Research Papers

Microalgal Biofuels: Photosynthetic Microalgae for Biofuel Production

  1. The genomic foundation of robust oil production in microalgae, in preparation.
  2. The discovery of functional features and their evolutionary signatures in microalgal genomes, in preparation.
  3. Global transcriptional landscape of stress-induced oil production in microalgae, in preparation.
  4. Wang DM, Lu YD, H He,Xu J. Establishing Oleaginous Microalgae Research Models for Consolidated Bioprocessing of Solar Energy. Advances in Biochemical Engineering/Biotechnology, 2012, 1-16, DOI: 10.1007/10_2011_122 Link

Cellulosic Biofuels: Microbial Degradation of Cellulose/Polysaccharides

  1. Xu C, Huang R, Teng L, Wang D, and Xu J (2013) Structure and regulation of the cellulose degradome in Clostridium cellulolyticum, Biotechnology for Biofuels 2013, 6:73, DOI:10.1186/1754-6834-6-73 Link
  2. Lin Lu and Xu J (2013) Dissecting and engineering metabolic and regulatory networks of thermophilic bacteria for biofuel production, Biotechnology Advances, DOI: 10.1016/j.biotechadv.2013.03.003 ScienceDirect
  3. Lin L, Song H, Tu Q, Qin Y, Zhou A, Liu W, He Z, Zhou J, and Xu J. The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria. PLoS Genetics, 7(10): e1002318. Link
  4. Lin L*., Song H*, Ji Y., He Z., Pu Y., Zhou J, and Xu, J. Ultrasound-mediated plasmid transformation in thermophilic anaerobic bacteria. PLoS One, Sep 4;5(9):e12582. Pubmed
  5. Xu CG, Qin Y, Li YD, Ji YT , Song HH*, Xu J* (2010) Factors influencing cellulosome activity in Consolidated-Bioprocessing production of cellulosic ethanol. Bioresource Technology, 101:9560-9. Pubmed
  6. Mcbride MJ, Xie G, Martens E, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, Staroscik AM, Hoover TR, Cheng YQ, Stein J (2009) Novel features of the polysaccharide digesting gliding bacterium Flavobacterium johnsoniae revealed by genome sequence analysis. Appl. Environ. Microbiol, (21):6864-75. Epub 2009 Aug 28.
  7. Feng X, Mouttaki, Lin L, Huang R, Wu B, Hemme C, He Z, Zhang B, Hicks L, Xu, J, Zhou J, Tang Y (2009) Characterization of the Central Metabolic Pathways in Thermoanaerobacter sp. X514 Isotopomer-Assisted Metabolite Analysis. Appl. Environ. Microbiol, 75(15):5001-8. Epub 2009 Jun 12.
  8. Xu J*, Mahowald MA*, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM,Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biology, 2007 Jun 19;5(7):e156 (*contributed equally). Pubmed.
  9. Selected peer commentaries: Walker A, Say hello to our little friends, Nat Rev Microbiol, 5:572-3 (2007) Pubmed
  10. Christopher H, Matthew F, Hu Q, Deng Y, Lin L, Tu Q, Housna M, Zhou A, Feng X, Zuo Z, Ramsay B, He Z, Wu L , Joy Van Nostrand, Xu J, Tang Y, Juergen W, Tommy P, and Zhou J. Correlation of genomic and physiological traits to biofuel yields in Thermoanaerobacter species. Applied and Environmental Microbiology, 2011, AEM.05677-11. Link
  11. Sonnenburg JL,Xu J, Leip DD, Chen CH, Westover BP, Buhler JD, Gordon JI. (2005). Adaptive foraging of a prominent human intestinal symbiont in gnotobiotic mice. Science, 307:1955-9. Pubmed
  12. Xu J, Chiang HC, Bjursell MK, Gordon JI. (2004). Message from a human gut symbiont: sensitivity is a prerequisite for sharing. Trends Microbiol,12:21-8. Pubmed
  13. Xu J and Gordon JI. (2003). Inaugural Article: Honor Thy Symbionts.Proc Natl Acad Sci USA 100:10452-9. Pubmed
  14. Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI. (2003). A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299:2074-6. Pubmed
  15. Hooper LV, Xu J, Falk PG, Midtvedt T, Gordon JI. (1999). A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc Natl Acad Sci USA 96:9833-8. Pubmed

Metagenomics and Single-cell genomics: Technology Development and Applications

  1. Wang Y, Chen Y, Rolfe S, Zhou Q, Ning K, Xu J, Huang WE (2012) Development of a toolbox for unravelling functional microbes and genes in a complex microbial community. PLoS ONE, in press.
  2. Li M, Xu J, Romero-Gonzalez M, Banwart S, Huang WE, Single cell Raman spectroscopy for cell sorting and imaging. Curr. Opin. Biotech. 2012,23(1),56-63. Link
  3. Dai X, Zhu YX, Luo, YF, Song L, Chen FR, Wang M, Li JB, Zeng XW, Dong ZY, Hu SN, Liu D, Li LY, Xu J*, Huang Li*, Dong XZ*. Metagenomic insights into efficient lignocellulose degradation in yak rumen, PLoS ONE 7(7): e40430. doi:10.1371/journal.pone.0040430.
  4. You N, Murillo G, Ning K, Zeng XW, Xu J, Zhang SD, Zhu JK, Cui XP (2012), SNP calling using genotype model selection on next generation sequencing data, Bioinformatics, doi: 10.1093/bioinformatics/bts001
  5. Wang, B., Zhang CX, Liu JL, ZengXW, Li FR, Wu YC, Lini XG, Zhu JG, Xiong ZQ, Xu J, Cai ZC, Jia ZJ (2011) Microbial Community Changes along a Land-Use Type Gradient of Desert Soil Origin. Pedosphere, submitted
  6. Chen XJ , Chen GL, Qiu MD, Guo J, Sun GP, Zeng XW, Xu J, Xu MY. Characterization of an enrichment culture debrominating deca-BDE with zero-valent iron as electron donor. PLoS ONE (2012).
  7. Jian XH, Pan HX, Ning TT, Shi YY, Chen YS, Li Y, Zeng XW, Xu J, Tang GL. Analysis of YM-216391 Biosynthetic Gene Cluster and Improvement of the Cyclopeptide Production in Heterologous Host. ACS Chem Biol.2012.DOI: 10.1021/cb200479f PubMed
  8. Huang S, Yang F, Zeng XW, Chen J, Li R, Ting W, Li C, Wei W, Liu JQ, Davis C., Chen L and Xu J. Preliminary Characterization of the Oral Microbiota of Chinese Adults with and Without Gingivitis. BMC Oral Health. 2011, 11:33 PubMed
  9. 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, ISME J, 2011.10.1038. Pubmed
  10. Xia WW, Zhang CX, Zeng XW, Feng YZ, Weng JH, Lin XG, Zhu JG, Xiong ZQ, Xu J, Cai ZC, Jia ZJ (2011) Autotrophic growth of soil Archaea during active nitrification. ISME J, 2011,1226-36. Pubmed
  11. Oh JD, Kling-Bäckhed H, Giannakis M, Xu JFulton R, Fulton L, Cordum H, Wang C, Elliott G, Edwards J, Mardis ER, Engstrand LG, and Gordon JI (2006). The complete genome sequence of a Helicobacter pylori isolate from a patient with chronic atrophic gastritis: characterization of genome evolution during disease progression. Proc Natl Acad Sci USA,103:9999-10004.
  12. Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, Bieri T, Meyer RR, Ozersky P, Armstrong JR, Fulton RS, Latreille JP, Spieth J, Hooton TM, Mardis ER, Hultgren SJ, and Gordon JI (2006). Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci USA 103:5977-82.
  13. Xu J and Gordon JI. (2005). MapLinker, a software tool to aid physical map-based whole-genome shotgun assembly. Bioinformatics 21:1265-6.
  14. Ippolito JE, Xu J, Jain S, Moulder K, Mennerick S, Crowley JR, Townsend RR, Gordon JI (2005). An integrated functional genomics and metabolomics approach for defining poor prognosis in human neuroendocrine cancers. Proc Natl Acad Sci USA 102:9901-6.
  15. Mitreva M, Arasu P, Hawdon J, Martin J, Dante M, Wylie T, Xu J, Stajich JE, Kapulkin V, Zhan B, Clifton SW, Waterston RH, Wilson RK, McCarter JP. (2005). Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics 6:58.
  16. Magrini V, Warren WC, Wallis J, Goldman WE, Xu J, Mardis ER, McPherson JD. Fosmid-based physical mapping of the Histoplasma capsulatum genome. (2004). Genome Res, 14:1603-9.

Methodology Development in Computational Biology

  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, accepted.
  2. Baoxing Song, Xiaoquan Su and Kang Ning. MetaSee: An interactive and extendable visualization toolbox for metagenomic sample analysis and comparison, PLOS ONE, 2012
  3. 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 2012, doi: 10.1093/bioinformatics/bts470
  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. J. Proteome Res, DOI: 10.1021/pr201052x (2012)
  5. Xiaoquan Su, Jian Xu and Kang Ning. Parallel-META: A High-Performance Computational Pipeline for Metagenomic Data Analysis. BMC Systems Biology, 2012, 6(Suppl1):S16 
  6. Na You, Gabriel Murillo, Kang Ning, Xiaoquan Su, Xiaowei Zheng, Jian Xu, Shoudong Zhang, Jiankang Zhu and Xinping Cui. SNP calling using genotype model selection on next generation sequencing data. Bioinforamtics, 2011, accepted.
  7. Xiaoquan Su, Jian Xu and Kang Ning1. An Open-source Collaboration Environment for Metagenomics Research. IEEE e-Science, 2011. Link
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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. (in press)
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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

Book Chapters

  1. Ning K and Xu J (2010) Bioinformatics in the metagenomics research for microbial communities: status and prospects, in Annual Advances (2011) of Industrial Biotechnology, ISBN 978-7-03-032516-7, Science Press (Beijing) 2011
  2. Wang DM and Xu J (2010) Dissection and engineering of algal feedstock for industry-scale oil production, in Annual Advances (2010) of Industrial Biotechnology, ISBN 978-7-03-028270-5, Science Press, Beijing, 2010
  3. Xu J (2009) The Genome and Gene Resources of Biomass Utilization, in Science & Technology on Bio-hylic and Biomass Resources in China: A Roadmap to 2050, ISBN 978-3-642-05339-9, Springer 2009
  4. Hu GR, Wang W, Xu J (2008) Elucidating the structure, function and regulation of microbial communities for bioenergy, in Annual Advances (2008) of Industrial Biotechnology, ISBN 978-7-03-022283-1, Science Press (Beijing) 2008