Index	Publication Since Joining Hubei University	Date
1	Yang S*#, Vera J. M*, Savvakis G., Moskvin O. V., Yang Y., McIlwain S. J., Lyu Y., Zinonos I., Hebert A. S., Coon J. J., Bates D. M., Sato T. K., Brown S. D., Himmel M. E., Zhang M., Landick R., Pappas K. M#, Zhang Y*#. 2018. Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. Biotechnology for Biofuels. 11：125	2018
2	2.Wang X*., He Q. *, Yang Y. *, Wang J., Haning K., Hu Y., Wu B., He M., Zhang Y., Bao J., Contreras L. M. # and Yang S#. 2018. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metabolic Engineering.	2018
3	Yang S#, M. A. Franden, Q. Yang, Y.-C. Chou, M. Zhang and P. T. Pienkos#. 2018. Identification of inhibitors in lignocellulosic slurries and determination of their effect on hydrocarbon-producing microorganisms. Frontiers in Bioengineering and Biotechnology 6:23. doi: 10.3389/fbioe.2018.00023.	2018
4	Yang Y, Hu M, Tang Y, Geng B, Qiu M, He Q, Chen S, Wang X#, Yang S#. 2018. Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis. Bioresources and Bioprocessing, 5(1):6.	2018
5	Cai, D., S. Hu, Y. Chen, L. Liu, S. Yang, X. Ma and S. Chen. 2018. Enhanced Production of Poly-γ-glutamic acid by Overexpression of the Global Anaerobic Regulator Fnr in Bacillus licheniformis WX-02. Applied Biochemistry and Biotechnology https://doi.org/10.1007/s12010-018-2693-7	2018
6	Huo, Y., Y. Zhan, Q. Wang, S. Li, Yang, S., C. T. Nomura, C. Wang and S. Chen. 2017. Acetolactate synthase (AlsS) in Bacillus licheniformis WX-02: enzymatic properties and efficient functions for acetoin/butanediol and L-valine biosynthesis. Bioprocess Biosyst Eng 41(1): 87-96.	2017
7	Xu, Q., E. P. Knoshaug, W. Wang, M. Alahuhta, J. O. Baker, Yang, S., T. Vander Wall, S. R. Decker, M. E. Himmel, M. Zhang, and H. Wei. 2017. Expression and secretion of fungal endoglucanase II and chimeric cellobiohydrolase I in the oleaginous yeast Lipomyces starkeyi. Microb Cell Fact 16(1): 126.	2017
8	Cho, S. H., K. Haning, W. Shen, C. Blome, R. Li, Yang S., and L. M. Contreras. 2017. Identification and characterization of 5′untranslated regions (5′UTRs) in Zymomonas mobilis as regulatory biological parts. Frontiers in Microbiology 8:2432.	2017
9	Yang, S. *#, Fei., Q.*, Zhang, Y., Contreras, L. M., Utturkar, S. M., Brown, S. D., Himmel, M.E., and Zhang, M#. 2016. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microbial Biotechnology. 9(6), 699–717.	2016
10	Yang, S. #, Mohagheghi, A., Chou, Y-C., Franden, M. A., Chen, X. W., Dowe, N., Himmel, M., and Zhang, M. # 2016. Metabolic engineering of Zymomonas mobilis for production of 2,3-butanediol from lignocellulosic biomass sugars. Biotechnology for Biofuels 9:189.	2016
11	Xu, Q., Resch, M., Podkaminer, K., Yang, S., Baker, J., Donohoe, B., Wilson, C., Klingeman, D. M., Olson, D., Decker, S., Giannone, R. J., Hettich, R. L., Brown, S. D., Lynd, L. R., Bayer, E. A., Himmel, M. E., and Bomble, Y. 2016. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. Science Advances. 2(2): e1501254.	2016
12	Yang, S. #, Wang, W. #, Wei, H., Wychen, S. V., Pienkos, P. T., Zhang, M., and Himmel, M. 2016. Impact of nitrogen deficiency strategies on lipid production for yeast and fungal species. Energies. 9:685.	2016
13	Shu, M., Shen, W., Yang, S., Wang, X., Wang, F., Wang, Y., and Ma, L. 2016. High-level expression and characterization of a novel serine protease in Pichia pastoris by multi-copy integration. Enzyme Microb Technol. 92:56-66.	2016

Index	Previous Publication	Date
Biofuels：
14	Yang, S.#, Franden, A., Chou, Y-C., Brown, S. D., Pienkos, P. T., and Zhang, M#. 2014. Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates. Biotechnology for Biofuels 7:140.	2014
15	Yang, S.#, Pan, C., Hurst, G. B., Dice, L., Davison, B. H., and Brown, S. D.#. 2014. Elucidation of Zymomonas mobilis physiology and stress responses to acetate by quantitative proteomics and transcriptomics. Front. Microbiol. 5:246.	2014
16	Yang, S., Pan, C., Tschaplinski, T. J., Hurst, G.B. Engle, N. L., Zhou, W., Dam, P., Xu, Y., Rodriguez, M. Jr., Dice, L., Johnson, C. M., Davison, B. H., and Brown, S. D. 2013. Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. PLoS ONE 8(7): e68886.	2013
17	Yang, S., Land, M. L., Klingeman, D. M., Pelletier, D. A., Lu, S. T., Martin, S. L., Guo, H. B., Smith, J. C., and Brown, S. D. 2010. Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 107: 10395–10400.	2010
18	Yang, S., Pelletier, D. A., Lu, S. T, and Brown, S. D. 2010. The Zymomonas mobilis regulator Hfq and related Saccharomyces cerevisiae proteins contribute to tolerance against multiple lignocellulosic pretreatment inhibitors. BMC Microbiology 10: 135.	2010
19	Yang, S., Pappas, K. M., Hauser, L. J., Land, M. L., Chen, G-L, Hurst, G.B. et al. 2009. Improved genome annotation for Zymomonas mobilis. Nature Biotechnology 27: 893 –4.	2009
20	Yang, S., Tschaplinski, T. J., Engle, N. L., Carroll, S. L., Martin, S. L., Davison, B. H., Palumbo, A. V., Rodriguez, M. Jr., and Brown, D., S. 2009. Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentation. BMC Genomics 10: 34. (Highly accessed).	2009
21	Wang, W*#., Yang, S.*#, Pienkos, P. T., and Johnson, D. 2014. Connecting lignin-degradation pathway with pretreatment inhibitor sensitivity of Cupriavidus necator. Front. Microbiol. 5:247.	2014
22	Yang, S.#, Guarnieri, M. T., Smolinski, S., Ghirardi, M., and Pienkos, P. T. 2013. De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq. Biotechnology for Biofuels 6:118.	2013
23	Wilson, C. M.*, Yang, S.*, Rodriguez, M. Jr., Ma, Q. , Johnson, C. M., Dice, L., Xu, Y., and Brown, S. D. 2013. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. Biotechnology for Biofuels 6:131.	2013
24	Yang, S., Giannone, R. J., Dice, L., Yang, Z. K., Engle, N. L., Tschaplinski, T. J., Hettich, R. L., and Brown, S. D. 2012. Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics 13:336.	2012
25	Chou, Y-C., Linger, J., Yang, S., and Zhang, M. 2015. Genetic engineering and improvement of a Zymomonas mobilis for arabinose utilization and its performance on pretreated corn stover hydrolysate. J. Biotechnol. Biomater. 5:2.	2015
26	Mohagheghi, A., Linger, J., Yang, S., Smith, H., Dowe, N., Zhang, M., and Pienkos, P. T. 2015. Improving a recombinant Zymomonas mobilis strain 8b through continuous adaptation on dilute acid pretreated corn stover hydrolysate. Biotechnology for Biofuels 8:55.	2015
27	Zeng, Y., Zhao, S., Yang, S., and Ding, S. 2014. Lignin plays the negative role in the biochemical process for producing lignocellulosic biofuels. Curr. Opin. Biotechnol. 27: 38-45.	2014
28	Mohagheghi, A., Linger, J., Smith, H., Yang, S., Dowe, N., and Pienkos, P. T. 2014. Improving xylose utilization by recombinant Zymomonas mobilis strain 8b through adaptation using 2-deoxyglucose. Biotechnology for Biofuels 7: 19.	2014
29	Wei, H., Fu, Y., Magnusson, L., Baker, JO., Maness, PC., Xu, Q., Yang, S., Bowersox, A., Bogorad, I., Wang, W., Tucker, MP., Himmel, ME., Ding, S. 2014. Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq. Front. Microbiol. 5:142.	2014
30	Guarnieri, M. T., Nag, A., Yang, S., and Pienkos, P. T. 2013. Proteomic analysis of Chlorella vulgaris: Potential targets for enhanced lipid accumulation. J Proteomics. pii: S1874-3919(13)00278-9.	2013
31	Brown, S. D., Guss, A. M., Karpinets, T. V., Parks, J. M., Smolin, N., Yang, S., Land, M. L., et al. 2011. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc. Natl. Acad. Sci. USA. 108: 13752-7.	2011
32	Bochner, B., Gomez, V., Ziman, M., Montgomery, S., Yang, S., and Brown, S. D. 2010. Phenotype MicroArray profiling of Zymomonas mobilis ZM4. Appl. Biochem. Biotech. 161:116-123.	2010
Molecular Microbe-Plant Interactions and others：
33	Yang, S., Peng, Q., Zhang, Q., Zou, L., Li, Y., Robert, C. et al. 2010. Genome-wide identification of HrpL-regulated genes in necrotrophic phytopathogen Dickeya dadantii 3937. PLoS ONE 5(10): e13472.	2010
34	Yang, S.*, Peng, Q.*, San Francisco, M., Wang, Y., Zeng, Q., and Yang, C.-H. 2008. Type III secretion system genes of Dickeya dadantii 3937 are induced by plant phenolic acids. PLoS ONE 3(8): e2973.	2008
35	Yang, S., Zhang, Q., Peng, Q., Yi, X., Chang, J. C., Reedy, R. M., Charkowski, A. O., and Yang, C.-H. 2008. Dynamic regulation of GacA in type III secretion system, pectinase gene expression, pellicle formation, and pathogenicity of Dickeya dadantii. Mol. Plant-Microbe Interact. 21: 133-142.	2008
36	Yang, S., Zhang, Q., Guo, J., Charkowski, A. O., Glick, B. R., Ibekwe, A. M., Cooksey, D. A., and Yang, C.-H. 2007. Global effect of indole-3-acetic acid (IAA) biosynthesis on multiple virulence factors of Erwinia chrysanthemi 3937. Appl. Env. Microbiol. 73:1079-1088.	2007
37	Peng, Q.*, Yang, S.*, Charkowski, A. O., Yap, M. N., Steeber, D. A., Keen, N. T., and Yang, C.-H. 2006. Population behavior analysis of dspE and pelD expression in Erwinia chrysanthemi 3937. Mol. Plant-Microbe Interact. 19: 451-7.	2006
38	Yang, S., Perna, N. T., Cooksey, D. A., Okinaka, Y., Lindow, S. E., Ibekwe, A. M., Keen, N. T., and Yang, C-H. 2004. Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array. Mol. Plant-Microbe Interact. 17: 999-1008.	2004
39	Chou, W-C., Ma, Q., Yang, S., Cao, S., Brown, S. D., and Xu, Y. 2015. Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum. Nucleic Acids Res. doi: 10.1093/nar/gkv177.	2015
40	Wei, H., Brunecky, R., Donohoe, BS., Ding, S., Ciesielski, PC., Yang, S., Tucker, MP., and Himmel, ME. 2015. Identifying the relatively abundant, ionically bound cell wall and intracellular glycoside hydrolases and carbohydrate esterases in late growth stage Arabidopsis stems: implications for the genetic engineering of bioenergy crops. Front. Plant Science. 6:315.	2015
41	Glasner, J. D., Yang, C.-H, Reverchon, S., Hugouvieux-Cotte-Pattat, N., Condemine, G., Bohin, J., Van Gijsegem, F., Yang, S., etc. 2011. Genome sequence of the plant pathogenic bacterium Dickeya dadantii 3937. J. Bacteriol. 193:2076-7.	2011
42	Okinaka, Y. Perna, N. T., Yang, S. Keen, N. T., and Yang, C-H. 2006. Identification of potential virulence genes in Erwinia chrysanthemi 3937; transposon insertion into plant up-regulated genes. J. Gen. Plant Pathol. 72:360-8.	2006
43	Schijven, J. F., Bradford, S. A., Yang, S. 2004. Release of Cryptosporidium and Giardia from dairy cattle manure: physical factors. J. Environ. Qual. 33:1499-1508.	2004
44	Yang, S., Fang, C., and Zhang, L. 2000. A staining method used for observing protoplast under the light microscope. Microbiology (Chinese) 27:55-7.	2000

Index	Patents
1	Yang, S., Linger, J., Franden, A., Pienkos, P. T., and Zhang, M. US14265039. Biocatalysts with enhanced inhibitor tolerance.
2	Brown, S., and Yang, S. US20130078691. Microorganisms having enhanced resistance to acetate and related compositions and methods of Use.
3	Brown, S., Guss, A., Yang, S., Karpinets, T., and Lynd, L. US20110287499. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol.
4	Brown, S., and Yang, S. US20100311137. Microorganisms having enhanced tolerance to inhibitors and stress.
5	Yang, C.-H., and Yang, S. US20100249234 and WIPO WO/2008/124836. Methods of reducing virulence in bacteria.

Index	Book Chapters	Date
1	Yang, S., Wang, W., Wei, H., Himmel, M., and Zhang, M. 2015. Identification of genetic targets to improve lignocellulosic hydrocarbon production in Trichoderma reesei using public genomic and transcriptomic datasets. P177-196. In Direct Microbial Conversion of Biomass to Advanced Biofuels. Edited by Michael E Himmel. Elsevier. New York, US.	2015
2	Yang, S., Klingeman, D. M., and Brown, S. D. 2012. Ethanol-tolerant gene identification in Clostridium thermocellum using pyro-resequencing for metabolic engineering. P111-136. In Methods in Molecular Biology: Microbial Metabolic Engineering. Edited by Cheng Q. Human Press. New York, US.	2012
3	Yang, S., Keller, M., and Brown, S. D. 2011. Genomics on pretreatment inhibitor tolerance of Zymomonas mobilis. P161-176. In: Microbial stress tolerance: from genomics to biofuels Microbiology monographs (Springer series). Edited by Liu Z. L. Springer. Heidelberg, Germany.	2011
4	Yang, C.-H., and Yang, S. 2008. Managing bacterial plant diseases by modulating quorum sensing and Type III secretory systems. P16-57. In: Biotechnology and Plant Disease Management. Eds. Punja Z.K., De Boer S.H., and Sanfacon H. CABI Publishing. Oxfordshire. UK.	2008

Index	Presentations: (>60 total, 45 first-authored in ASM, APS, SIMB, and ICMS etc.)
1	Invited talks on next-generation sequencing and systems biology for biofuel biocatalyst development at international conference of: ACS Annual Meeting; Society for Industrial Microbiology & Biotechnology (SIMB) Annual Meeting; Symposium on Biotechnology for Fuels and Chemicals; as well as DuPont, IneosBio, Wuhan University, and Beijing Institute of Genomics etc.