2006 Ning K, Leong HW. Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm. Bmc Bioinformatics. 7: S12. PMID 17217504 DOI: 10.1186/1471-2105-7-S4-S12  1
2006 Ning K, Ng HK, Leong HW. Finding patterns in biological sequences by longest common subsequences and shortest common supersequences Proceedings - Sixth Ieee Symposium On Bioinformatics and Bioengineering, Bibe 2006. 53-60. DOI: 10.1109/BIBE.2006.253315  1
2006 Ning K, Chua HN. Automated identification of protein classification and detection of annotation errors in protein databases using statistical approaches Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3886: 123-138. DOI: 10.1007/11683568_11  1
2006 Chong KF, Ning K, Leong HW, Pevzner P. Characterization of multi-charge mass spectra for peptide sequencing Series On Advances in Bioinformatics and Computational Biology. 3: 109-119.  1
2006 Ning K, Chong KF, Leong HW. A database search algorithm for identification of peptides with multiple charges using tandem mass spectrometry Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3916: 2-13.  1
2005 Ning K, Choi KP, Leong HW, Zhang L. A post-processing method for optimizing synthesis strategy for oligonucleotide microarrays. Nucleic Acids Research. 33: e144. PMID 16192568 DOI: 10.1093/nar/gni147  1
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