Book chapter

1. Ju F, Fang, HHP, Zhang T*. Application of Metagenomics in Environmental Anaerobic Technology. Book chapter V of “Anaerobic Biotechnology: Environmental Protection and ResourceRecovery”, Imperial College Press, October, 2015. ISBN: 978-1-78326-790-3

2. Zhang HL, Zhou NJ, Ju F*. Immunoreaction-based Sensors to Improve Bacterial Detection. Book chapter of “Handbook of BiochipsSpringerMay 2020. ISBN:978-1-4614-6623-9

3. Huang XY, Zhang L, Yuan L, Ju F*. (2021). Quantitative Metagenomics and MetatranscriptomicsMethods of Microbiome. Bio-101: e2003693. DOI: 10.21769/BioProtoc.2003693

4. Zhang L, Ju F*. (2021). RNA-Stable Isotope Probing for Microbial Communities. Bio-101:e2003692. DOI: 10.21769/BioProtoc. 2003692

5. Zhao Z, Ju F*. (2020). Isolation and Extraction of IntracellularAbsorbed-extracellular and Free-extracellular Environmental DNA from AquaticMicrobial Community. Bio-101: e2003587. DOI: 10.21769/BioProtoc. 2003587

Journal Papers

Journal name (no. of articles): Microbiome (1), Water Research (5), The ISME Journal (4), Environmental Science & Technology (9), Science of the Total Environment (5), Applied Microbiology and Biotechnology (6), Environmental Microbiology (2), Journal of Hazardous Materials (2), Scientific Reports (2) and other journals.

1. He YZ , Jin H, Gao H, Zhang GQ, Ju F*. 2021. Profiling microbial removal of micropollutants in sand filters: Biotransformation pathways and associated bacteria.   Science of the Total Environment

2. Zhang L, Yin W, Wang C, Zhang A, Zhang H, Zhang T, Ju F*. 2021. Untangling Microbiota Diversity and Assembly Patterns in the World's Largest Water Diversion Canal. Water Research. 117617

3. Yuan L, Wang YB, Zhang L, Alejandro P, Zhou JZ, Smets BF, Bürgmann H, Ju F*. 2021. Pathogenic and indigenous denitrifying bacteria are transcriptionally active and key multi-antibiotic resistant players in wastewater treatment plants. Environmental Science & Technology. 55(15): 10862-10874

4. Yan XY, Wang H,   Zhang L, Kong LW, Chen Y*,   He Q,   Li L, Grossart H-P, Ju F*. 2021. Marine algae facilitate transfer of microplastics and associated pollutants into food webs. Science of the Total Environment. (787): 147535

5. Zhang RS#, He YZ#, Yao LX#, Chen J, Zhu SH, Rao XX, Tang PY, You J, Hua GQ, Zhang L, Ju F*, Wu LF* . 2021. Metformin chlorination byproducts in drinking water exhibit marked toxicities of a potential health concern. Environment International. (146): 106244

6. Gao CH, Cao H, Ju F, Xiao KQ, Cai P, Wu Y, Huang Q. 2021. Emergent transcriptional adaption facilitates convergent succession within a synthetic community. ISME Communications. 1 (1): 1-5

7. Lee J, Ju F, Maile-Moskowitz A, Beck K, Maccagna A,  McArdell C, Molin MD, Fenicia F, Vikesland P, Pruden A, Stamm, C, Buergmann H. 2021. Unraveling the riverine antibiotic resistome: the downstream fate of anthropogenic inputs. Water Research. (197): 117050

8. Wang Y, Qin W, Jiang X, Ju F, Mao Y, Zhang A, Stahl DA, Zhang T. 2021. Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis. Environmental Science & Technology. 55 (4): 2662-2673

9. CaoY, Yu X, Ju F, Zhan H, Jiang B, Kang H, Xie Z. 2020. Airborne Bacterial Community Diversity, Source and Function along the Antarctic Coast. Science of The Total Environment. 142700

10. Wang CX, Wang YB, Wang YL, Cheung KK, Ju F, Xia Y, Zhang T. 2020. Genome-centric microbiome analysis reveals solid retention time (SRT)-shaped species interactions and niche differentiation in food waste and sludge co-digesters.Water Research. (181) : 115858

11. Hu WC, Liang JS, Ju F, Wang QJ, Liu RP, Bai YH*, Liu HJ, Qu JH, 2020. Metagenomics unravels differential microbiome composition and metabolic potential in rapid sandfilters purifying surface water versus groundwater. Environmental Science &Technology. 54(8): 5197-5206

12. Ju F, Zhang T. 2019. Advances in meta-omics research on activated sludge microbial community. Microbiology China. 46(8): 2038-2052

13. Ju F, Beck K, Yin X, McArdell Christa, Singer H, Johnson D, Zhang T, Buergmann H*. 2019. Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange and upregulated expression in the effluent. The ISME Journal. 13 (2): 346-360

14. Zhao F#, Ju F#, Huang K, Mao Y, Zhang XX*., Ren H, Zhang T*. 2019. Comprehensive insights into the key components of bacterial assemblages in pharmaceutical wastewater treatment plants. Science of The Total Environment. 651, 2148-2157.10492–10502

15. Guo F, Zhang T, Li B, Wang Z, Ju F, Liang Y, 2019. Mycobacterial species and their contribution to cholesterol degradation in wastewater treatment plants. Scientific reports. 9 (1): 836

16. Ju F, Wang Y, Zhang T. 2018. Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics. Biotechnology for Biofuels. 11 (1): 135

17. Jiang XT, Ye L, Ju F, Wang YL, Zhang T*. 2018. Toward an intensive longitudinal understanding of activated sludge bacterial assembly and dynamics. Environmental Science & Technology. 52(15): 8224-8232

18. Jiang XT, Ye L, Ju F, Li B, Ma LP, ZhangT*. 2018. Temporal dynamics of activated sludge bacterial communities in twodiversity variant full-scale sewage treatment plants. Applied microbiology and biotechnology. 1-10

19. Huang K, Mao Y, Zhao F, Zhang XX, Ju F, Ye L, Wang Y, Li B, Ren H, Zhang T. 2018. Free-living bacteria and potential bacterial pathogens in sewage treatment plants. Applied microbiology and biotechnology. 102 (5): 2455-2464

20. Ju F, Lau, F, Zhang T*. 2017. Linking microbial community, environmental variables and methanogenesis in anaerobic biogas digesters of chemically enhanced primary treatment sludge. Environmental Science & Technology. 51 (7): 3982-3992

21. Hu A, Ju F, Hou L, Li J, Yang X, Wang H,Mulla SI, Sun Q, Bürgmann H*, Yu CP*. 2017. Strong impact of anthropogenic contamination on the cooccurrence patterns of a riverine microbial community. Environmental Microbiology. 19(12): 4993-5009

22. Ju F, Li B, Ma LP, Wang YB, Huang DP,Zhang T*. 2016. Antibiotic resistance genes and human bacterial pathogens:co-occurrence, removal, and enrichment in municipal sewage sludge digesters.Water Research. 91, 1-10   

23. Ju F, Wang YB, Lau FTK, Fung WC, Huang DP, Xia Y, Zhang T*. 2016. Anaerobic digestion of chemically enhanced primarytreatment (CEPT) sludge and the microbial community structure. Applied Microbiology and Biotechnology. 100 (20), 8975-8982

24. Li B#, Ju F# , Cai L , Zhang T*. 2015. Profile and fate of bacterial pathogens in sewage treatment plants revealed by high-throughput metagenomic approach. Environmental Science & Technology.49 (17), 10492–10502

25. Li B, Yang Y, Ma LP, Ju F, Guo F, TiedjeJ. Zhang T*. 2015. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. The ISME Journal. 9(11):2490-2502

26. Ju F, Zhang T*. 2015. Experimental design and bioinformatics analysis for the application of metagenomics inenvironmental sciences and biotechnology. Environmental Science &Technology. 49(21), 12628-12640

27. Ju F, Zhang T*. 2015. 16s rRNA gene high-throughput sequencing data mining of microbial diversity and interactions. Applied Microbiology and Biotechnology. 99(10): 4119-4129

28. Ju F, Zhang T*. 2015. Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant. The ISME Journal. 9: 683-695

29. Wang YB, Xia Y, Ju F, Zhang T*. 2015.Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation. Applied Microbiology and Biotechnology. 99(24):10871-10879

30. Chao YQ, Ma LP, Yang Y, Ju F, Zhang XX,Wu, WM, Zhang T*. 2014. Metagenomic analysis reveals significant changes ofmicrobial compositions and protective functions during drinking watertreatment. Scientific Reports. srep03550

31. Ju F, Xia Y, Guo F, Wang ZP, Zhang T*.2014. Taxonomic relatedness shapes bacterial assembly in activated sludge ofglobally distributed wastewater treatment plants. Environmental Microbiology.16(8):2421-2432

32. Ju F, Guo F, Ye L, Xia Y, Zhang T*.2014. Metagenomic analysis on seasonal microbial variations of activated sludgefrom a full-scale wastewater treatment plant over four years. Environmental Microbiology Reports. 6(1): 80-89

33. Peng XX, Guo F, Ju F, Zhang T*. 2014. Shifts in the microbial community, nitrifiers and denitrifiers in the biofilmin a full-scale rotating biological contactor. Environmental Science &Technology. 48 (14): 8044-8052

34. Cai L, Ju F, Zhang T*. 2014. Tracking human sewage microbiome in a municipal wastewater treatment plant. Applied Microbiology and Biotechnology. 98(7): 3317-3326

35. Ju F, Zhang T*. 2014. Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing. Microbial Ecology. 68(2): 235-246

36. Fang H, Cai L, Yang Y, Ju F, Li XD, YuYL, Zhang T*. 2014. Metagenomic analysis reveals potential biodegradation pathways of persistent pesticides in freshwater and marine sediments. Scienceof the Total Environment. 470-471: 983-992

37. Yang Y, Li B, Ju F, Zhang T*. 2013. Exploring variation of antibiotic resistance genes in activated sludge over afour-year period through a metagenomic approach. Environmental Science &Technology. 18(47),10197-10205

38. Ju F, Hu YY*, Cheng, JH. 2011. Removalof chelated Cu (II) from aqueous solution by adsorption–coprecipitation with iron hydroxides prepared from microelectrolysis process. Desalination. 274(1):130-135

39. Ju F, Hu YY*. 2011. Removal of EDTA-chelated copper from aqueous solution by interior microelectrolysis. Separation andPurification Technology. 78(1): 33-41