Huansheng Cao, Ph.D. Center for Fundamental and Applied Microbiomics Biodesign Institute Arizona State University 781 S Terrace Rd, Tempe, AZ 85281 Phone: (480) 727-8381; Email: [email protected] Home page: http://csbl.bmb.uga.edu/~hshcao

CURRENT POSITION Assistant Research Professor, Biodesign Institute, Arizona State University July, 2017-

EDUCATION Ph.D. Cell and Molecular Biology, Fordham University 2006-2012 Dissertation: Effects of population size on fitness effects of mutations and long- term fitness trajectories in E. coli populations for 4,000 generations Advisors: Professors James D Lewis and Gordon R Plague Ph.D. Limnology, Chinese Academy of Sciences 2003-2006 Dissertation: Development and formation of Microcystis aeruginosa blooms and major stage-specific driving factors Advisor: Professor Fanxiang Kong M.Eng. Environmental Science, Jinan University, China 2002-2003 Thesis: Induction of hairy roots from hairy roots of pharmaceutical plant Trichosanthes bracteata Voigt for treatment of sewage Advisor: Professor Mingfang Xu B.S. Biochemistry, Yantai University, China 1996-2000 Thesis: Extraction and analyses of asterosaponin from Yellow Sea starfish Advisor: Professor Chenghua Guo

PROFESSIONAL EXPERIENCE 2014–2017 University of Georgia Bioinformatics Post-Doctorate Research Associate Computational Systems Biology Laboratory, Institute of Bioinformatics, and Department of Biochemistry and Molecular Biology, Advisor: Professor Ying Xu 2012–2014 Northern Illinois University Bioinformatics Post-Doctorate Research Associate Department of Biological Sciences Advisor: Professor Yanbin Yin 2011–2012 Fordham University Research Fellow Department of Biological Sciences 2006–2011 Fordham University Teaching Fellow Department of Biological Sciences

RESEARCH INTERESTS • Basic Systems Biology Interests o microbiome studies using genomics, phylogenetics, transcriptomics, and metabolomics (under global change or other environments)

o elucidation of microbial metabolic network structure and associated regulatory systems o multi-omics data mining and computational integration based on metabolic network flux and topology o evolutionary and functional genomics based on metabolic network flux and topology o characterization of bacterial genomic organization and associated regulatory systems o robustness and evolvability of biological systems under environmental change and the systems determinants (genomics, transcriptomics, and metabolomics) • Applied Systems Biology Interests o population genetics, conservation biology, and evolutionary ecology at the molecular, population, community, and ecosystem levels under global change o development and application of next-generation bioengineering pipeline based on large-scale metabolic network reconstruction and flux optimization o systems study of toxicity of biofuels and environmental stressors in terms of tradeoff between survival and growth on the balance of energy and mass o evolutionary ecology of toxic blooms under increasing water eutrophication and global climate change o pathogen control by development of antibiotics against key reactions as new targets

RESEARCH EXPERIENCE Bioinformatics Research Associate (with Dr. Ying Xu) 2014-present Department of Biochemistry and Molecular Biology, University of Georgia • Systems-level elucidation of biofuel ethanol stress and adaptation in E. coli by integrating of phenotypic data (ethanol-tolerance genes, growth rate, stress response genes) with multi-omics data (transcriptomics, genomics, and proteomics) in non- evolved and evolved strains • Flux balance & topology decomposition analyses of bacterial genome-scale metabolic networks in support of genetic engineering • Development of next-generation pipeline for bioengineering by large-scale reconstruction of metabolic networks and flux optimization • Computational study of seed development in biofuel plant switchgrass using both microarray and RNA-seq transcriptomes and metabolic network Bioinformatics Research Associate (with Dr. Yanbin Yin) 2012-2014 Department of Biological Sciences, Northern Illinois University • Functional genomics comparison between blooming and non-blooming cyanobacteria to identify major bloom-driving pathways • Transcriptomic, metabolomics, and phenotypic responses in the top water-bloom cyanobacterium Microcystis aeruginosa in extra-eutrophic conditions • Molecular evolution of genes encoding cellulose-active enzymes and cellulosome genes in three domains of life and five species of Clostridium genus • Whole-genome sequencing and annotation of water-bloom cyanobacterium Aphanizomenon flos-aquae NIES-81 and plant pathogen Penicillium expansum PhD Student/Research Fellow (with Drs. Gordon Plague and James D Lewis) 2006-2012 Department of Biological Sciences, Fordham University • Fitness effects of mutations at high and low population density in E. coli using genome resequencing and transcriptomics • Evolutionary trajectories of E. coli populations in high and low density and rich and minimal medium for 4,000 generations

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• Clonal interference of E. coli populations at high and medium populations in rich and minimal medium MEng Student/Research Fellow (Dr. Mingfang Xu) 2003-2006 Institute of Hydrobiology, Jinan University, China • Induction hairy roots in medical Thesis: Induction of hairy roots from hairy roots of pharmaceutical plant Trichosanthes bracteata Voigt for treatment of sewage • Preparation and application of nanocrystalline TiO2 photocatalysis for degradation of crude oil poIlutants BS Biochemistry Student (with Dr. Chenghua Guo) 2003 Life Sciences College, Yantai University, China • Extraction and analyses of asterosaponin from Yellow Sea starfish

RESEARCH FUNDING • National Natural Science Foundation of China: Co-PI (PI: Dr. Aiju Liu of Shandong University of Technology), Jan. 2017 – Dec. 2020. $95,426 (Chinese Yuan: ¥660,000). Grant No: 41671322. Ecotoxic effects of combined contaminations of antibiotics and heavy metals on soil microbiome and the underlying mechanism studied with ecotoxicogenomics and metagenomics • Research Fellowship, Fordham University (research-proposal-based award, five awards each year in the Graduate School of Arts and Sciences, funding rate: 20%) • Fordham University, Calder Graduate Research Grant, $1,200, 2011–2012, (25% funding rate) • National Natural Science Foundation of China: Co-PI (PI: Dr. Zhou Yang of Nanjing Normal University), Jan. 2005 – Dec. 2007. Chinese Yuan: ¥220,000. Grant No: 30400062. Induction of colonies in water-bloom cyanobacterium Microcystis aeruginosa by zooplankton.

PUBLICATIONS (+: equal contribution) Computational Systems Biology 1. Cao H+, Du W+, Yang Y, Shang Y, Li G, Zhou Y, Ma Q, and Xu Y. Systems-Level Understanding of Ethanol-Induced Stresses and Adaptation in E. coli. Scientific Reports (impact factor 5.2), 7:44150 | DOI: 10.1038/srep44150. 2017. 2. Cao H, Ma Q, X Chen, and Xu Y. DOOR: A microbial operon database for gene organization and function discovery. Briefings in Bioinformatics (IF 8.4), accepted. 3. Cao H, Shimura Y, Steffen MM, Li G, Ma Q, Masanobu K, and Yin Y. Cyanobacterial harmful algal blooms are driven by superior resource-utilizing metabolic capabilities revealed by comparative genomics and transcriptomics. DNA Research. (IF 5.5) in revision. ● This article reconstructs and evaluates all bloom-driving metabolic pathways and identifies six top bloom driving pathways. 4. Cao H, Ekstrom A, and Yin Y. Plant carbohydrate active enzyme (CAZyme) repertoires: a comparative study. In G. Sablok et al. (eds.), Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches. Springer DOI 10.1007/978-3-319-17157-9_8. 2015. (Downloads from publisher site: 735) 5. Cao H and Yin Y, Rapid evolution of cellulosome modules by comparative analyses of five Clostridiales genomes. BioEnergy Research 7: 1369–1381, 2014. 6. Cao H, Shimura Y, Masanobu K, and Yin Y. Draft genome sequence of the toxic bloom- forming Aphanizomenon flos-aquae NIES-81. Genome Announcements 2: e00044-14. 2014. (Citation: 6)

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7. Yu J, Jurick WM, Cao H, Yin Y, Gaskins VL, Losada L, Zafr N, Kim N, Bennett JW, and Nierman WC. 2014. Draft genome sequence of Penicillium expansum (R19) that causes postharvest decay of apple fruit. Genome Announcements 2: e00635-14 (contribution: genome annotation). 2014. (Citation: 5) 8. Yin Y, Jones MA, Cao H, and Rupani M. 2014. A survey of the genomes and transcriptomes of diverse plants and algae revealed new insights into the evolution of the cellulose synthase superfamily. BMC Genomics, 15: 260. 2014. (Citation: 12) Genetics and Evolution 9. Cao H and Plague GR. The fitness effects of a point mutation in Escherichia coli change with founding population density. Genetica 144: 417-424. 2016. 10. Cao H, Houssin M, Butler K, and Lewis JD. 2014. Variation in the fitness effects of mutations with population density and size in Escherichia coli. Plos ONE doi: e105369. ● This works discovers for the first time fitness effects vary with population density; 500 views within first two months of publication according to journal metrics. 11. Plague G, Dougherty K, Boodram K, Boustani S, Cao H, Manning S, and McNally C. Relaxed natural selection alone does not permit transposable element expansion within 4,000 generations in Escherichia coli. Genetica 139: 895-902. 2011. (Citation: 4) Ecology/Toxicology/Pathology 12. Xu G, Xia Y, Tang Y, Cao H, Ma Q, Xu Y, Zhang N, and Xu H. Bibliometric screening of Helicobacter pylori pathogenic genes through pathway enrichment and operon analysis. Clinical Laboratory 62:xx-xx. 2016 13. Liu A, Cao H, Yang Y, Ma X, and Liu X. Combinational effects of sulfomethoxazole and copper on soil microbial community and function. Environmental Science and Pollution Research 23: 4235–4241. 2016. (IF: 2.8; citation: 1; view: 218) 14. Cao H+, Lü K+, Xiang F, and Yang Z. Life history response of the crustacean Daphnia similoides to secondary pollutants derived from degradation of cyanobacterial blooms and their post-exposure recovery. Environmental Toxicology and Chemistry 33: 2497–2505. 2014. (IF: 2.8) ● This article shows stressed Daphnia can recover quickly. 15. Lyu K, Cao H, Wang Q, Chen R, Minter EJA, and Yang Z. Differences in long-term impacts of un-ionized ammonia on life-history traits of three species of Daphnia. International Review of Hydrobiology 98: 253–261. 2013. 16. Lyu K, Cao H, Chen R, Wang Q, and Yang Z. Combined effects of hypoxia and ammonia to Daphnia similis estimated with life-history traits. Environmental Science and Pollution Research 20:5379-5387. 2013. (IF: 2.8; citation: 15; view: 358) 17. Cao H and Z Yang. Variation in colony size of Microcystis aeruginosa in a eutrophic lake during recruitment and bloom formation. Journal of Freshwater Ecology 25: 331-335. 2010. (Citation: 7) 18. Tan X, Kong F, Zeng Q, Cao H, Qian S, and Zhang M. Seasonal variation of Microcystis in Lake Taihu and its relationships with environmental factors. Journal of Environmental Sciences 21: 892-899. 2009. (Citation: 38) 19. Yang Z, Kong F, Shi X, Zhang M, Xing P, and Cao H. Changes in the morphology and polysaccharide content of Microcystis aeruginosa (cyanobacteria) during flagellate grazing. Journal of Phycology 44: 716-720. 2008. (Citation: 89) ● This article shows the enlargement of Microcystis aeruginosa colony can be induced indirectly by flagellates. 20. Tan X, Kong F, Cao H, Yu Y, and Zhang M. Recruitment of bloom-forming cyanobacteria and its driving factors. African Journal of Biotechnology 7: 4726-4731. 2008.

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21. Cao H, Tao Y, Kong F, and Yang Z. Relationship between temperature and cyanobacterial recruitment from sediments in laboratory and field studies. Journal of Freshwater Ecology 23: 405-412. 2008. (Citation: 34) ● This article shows the cumulative relationship between recruitment and temperature. 22. Zhang M, Kong F, Tan X, Yang Z, Cao H, and Xing P. Biochemical, morphological, and genetic variations in Microcystis aeruginosa due to colony disaggregation. World Journal of Microbiology and Biotechnology 23: 663-670. 2007. (Citation: 44) 23. Xing P, Kong F, Cao H, Zhang M, and Tan X. Variations of bacterioplankton community composition during Microcystis spp. blooms in a shallow eutrophic lake. Journal of Freshwater Ecology 22: 61-67. 2007. (Citation: 7) 24. Yang Z, Kong F, Shi X, and Cao H. Morphological response of Microcystis aeruginosa to grazing by different sorts of zooplankton. Hydrobiologia 563: 225-230. 2006. (Citation: 93). ● This article shows colony enlargement of M. aeruginosa is induced by grazing. 25. Cao H, Kong F, Luo L, Shi X, Yang Z, Zhang X, and Tao Y. Effects of wind and wind- induced waves on vertical phytoplankton distribution and surface blooms of Microcystis aeruginosa in Lake Taihu. Journal of Freshwater Ecology 21: 231-238. 2006. (Citation: 57) ● This article provides the threshold values of wind and waves for surface bloom formation. 26. Yang Z, Kong F, Cao H, and Shi X. Observation on colony formation of Microcystis aeruginosa induced by filtered lake water under laboratory conditions. Annales de Limnologie - International Journal of Limnology 41: 169-173. 2005. (Citation: 19) 27. Tan J, Kong F, Cao H, Yu Y, and Han X. Effects of acid precipitation and aluminum on carbohydrate metabolism in mycorrhizae of Pinus massioniana. Bulletin of Environmental Contamination and Toxicology 74: 614-622. 2005. 28. Cao H, Kong F, Tan J, Zhang X, Tao Y, and Yang Z. Recruitment of total phytoplankton, chlorophytes and cyanobacteria from lake sediments recorded by photosynthetic pigments in a large, shallow lake (Lake Taihu, China). International Review of Hydrobiology 90: 347-357. 2005. (Citation: 41). ● This article is the first work on recruitment of phytoplankton in shallow lakes. Manuscripts submitted or in preparation 29. Li G+, Cao H+, and Xu Y. Elucidation of organizing principles of the metabolic system in E. coli (submitted to Molecular Systems Biology) 30. Yu +, Cao H+, Liu C, Zhang H, Chen X, Ma Q, and Xu Y, Computational elucidation of regulatory network responding to acid stress in food strain Lactococcus lactis MG1363 (submitted) 31. Zuo C+, Cao H+, and Xu Ying. Seed development in the bioenergy plant switchgrass revealed by transcriptomic analysis of microarray and RNA-seq data (submitted). 32. Cao H+, Li G+, Yang J, Xie J, Shang Y, Q Ma, and Y Yin. Systematic physiological modulations to extra eutrophication in Microcystis aerugionsa NIES-843 revealed by transcriptomics and metabolic network analyses (being finalized) 33. Cao H+, Li G+, Du W, and Xu Y. Computational development of next-generation pipeline for bioengineering. (in preparation) 34. Driscoll C, Cao H, others. Genomic comparison of Nostocales species reveals discrepancy between morphology and phylogeny and diversity in physiological capability. (manuscript being finalized) 35. Cao H+, Li G+, Du W+, and Xu Y. HABmeta: a metabolic network database of harmful bloom algae. (in preparation)

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Earlier Publications in Chinese 36. Kong F, Cao H, and Tan X. 2010. Advances in recruitment of bloom-forming cyanobacteria and bloom forecast. Environmental Monitoring and Forewarning 2: 1- 4. 37. Xing P, Kong F, Cao H and Zhang M. 2007. Relationship between bacterioplankton and phytoplankton community dynamics during late spring and early summer in Lake Taihu. Acta Ecologica Sinica 27: 1696-1702. 38. Tan X, Kong F, Cao H, Shi X, Yu Y, and Zhang M. 2006. Influence of temperature on the competition between two species of algae assayed by flow cytometry. Journal of Lake Science 18: 419-424. 39. Cao H, Kong F, Tan X, Yang Z, Zhang Z, and Xing P. 2006. Comparison of recruitment from sediments with pelagic growth of cyanobacteria in Lake Taihu, China. Journal of Lake Science 18: 585-589. 40. Zhang X, Kong F, Cao H, Tan J, Tao Y, and Wang M. 2005. Recruitment dynamics of bloom-forming cyanobacteria in Meiliang Bay of Taihu Lake. Chinese Journal of Applied Ecology 16: 1346-1350. 41. Wang D, Kong F, Liu A, Tan J, and Cao H. 2005. Analysis of the influence of the ecological dredging to ecosystem of Lake Wuli, Lake Taihu. Journal of Lake Science 17: 263-268. 42. Tao Y, Kong F, Cao H, and Zhang X. 2005. Simulative recruitment of Microcystis from the surface sediment in Lake Taihu. Journal of Lake Science 17: 231-236. 43. Xu M, Cao H, and Li D. 2003. The study on the effect of different conditions on induction of hairy roots of Trichosanthes bacterata Voigt. Ecologic Science 22: 209-212. 44. Cao H, Xu M, and Li D. 2002. Medicinal value analysis of Trichosanthes bracterata Voigt. Pharmaceutical Biotechnology 9: 292-296. 45. Cao H and Xu M. 2002. Advances in the application of biosensor in monitoring aquiculture environment. Marine Environmental Science 21: 75-80.

ACADEMIC PRESENTATIONS Invited Talks 1. Cao H. Toward systems ecology of cyanobacterial blooms: integrating driving factors and ecophysiology at the systems level. School of Biological Sciences, Nanjing Normal University, June 9, 2017 2. Cao H. Toward systems-level integration of multi-omics data: applications in ethanol stress/adaption and microbial metabolic structure. Department of Science, John Jay College of Criminal Justice, City University of New York, March 10, 2017 3. Cao H. Toward systems ecology of cyanobacterial blooms: integrating driving factors and ecophysiology at the systems level. Department of Biological Sciences, University of Cincinnati, March 5, 2017 4. Cao H. Systems-level understanding of ethanol stresses and adaptation in E. coli by integrating genomic, transcriptomic, and protein data. Department of Environmental Health Science, College of Public Health, University of South Carolina, Feb 1, 2017 5. Cao H. Systems-level understanding of ethanol stress and adaptation in E. coli and heterogeneous architecture of bacterial metabolic networks. Biodesign Institute, Arizona State University, Jan. 24, 2017 6. Cao H. A primer to bioinformatics: learning by doing. Department of Biology, Stonehill College, Boston, MA, Jan 20, 2017 7. Cao H+, Du W+, Yang Y, Shang Y, Li G, Zhou Y, Ma Q, and Xu Y. Systems-Level Understanding of Ethanol-Induced Stresses and Adaptation in E. coli. Integrative BioSystems Institute, Georgia Institute of Technology, Atlanta, GA, December 7, 2016

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8. Cao H, Li G, and Xu Y. Development of next-generation pipeline for biological engineering. Dr. Yanjun Yan’s lab in the College of Engineering at the University of Georgia, Athens, GA, September 10, 2016 9. Cao H. Fitness effect of mutations and evolutionary trajectories of E. coli populations are high and low Nes. Dr. Siobain Duffy lab, Rutgers, New Brunswick, NJ, April, 2012 10. Cao H. Fitness effect of a crp mutation depends not only on environment, but also population size. Fordham University GSAS Communitas, Bronx, NY, March 30, 2011 11. Cao H. Variation of fitness effects of mutations and implications to cancer and pathogenesis. Fordham University Summer Research Program, Armonk, NY, July 16, 2011 12. Cao H. Evolutionary trajectories of pathogenic E. coli populations in rich and minimal medium for 4,000 generations. Fordham University Summer Research Program, Armonk, NY, June 11, 2010 Talks 1. Cao H, Kong F, and Zhang X. Seasonal variations of cyanobacteria recorded by phycocyanin and colony enlargement of Microcystis aeruginosa in Lake Taihu. International Symposium on the Eutrophication Process and Control in Large Shallow Lakes (With special reference to Lake Taihu, a large shallow subtropical Chinese lake). Nanjing, China. 2005 2. Cao H, Kong F, and Zhang X. Recruitment of phytoplankton and dominance establishment of Microcystis in Taihu. The 12th International Symposium on River and Lake Environments-Freshwater Environment and Biodiversity. Wuhan, China. 2004 Posters 1. Cao H, Chen X, Li G, Zuo C, Ma Q, and Xu Y. An integrated computational suite of webservers and tools developed by CSBL. U.S. Department of Energy BioEnergy Science Center Retreat, Chattanooga, TN, June 12, 2016 2. Cao H, Li G, Ma Q, and Xu Y. A new computational framework of metabolic network analysis. U.S. Department of Energy BioEnergy Science Center Retreat, Chattanooga, TN, June 12, 2016 3. Cao H, Du W, and Xu Y. Ethanol toxicity and adaptation in E. coli revealed by transcriptomic, genomics and literature data. Department of Biochemistry and Molecular Biology Retreat, Helen, GA, May 16, 2016 4. Cao H, Xu Y. Dense modules in bacterial metabolic networks and network evolution. Department of Biochemistry and Molecular Biology Retreat, Athens, GA, March 16, 2015 5. Cao H, and Y Yin. Physiological modulations to extra eutrophication in Microcystis aerugionsa NIES-843 revealed by transcriptomics analyses (being finalized). Sigma conference, Northern Illinois University, April 12, 2014 6. Cao H, and Y Yin. Comparative genomics of water-bloom cyanobacterial for identification of important driver pathways. 19th Annual Phi Sigma Research Symposium, Northern Illinois University, April 12, 2013 7. Cao H and Yanbin Yin. Sequence evolution and diversity of cellulosome modules in metagenomes. Society for Molecular Biology and Evolution Conference. Chicago, IL, July 12, 2013 8. Cao H, Butler K, Housin M, and Lewis JD. Effective population size-dependent mutational fitness effects in Escherichia coli: Common and gene function-related. Society for Molecular Biology and Evolution Conference. Chicago, IL, July 12. 9. Cao H, Dougherty KM, and Plague GR. Fitness evolution in experimental bacterial pathogens. Ecology & Evolution of Infectious Diseases Conference. Atlantic City, NJ, March 22.

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TEACHING EXPERIENCE Guest Lecturer Northern Illinois University, Department of Biological Sciences Genetics (BIOS308, 5 credits, 60 students; five lectures) Spring 2014 Teaching Fellow Fordham University, Department of Biological Sciences Human Physiology Lab (BISC3242, 3 credits, 24 students) 2009-2011 Microbiology Lab (BISC3653, 3 credits, 24 students) 2008-2009 Teaching Fellow Fordham University, Department of Biological Sciences Introductory Biology Lab (BISC1413/1414, non-bio majors) (3 credits, 24 students; team taught with two other peers) 2007-2008 Teaching Assistant Fordham University, Department of Biological Sciences Introductory Biology Lab (BISC 1413/1414, bio majors) (3 credits, 24 students) 2006-2007

MENTORING EXPERIENCE The University of Georgia Visiting Scholars Hongxi Liu Associate Professor, Changchun Institute of Technology, China 2015-present Co-advisor on Computational metabolomics data analysis (Mass Spectrophotometry and NMR data) Yan Xia Associate Professor, First Hospital of Jilin University, China 2015-present Co-advisor on Computational human gut microbiome data analysis (metagenomics and meta-transcriptomic data) Ph.D. students Yu Shang Visiting Student, Jilin University, Changchun, China 2014-present Primary advisor on Computational analysis of gene regulatory network analysis using deep learning Gaoyang Li Visiting Student, Jilin University, Changchun, China 2014-present Co-advisor on Topological analysis of metabolic network of E. coli Primary advisor on Development of next-generation pipeline for biological engineering Chunman Zuo Visiting Student, Jilin University, China 2014-present Primary advisor on Systems analysis of biofuel plant switchgrass using metabolic network-guided transcriptomic analysis, Undergraduate Students J. Meersman Research Student of Department of Biochemistry and Molecular Biology University of Georgia Fall 2016 Primary advisor on Metabolic network analysis of E. coli S. Alexander Research Student of Department of Biochemistry and Molecular Biology University of Georgia Fall 2016 Primary advisor on Metabolic network analysis of cyanobacteria Northern Illinois University Graduate Student Rahil Taujale Graduate Student of the Department of Biological Sciences 2013-2014 Co-advisor on Glycosyltransferase family in Charophycean green algae Page 8 of 11 CV Cao Dec 2016

Undergraduate Student Alex Ekstrom Research Student of the Department of Biological Sciences 2013-2014 Co-advisor on database for plant carbohydrate-active enzymes Joel Dennison Research Student of the Department of Biological Sciences Summer 2013 Primary advisor on Computational curation of water-bloom driving pathways in cyanobacteria. Fordham University Undergraduate Students Mithi Hossain Research Intern, Department of Biological Sciences Summer 2012 Primary advisor on Fitness effects of mutations in E. coli at high and low population density Kevin Butler Research Intern, Department of Biological Sciences Summer 2012 Primary advisor on Fitness effects of mutations in E. coli at high and low population density High School Students F. Holmes Research Intern Summer 2010 Primary advisor on Growth of evolved E. coli populations and growth curve mathematical fitting to extract duration of lag and log phase Robert Taylor Research Intern Summer 2009 Primary advisor on Growth rate measurements of evolved E. coli populations in MOPS minimal and rich medium Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences Undergraduate Students Xiao Tan Nanjing Normal University, thesis student 2005 Primary advisor on Influence of temperature on the competition between Microcystis aeruginosa and Chlorella sp. assayed by flow cytometry Xiaoping Chen Nanjing Normal University, thesis student 2004 Primary advisor on Recruitment of phytoplankton from overwintering stocks in sediments of Lake Taihu, China

SOFTWARE DEVELOPMENT R package: DDMAKER 2.0, for identification of clinical markers in extracellular circulation (https://github.com/yu-shang/DDMarker) R package: Delta (DEep Learning biclusTer Algorithm based on gravitation field) (https://github.com/yu-shang/delta) RESEARCH SKILLS Bioinformatics Skills Languages PERL, R, MATLAB, and Python in Linux, MAC, and Windows operating systems Analyses Next generation sequencing analyses, metabolomics, protein structure, phylogeny, gene regulation, DNA organization, systems biology (integration of OMICS), NMR and MS data analysis and network analyses (topology and flux) Tools Genome assembly and annotation, RNAseq/Microarray packages, phylogeny analysis and visualization, DNA/RNA/protein structure analysis/simulation,

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pathways tools, gene regulation tools, and metabolomics tools, database building programs/tools Resources Online databases for genomes, proteins, shorts reads/microarrays, gene regulation, pathways, metabolites/compounds, enzymes, metabolic networks Experimentation Skills Ecology Field survey/manipulation and laboratory simulations, water quality assessment and monitoring Evolution Experimental evolution, phenotypic and genotypic analyses Physiology Biochemical, molecular, and cell techniques for growth and physiological assessment, metabolomics, DNA/RNA processing, genome and gene manipulations, gene expression, protein analyses, Chip-seq, systems integration and analysis, etc.

AWARDS AND HONORS In USA 2014 Nomination for Northeastern Association of Graduate Schools Dissertation Award (one from each participating institution each year) 2010 Kathleen O'Connell Tamburro, M.D. and Carlo H. Tamburro Memorial Scholarship, Fordham University (two awards in the Graduate School of Arts and Sciences each year) 2010 Burroughs Wellcome Fund Travel Scholarship 2006 Schering-Plough Award, Fordham University 2006–2011 Graduate Teaching Assistantship, Fordham University

In China 2008 Award for the Advancement of Science and Technology (2nd place, Award no. 20080593, with Kong F, Ma R, Chen J, Gao G, Wu X, Zhang M, Yu Y, Ji J, Cao H, Yang Z, Xing P, and Tao Y), Jiangsu Province, China 2006 Excellent Graduate Award, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences (two out of my cohort) 2006 Chinese Academy of Sciences, Nanjing Academy Award (two each year) 1997 Excellent Youth League Member, Yantai University 1997 Excellent Editor for ‘Communications of the Student Government’, Yantai University

RELATED PROFESSIONAL EXPERIENCE 2016 Integration of DBCAN into Kbase, DOE BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 2015 Learn how to effectively apply for NSF funding, Spelman College, Atlanta, GA 2015 Teaching the STEM Undergraduates, Online CIRTL teaching course at the University of Georgia, Athens, GA 2014 The College Classroom, Online CIRTL teaching course at University of Georgia, Athens, GA 2014 Career Development Workshop: Getting a head start towards tenure: expectations and strategies for the first 3 years as a professor, University of Georgia, Athens, GA

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PROFESSIONAL SERVICE Seminar Organizing 2015-present Professor Ying Xu’s lab bi-weekly seminar series, invited and hosted 20+ seminar speakers (faculty members from) 2009 Fordham University, Department of Biological Sciences, hosting student-selected speaker Dr. Paul Turner from Yale University Editorial Service 2015 Guest Editor for the Scientific World Journal Grant Review 2014 Earth and Life Sciences Division of the Netherlands Organisation for Scientific Research (NWO), The Netherlands (1) 2015-2017 Research Grants Council of Hong Kong, Hong Kong, China (3) Journal Peer Review Bioinformatics Journals Bioinformatics (1) Briefings in Bioinformatics (1) BMC Genomics (25) BMC Research Notes (2) IEEE/ACM Transactions on Computational Biology and Bioinformatics (1) Journal of Bioinformatics and Computational Biology (4) Mathematical Biosciences (1) Nucleic Acids Research (1) PLoS ONE (1) Scientific Reports (2) Experimentation journals Algal Research (1) Aquatic Toxicology (1) Biochemical Systematics and Ecology (12) Bulletin of Environmental Contamination and Toxicology (2) Chemosphere (3) Ecological Indicators (3) Environmental Pollution (3) Environmental Science and Pollution Research (2) Fundamental and Applied Limnology (1) Journal of Freshwater Ecology (1) Limnology and Oceanography (1) Marine Biology Research (1) Phycological Research (1) Water Research (2)

PROFESSIONAL ASSOCIATIONS 2013-present Society of Molecular Biology and Evolution 2014-present American Society of Microbiology 2011-2012 Sigma Xi, the Scientific Research Society 2005–present Ecological Society of China

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