Education

09/2014 - 09/2018 Ph.D., Biological Sciences, The University of Hong Kong, Hong Kong SAR, China

09/2010 - 07/2014 B.S. (Hons., First Class), Applied Biology-Environmental Sciences, Hong Kong Baptist University, Hong Kong SAR, China

Research Experience

09/2026 - Present Professor, Institute for Advanced Study, Shenzhen University, Shenzhen, China

11/2021 - 09/2026 Computational Scientist, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.

09/2018 - 10/2021 Postdoctoral Research Associate, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA. Supervisor: Janet Jansson

10/2016 - 07/2018 Visiting Graduate Student, Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA. Supervisor: James Tiedje and Jim Cole

07/2013-07/2014, Intern, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China. Supervisor: Yu Jun

07/2012-09/2012, Intern, Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China. Supervisor: Liang Yan

Research Interests

1. Viral Auxiliary Metabolic Genes and Host Metabolic Reprogramming: Characterizing viral auxiliary metabolic genes at the molecular, structural, and functional levels to understand how viral proteins interact with host cellular machinery and reprogram host metabolism during infection.

2. Viral Ecology and Virus-Microbiome Interactions: Understanding how viruses shape microbial community structure, function, and resilience across diverse microbiome systems, and how virus-host interactions respond to environmental, physiological, and ecological perturbations.

3. Cross-Scale Modeling of Virus-Microbiome Systems: Integrating molecular mechanisms, multi-omics data, genome-scale metabolic models, and community-level information to connect viral genetic variation and protein function with host physiology, microbial interactions, and system-level processes.

4. Phage Engineering and Microbiome Functional Control: Developing predictive approaches to enable capability of using phages to steer microbiome composition, metabolic functions, and process performance, with applications across environmental and human-associated systems.

Publications

1. Rodríguez-Ramos J.A., Zimmerman A.E., Wu R., Bell S.L., Alfaro T.D., Reichart N.J., Hofmockel K.S., Nelson W.C. Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities. Nat. Commun. 2026, 17, 7551.

2. Veličković M., Thairu M.W., Gao Y., Clendinen C.S., Munoz N., Lalli P.M., Nicora C.D., Stratton K.G., Monroe M.E., Moore R.J., Currie C.R., Wu R. (corresponding author), Burnum-Johnson K.E. Deciphering taxon-specific metabolic shifts during pathogenic fungal infection in leaf-cutter ant fungal gardens. ISME Commun. 2026, 6(1), ycag213.

3. Gao Y., Kim J., Wu R. (co-first author), Chowdhury N.B., Lee J.-Y., Nicora C.D., Moore R.J., Monroe M.E., Jansson J.K., Burnum-Johnson K.E. Metaproteomics uncovers the functional capacity of a soil microbiome. Sci. Rep. 2026, 16, 22142.

4. Rozum J.C., Sineath W., Bohutskyi P., Quenneville J., Kim D.N., Johnson C.G., Mehta A.P., Evans J., Pollock D., Qian W.-J., Cheung M.S., Wu R. (corresponding author), Feng S. (corresponding author). Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophages. Sci. Adv. 2026, 12(14), eaeb7646.

5. Qi H., Wu R., Liao J., Alvarez P.J.J., Yu P. Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge. Bioresour. Technol. 2026, 449, 134410.

6. Boise N.R., Leiser O.P., Jones K., Peter-Frank M., Leach D., Crafton-Tempel S., Regier P., Wu R., Phillips C., Cheung M.S., Johnson C.G.M., Edmundson S.J., Pollock D.D. Sampling microbial dynamics in the Salish Sea estuary: evaluating methods to capture cyanobacteria and cyanophage. Front. Mar. Sci. 2026, 13, 1769457.

7. Fiamenghi M.B., Camargo A.P., Ivanova N.N., Graham E.B., Wu R., Hofmockel K.S., Kyrpides N.C. A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes. Nat. Commun. 2025, 16, 10089.

8. Touceda-Suárez M., Perry M.A., Frizzo R., Lotz-McMillen J.H., Gilmore R.A., Bennett S.M., Basso J.T.R., Donovan W., Fudyma J.D., Geonczy S.E., Gittrich M., Gogul G., Hazard C., Hillary L.S., Jameson E., Jiraska L., Johnson S.S., Kosmopoulos J.C., Leleiwi I., Ma B., Mageeney C.M., Millard A., Neri U., Rodríguez-Ramos J., Roux S., Tong D., Wang Y., Williamson K., Wu R., Martins P.D., Sapkota R., Emerson J.B., Trubl G. Meeting report: International soil virus conference. Virus Res. 2025, 354, 199544.

9. Veličković M., Kadam L., Kim J., Zemaitis K.J., Veličković D., Gao Y., Wu R., Fillmore T.L., Orton D., Williams S.M., Monroe M.E., Moore R.J., Piehowski P.D., Bramer L.M., Myatt L., Burnum-Johnson K.E. Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution. Nat. Commun. 2025, 16, 2061.

10. Huang D., Liao J., Balcazar J.L., Ye M., Wu R., Wang D., Alvarez P.J.J., Yu P. Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress. Microbiome 2025, 13, 34.

11. Wu R., Veličković M., Burnum-Johnson K.E. From single cell to spatial multi-omics: unveiling molecular mechanisms in dynamic and heterogeneous systems. Curr. Opin. Biotechnol. 2024, 89, 103174.

12. Veličković M., Wu R., Gao Y., Thairu M.W., Veličković D., Munoz N., Clendinen C.S., Bilbao A., Chu R.K., Lalli P.M., Zemaitis K., Nicora C.D., Kyle J.E., Orton D., Williams S., Zhu Y., Zhao R., Monroe M.E., Moore R.J., Webb-Robertson B.M., Bramer L.M., Currie C.R., Piehowski P.D., Burnum-Johnson K.E. Mapping microhabitats of lignocellulose decomposition by a microbial consortium. Nat. Chem. Biol. 2024, 20(8), 1033-1043.

13. Wu R., Zimmerman A.E., Hofmockel K.S. The direct and indirect drivers shaping RNA viral communities in grassland soils. mSystems 2024, 9(8), e0009924.

14. Qi H., Wu R., Ye M., Huang D., Wang L., Liao J., Yu P. Symbiotic bacteriophages exhibit multiple adaptive strategies in activated sludge flocs and contribute to floc stability. Chem. Eng. J. 2024, 492, 152448.

15. Graham E.B., Camargo A.P., Wu R., Neches R.Y., Nolan M., Paez-Espino D., Copeland A., Kyrpides N., Jansson J.K., McDermott J.E., Hofmockel K.S., Soil Virosphere Consortium. A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. Nat. Microbiol. 2024, 9(7), 1873-1883.

16. Graham E.B., Garayburu-Caruso V.A., Wu R., Zheng J., Jones G. Genomic fingerprints of the world's soil ecosystems. mSystems 2024, 9(6), e0111223.

17. Chen T., Wu R., Cheng L., Liao Q., Chen Z. Editorial: Vaginal microecological disorder and gynecological diseases. Front. Cell. Infect. Microbiol. 2023, 13, 1292815.

18. Wu R., Davison M.R., Nelson W.C., Smith M.L., Lipton M.S., Jansson J.K., McClure R.S., McDermott J.E., Hofmockel K.S. Hi-C metagenome sequencing reveals soil phage-host interactions. Nat. Commun. 2023, 14, 7666.

19. Jansson J.K., Wu R. Soil viral diversity, ecology and climate change. Nat. Rev. Microbiol. 2023, 21(5), 296-311.

20. Wu R., Trubl G., Taş N., Jansson J.K. Permafrost as a potential pathogen reservoir. One Earth 2022, 5(4), 351-360.

21. Wu R., Smith C.A., Buchko G.W., Blaby I.K., Paez-Espino D., Kyrpides N.C., Yoshikuni Y., McDermott J.E., Hofmockel K.S., Cort J.R., Jansson J.K. Structural characterization of a soil viral auxiliary metabolic gene product, a functional chitosanase. Nat. Commun. 2022, 13, 1-14.

22. Lee J.Y., Mitchell H.D., Burnet M.C., Wu R., Jenson S.C., Merkley E.D., Nakayasu E.S., Nicora C.D., Jansson J.K., Burnum-Johnson K.E., Payne S.H. Uncovering hidden members and functions of the soil microbiome using de novo metaproteomics. J. Proteome Res. 2022, 21(8), 2023-2035.

23. Wu R. (corresponding author), Bottos E.M., Danna V.G., Stegen J.C., Jansson J.K., Davison M.R. RNA viruses linked to eukaryotic hosts in thawed permafrost. mSystems 2022, 7(6), e00582-22.

24. Wu R., Davison M.R., Nelson W.C., Graham E.B., Fansler S.J., Farris Y., Bell S.L., Godinez I., McDermott J.E., Hofmockel K.S., Jansson J.K. DNA viral diversity, abundance, and functional potential vary across grassland soils with a range of historical moisture regimes. mBio 2021, 12(6), e02595-21.

25. Wu R., Davison M.R., Gao Y., Nicora C.D., McDermott J.E., Burnum-Johnson K.E., Hofmockel K.S., Jansson J.K. Moisture modulates soil reservoirs of active DNA and RNA viruses. Commun. Biol. 2021, 4, 1-11.

26. Wu R., Chai B., Cole J.R., Gunturu S.K., Guo X., Tian R., Gu J.-D., Zhou J., Tiedje J.M. Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming. ISME J. 2020, 14(7), 1651-1662.

27. Nelson W.C., Anderson L.N., Wu R., McDermott J.E., Bell S.L., Jumpponen A., Fansler S.J., Tyrrell K.J., Farris Y., Hofmockel K.S. Terabase metagenome sequencing of grassland soil microbiomes. Microbiol. Resour. Announc. 2020, 9(32), e00718-20.

28. Wu R., Meng H., Wang Y., Gu J.-D. Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests. Appl. Microbiol. Biotechnol. 2019, 103(10), 4229-4240.

29. Meng H., Zhou Z., Wu R., Wang Y., Gu J.-D. Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene. Appl. Microbiol. Biotechnol. 2019, 103(2), 995-1005.

30. Wu R., Meng H., Wang Y., Gu J.-D. Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils. Appl. Microbiol. Biotechnol. 2018, 102(12), 5309-5322.

31. Luo L., Wu R., Gu J.-D., Zhang J., Deng S., Zhang Y., Wang L., He Y. Influence of mangrove roots on microbial abundance and ecoenzyme activity in sediments of a subtropical coastal mangrove ecosystem. Int. Biodeterior. Biodegradation 2018, 132, 10-17.

32. Meng H., Wu R., Wang Y., Gu J.-D. A comparison of denitrifying bacterial community structures and abundance in acidic soils between natural forest and re-vegetated forest of Nanling Nature Reserve in southern China. J. Environ. Manage. 2017, 198, 41-49.

33. Wu R., Meng H., Wang Y., Lan W., Gu J.-D. A more comprehensive community of ammonia-oxidizing archaea revealed by genomic DNA and RNA analyses of amoA gene in subtropical acidic forest soils. Microb. Ecol. 2017, 74(4), 910-922.

34. Zhang X., Wu W.K., Xu W., Man K., Wang X., Han J., Leung W.Y., Wu R., Liu K., Yu J. CXC motif chemokine 10 impairs autophagy and autolysosome formation in non-alcoholic steatohepatitis. Theranostics 2017, 7(11), 2822-2836.

35. Luo L., Meng H., Wu R., Gu J.-D. Impact of nitrogen pollution/deposition on extracellular enzyme activity, microbial abundance and carbon storage in coastal mangrove sediment. Chemosphere 2017, 177, 275-283.

36. Meng H., Wang Y., Chan H., Wu R., Gu J.-D. Co-occurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in subtropical acidic forest soils. Appl. Microbiol. Biotechnol. 2016, 100(17), 7727-7739.

37. Luo L., Wu R., Meng H., Li X., Gu J.-D. Seasonal and spatial variations in diversity and abundance of bacterial laccase-like genes in sediments of a subtropical mangrove ecosystem. Int. Biodeterior. Biodegradation 2016, 114, 260-267.

38. Wu R., Nakatsu G., Zhang X., Yu J. Pathophysiological mechanisms and therapeutic potentials of macrophages in non-alcoholic steatohepatitis. Expert Opin. Ther. Targets 2016, 20(5), 615-626.

39. Tong G., Du F., Liang Y., Hu Q., Wu R., Guan J., Hu X. Polymorphous ZnO complex architectures: selective synthesis, mechanism, surface area and Zn-polar plane-codetermining antibacterial activity. J. Mater. Chem. B 2013, 1(4), 454-463.

40. Tong G., Du F., Wu W., Wu R., Liu F., Liang Y. Enhanced reactive oxygen species yields and antibacterial activity of spongy ZnO/ZnFe2O4 hybrid micro-hexahedra selectively synthesized through a versatile glucose-engineered co-precipitation/annealing process. J. Mater. Chem. B 2013, 1(20), 2647-2657.

Award and Service

1. Outstanding Contribution Award, U.S. Pacific Northwest National Laboratory, 2023

2. Rockstar Award, U.S. Pacific Northwest National Laboratory, 2023

3. Rockstar Award, U.S. Pacific Northwest National Laboratory, 2022

4. Outstanding Abstract Award, American Society of Microbiology，2018

5. Guest Editor, Frontiers in cellular and infection microbiology，2023

6. Associate Editor, Journal of Environmental Management, 2024

Selected Invited Talks

1. NIH Human Virome Program Annual Meeting, 2026, Rockville, MD, USA.

2. International Soil Virus Conference, 2024, Livermore, CA, USA.

3. American Society of Microbiology, 2024, Atlanta, GA, USA.

4. Lawrence Berkeley National Laboratory Ecology Department Webinar, 2023, Virtual.

5. Early Career Researcher Viromics Webinar, Ohio State University, 2023, Virtual.

6. Chinese Academy of Sciences Seminar, 2023, Virtual.

7. Viral EcoGenomics & Applications, 2022, Berkeley, CA, USA.

8. EMSL Summer School: Soil Exposed, 2022, Virtual.

9. International Forum on Advanced Environmental Sciences and Technology, 2022, Virtual.

10. Phages for Health & Energy Symposium, 2021, Virtual.

11. 24th Biennial Evergreen Phage Meeting, 2021, Virtual.