1.    Qin, J., Zhao, B., Wang, X., Wang, L., Yu, B., Ma, Y., Ma, C., Tang, H., Sun, J., Xu, P. Non-sterilized fermentative production of polymer-grade L-lactic acid by a newly isolated thermophilic strain Bacillus sp. 2-6. PLoS ONE, 2009, 4 (2).

2.    Wortman, J.R., Gilsenan, J.M., Joardar, V., …, Sun, J., Taheri-Talesh, N., Takeshita, N., Ussery, D., vanKuyk, P.A., Visser, H., van de Vondervoort, P.J., de Vries, R.P., Walton, J., Xiang, X., Xiong, Y., Zeng, A.P., Brandt, B.W., Cornell, M.J., van den Hondel, C.A., Visser, J., Oliver, S.G., Turner, G. The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal genetics and biology, 2009, 46 Suppl 1, pp. S2-13.

3.    Flipphi, M., Sun, J., Robellet, X., Karaffa, L., Fekete, E., Zeng, A.P., Kubiecek, C.P. Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp. Fungal genetics and biology, 2009, 46 Suppl 1, pp. S19-S44.

4.    Seidl V, Song L, Lindquist E, Gruber S, Koptchinskiy A, Zeilinger S, Schmoll M, Martínez P, Sun J, Grigoriev I, Herrera-Estrella A, Baker SE, Kubicek CP. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey. BMC Genomics. 2009, 10:567.

5.    Bizukojc M, Dietz D, Sun J, Zeng AP. Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions. Bioprocess Biosyst Eng. 2009 Aug 13. [Epub ahead of print]

6.    Sun J, Lu X, Rinas U and Zeng AP. Metabolic pecularities of Aspergillus niger disclosed by comparative metabolic genomics. Genome Biology. 8:R182

7.    Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den BM, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, D'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H (2007). Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol 25:221-231.

8.    Sun J, Wang W, Hundertmark C, Zeng AP, Jahn D, Deckwer WD. (2006) A protein database constructed from low-coverage genomic sequence of Bacillus megaterium and its use for accelerated proteomic analysis. J. Biotechnol. 124:486-495

9.    Wang W, Sun J, Hollmann R, Zeng AP, Deckwer WD. (2006) Proteomic characterization of transient expression and secretion of a stress-related metalloprotease in high cell density culture of Bacillus megaterium. J. Biotechnol. 126:313-324.

10.Zheng P, Sun J, van den Heuvel J, Zeng AP. (2006) Discovery and investigation of a new, second triose phosphate isomerase in Klebsiella pneumoniae. J. Biotechnol. 125:462–473

11.Zheng P, Menzel K, Sun J, van den Heuvel J, Zeng AP. (2006) Overexpression of genes of the dha regulon and its effects on cell growth, glycerol fermentation to 1,3-propanediol and plasmid stability in Klebsiella pneumoniae.Process Biochemistry. 41:2160–2169

12.Sun J, Gunzer F, Westendorf AM, Buer J, Scharfe M, Jarek M, G？？ling F, Bl？cker H, Zeng AP. (2005) Genomic peculiarity of coding sequences and metabolic potential of the probiotic Escherichia coli strain Nissle 1917 inferred from raw genome sequence.
J. Biotechnol. 117:147–161

13.Sun J, Zeng AP. (2004). IdentiCS - identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics. 5:112

14.Sun J, Daniel R, Wagner-D？bler I, and Zeng AP. (2004) Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways. BMC Evolutionary Biology 4:36

15.Sun J, van den Heuvel J, Soucaille P, Qu Y, Zeng AP. (2003) Comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria. Biotechnol Prog. 19:263-272

16.Wang W, Sun J, Hartlep M, Deckwer WD, Zeng AP. (2003) Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Biotechnol Bioeng. 83:525-536

17.Wang W*, Sun J*, Nimtz M, Deckwer WD, Zeng AP. (2003) Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences. Proteome Sci. 1:6 *: equal contributor

18.Zeng, A.-P., Sun, J. Continuous Culture, a book chapter in Manual of Industrial Microbiology and Biotechnology, 3rd Ed., edited by R. H. Baltz et al. ASM press, 2010.

19.Sun J and Zeng AP (2008) Systems Biotechnology. In: 2008 Report on the Development of Industrial Biotechnology. Ed. The Bureau of Life Science & Biotechnology, Chinese Academy of Sciences, Science Press, Beijing. (in Chinese)

20.Ma H, Rosa da Silva M,Sun J, Kumar B, Zeng AP (2007) Reconstruction and Structural Analysis of Metabolic and Regulatory Networks. In: "Introduction to Systems Biology". Eds. Sangdun Choi, Humana Press.

21.da Silva MR, Ma H,Sun J, He F, Zeng AP (2006) Metabolic network. In B. H. Junker, F. Schreiber (eds.)Biological Network Analysis, Wiley: 233-253.

22.Zeng, AP;Sun, J; Wang, W; Ma, H; Deckwer, WD (2006) Chapter 2. Application of Genomic and Proteomic Data for Bioprocess Analysis and Optimization. In: Yang, S. T. (ed.)Bioprocessing for value-added products from renewable resources. Elservier Inc,USA, 25-48.