Computational Scientist
Computational Scientist


Ruonan Wu is a computational scientist on the Microbiome Science team within the Biological Sciences Division at PNNL. After attending college at Hong Kong Baptist University (HKBU), Wu earned a PhD in environmental microbiology with a joint study at the University of Hong Kong (HKU, Ji-Dong Gu’s Laboratory, 2014-2016) and Michigan State University (James Tiedje’s Laboratory 2016-2018). During her undergrad and graduate studies, she developed both wet-laboratory and bioinformatics skills, and applied them to various multidisciplinary studies, such as investigating antibacterial properties of self-synthesized nanoparticles, innate immunity along the progression of nonalcoholic steatohepatitis, nitrogen cycle in extreme environments, and targeted detection of CRISPR-CAS in soil.

Currently, Wu is mentored by Janet Jansson and mainly works on the virome task of the U.S. Department of Energy’s Office of Science-funded Phenotypic Response of the Soil Microbiome to Environmental Perturbations Science Focus Area. She’s also co-principle investigator of a Laboratory Directed Research and Development project for computational workflow development to uncover unknown RNA viruses in permafrost. Her work aims to integrate the efforts from both multi-omic data mining and current advances in molecular virology to uncover the cryptic viruses in environments and understand their ecological impacts on microbiomes.

Disciplines and Skills

  • Data management practices and high-performance computing clusters
  • Processing and analyzing high-throughput multi-omic data
  • Designing computational workflow for biological data integration and interpretation
  • Good communication skills with experience working on collaborative projects with research groups inside and outside of PNNL


  • PhD in Environmental Microbiology, HKU, 2018
  • BA in Applied Biology, HKBU, 2014

Affiliations and Professional Service

  • American Society of Microbiology (ASM)
  • American Geophysical Union
  • International Society for Microbial Ecology
  • Reviewer of International Biodeterioration & Biodegradation

Awards and Recognitions

  • Outstanding Abstract Award at ASM Microbe 2018
  • Conference Support for Research Postgraduate Students, HKU, 2017
  • Pilot Scheme for Postgraduate Students, HKU, 2016
  • University Postgraduate Fellowship, HKU, 2014-2018
  • Postgraduate Scholarship, HKU, 2014-2018
  • Mr. Lui Ming Fong Memorial Scholarship, HKBU, 2014
  • MI Asia Award, 2014
  • Lee Koon Shin Scholarship, HKBU, 2013
  • Sponsorships for Outstanding Mainland Students, HKBU, 2013
  • Summer Undergraduate Research Fellowship, HKBU, 2012



  • Wu R., M.R. Davison, W.C. Nelson, E.B. Graham, S.J. Fansler, Y. Farris, and S.L. Bell, et al. 2021. "DNA viral diversity, abundance and functional potential vary across grassland soils with a range of historical moisture regimes." mBio 12, no. 6:e02595-21. PNNL-SA-166275. doi:10.1128/mBio.02595-21
  • Wu R., M.R. Davison, Y. Gao, C.D. Nicora, J.E. McDermott, K.E. Burnum-Johnson, and K.S. Hofmockel, et al. 2021. "Moisture Modulates Soil Reservoirs of Active DNA and RNA Viruses." Communications Biology 4, no. 1:992. PNNL-SA-160635. doi:10.1038/s42003-021-02514-2


  • Davison M.R., R. Wu, V.G. Danna, and I.G. Godinez. 2020. Uncovering novel RNA viruses in permafrost. PNNL-30560. Richland, WA: Pacific Northwest National Laboratory. Uncovering novel RNA viruses in permafrost
  • Nelson W.C., L.N. Anderson, R. Wu, J.E. McDermott, S.L. Bell, A. Jumpponen, and S.J. Fansler, et al. 2020. "Terabase Metagenome Sequencing of Grassland Soil Microbiomes." Microbiology Resource Announcements 9, no. 32:Article No. e00718-20. PNNL-SA-153752. doi:10.1128/MRA.00718-20
  • Ruonan Wu, Benli Chai, James R. Cole, Santosh K. Gunturu, Xue Guo, Renmao Tian, Ji-Dong Gu, Jizhong Zhou, and James M. Tiedje. Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming. The ISME Journal (2020): 1-12.


  • Graham, Emily B., David Paez-Espino, Colin Brislawn, Russell Y. Neches, Kirsten S. Hofmockel, Ruonan Wu, Nikos C. Kyrpides, Janet K. Jansson, and Jason E. McDermott. Untapped viral diversity in global soil metagenomes. bioRxiv (2019): 583997.
  • Meng, Han, Zhichao Zhou, Ruonan Wu, Yongfeng Wang, and Ji-Dong Gu. Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene. Applied microbiology and biotechnology (2019):103, no. 2, 995-1005.
  • Ruonan Wu, Han Meng, Yongfeng Wang, Jidong Gu: Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests. Applied microbiology and biotechnology(2019):103 (10), 4229-4240


  • Ruonan Wu, Han Meng, Yongfeng Wang, Jidong Gu: Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils. Applied Microbiology and Biotechnology (2018): 1-14
  • Luo, Ling, Ruonan Wu, Ji-Dong Gu, Jing Zhang, Shihuai Deng, Yanzong Zhang, Lilin Wang, and Yan He. Influence of mangrove roots on microbial abundance and ecoenzyme activity in sediments of a subtropical coastal mangrove ecosystem. International Biodeterioration & Biodegradation 132 (2018): 10-17.


  • Ruonan Wu, Han Meng, Yongfeng Wang, Wensheng Lan, and Jidong Gu. A more comprehensive community of ammonia-oxidizing archaea (AOA) revealed by genomic DNA and RNA analyses of amoA gene in subtropical acidic forest soils. Microbial Ecology 74, no. 4 (2017): 910-922.
  • Han Meng, Ruonan Wu, Yongfeng Wang, and Jidong Gu. 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. Journal of Environmental Management 198 (2017): 41-49.
  • Ling Luo, Han Meng, Ruonan Wu, and Jidong Gu. Impact of nitrogen pollution/deposition on extracellular enzyme activity, microbial abundance and carbon storage in coastal mangrove sediment. Chemosphere 177 (2017): 275-283.
  • Xiang Zhang, William KK Wu, Weiqi Xu, Kwan Man, Xiaojuan Wang, Juqiang Han, Wing Yan Leung, Ruonan Wu, Ken Liu, and Jun Yu. CXC motif chemokine 10 impairs autophagy and autolysosome formation in non-alcoholic steatohepatitis. Theranostics 7, no. 11 (2017): 2822.


  • Ling Luo, Ruonan Wu, Han Meng, Xiaoyan Li, and Jidong Gu. Seasonal and spatial variations in diversity and abundance of bacterial laccase-like genes in sediments of a subtropical mangrove ecosystem. International Biodeterioration & Biodegradation 114 (2016): 260-267.
  • Ruonan Wu, Nakatsu Geicho, Xiang Zhang, and Jun Yu. Pathophysiological mechanisms and therapeutic potentials of macrophages in non-alcoholic steatohepatitis. Expert Opinion on Therapeutic Targets 20, no. 5 (2016): 615-626.
  • Han Meng, Yongfeng Wang, Howang Chan, Ruonan Wu, and Jidong Gu. Co-occurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in subtropical acidic forest soils. Applied Microbiology and Biotechnology 100, no. 17 (2016): 7727-7739.


  • Ruonan Wu, Xiang Zhang, Eagle SH Chu, Joseph JY Sung, and Jun Yu. Sa1712 Inducible Macrophage Ablation Protects Mice From Non-Alcoholic Steatohepatitis. Gastroenterology 146, no. 5 (2014): S-957.


  • Guoxiu Tong, Fangfang Du, Wenhua Wu, Ruonan Wu, Fangting Liu, and Yan Liang. Enhanced reactive oxygen species (ROS) yields and antibacterial activity of spongy ZnO/ZnFe2O4 hybrid micro-hexahedra selectively synthesized through a versatile glucose-engineered co-precipitation/annealing process. Journal of Materials Chemistry B 1, no. 20 (2013): 2647-2657.
  • Guoxiu Tong, Fangfang Du, Yan Liang, Qian Hu, Ruonan Wu, Jianguo Guan, and Xian Hu. Polymorphous ZnO complex architectures: selective synthesis, mechanism, surface area and Zn-polar plane-codetermining antibacterial activity. Journal of Materials Chemistry B 1, no. 4 (2013): 454-463.