Computational Scientist
Computational Scientist


Ryan McClure’s research history is focused on host/pathogen interactions, natural microbial communities, network biology, and large-scale omics studies. He’s experienced in managing multiple projects at once and guiding experiments and studies from initial design, to data collection and analysis, to publication. McClure is able to work independently and lead others, as well as learn from colleagues and contribute as a team member to larger experiments and projects.


  • PhD in Microbiology, Boston University
  • BS in Biochemistry, Michigan State University



  • Berg G, Rybakova D, Fischer D, Cernava T, Champomier-Vergès MC, Charles T, Chen X, Cocolin L, Eversole K, Herrero-Corral G, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin JA, Maguin E, Mauchline T, McClure R, Mitter B, Ryan M, Sarand I, Smidt H, Schelkle B, Roume H, Kiran SG, Selvin J, de Souza RSC, van Overbeek L, Singh B, Wagner M, Walsh A, Sessitsch A, Schloter M. 2020.  Microbiome definition re-visited: old concepts and new challenges.  Microbiome 8, 103 (2020). doi:10.1186/s40168-020-00875-0.  PNNL-SA-151555
  • Naylor D, Fansler S, Brislawn C, Nelson WC, Hofmockel KS, Jansson JK, McClure R. (2020). Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules. mBio.doi:10.1128/mBio.01349-20.  PNNL-SA-150380.
  • McClure R., J.-Y. Lee, T. Chowdhury, E. Bottos, R. White III, Y.-M. Kim, C. Nicora, T. Metz, K.S. Hofmockel, J.K. Jansson and H.S. Song (2020). Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations. Scientific Reports. doi:10.1038/s41598-020-67878-7.  PNNL-SA-153633
  • Naylor, D., N. Sadler, A. Bhattacharjee, E.B. Graham, C.R. Anderton, R. McClure, M. Lipton, K.S. Hofmockel, and J.K. Jansson. (2020) Soil microbiomes under climate change and implications for carbon cycling. Annual Review of Environment and Resources. doi:10.1146/annurev-environ-012320-082720.  PNNL-SA-150059
  • McClure R.S., A. Sunkavalli, P. Balzano, P. Massari, C. Cho, W.M. Nauseef, and M.A. Apicella, et al. 2020. "Global Network Analysis of Neisseria Gonorrhoeae Identifies Coordination Between Pathways, Processes and Regulators Expressed During Human Infection." mSystems 5, no. 1:Article No.e00729-19. doi:10.1128/mSystems.00729-19.  PNNL-SA-144073


  • Bohutskyi P., R.S. McClure, E.A. Hill, W.C. Nelson, W.B. Chrisler, J. Nunez, and R.S. Renslow, et al. 2019. "Metabolic effects of vitamin B12 on physiology, stress resistance, growth rate and biomass productivity of Cyanobacterium stanieri planktonic and biofilm cultures." Algal Research 42. PNNL-SA-136164. doi:10.1016/j.algal.2019.101580
  • McClure R.S., J.P. Wendler, J.N. Adkins, J.A. Swanstrom, R. Baric, B. Kaiser, and K.L. Oxford, et al. 2019. "Unified Feature Association Networks through Integration of Transcriptomic and Proteomic Data." PLoS Computational Biology 15, no. 9:e1007241. PNNL-SA-137420. doi:10.1371/journal.pcbi.1007241
  • Minutoli M., M. Halappanavar, A. Kalyanaraman, A. Visweswara Sathanur, R.S. McClure, and J.E. McDermott. 2019. "Fast and Scalable Implementations of Influence Maximization Algorithms." In IEEE International Conference on Cluster Computing (CLUSTER 2019), September 23-26, 2019, Albuquerque, NM. Piscataway, New Jersey:IEEE. PNNL-SA-141177. doi:10.1109/CLUSTER.2019.8890991
  • Shankar P., M. Geier, L. Truong, R.S. McClure, P. Pande, K.M. Waters, and R. Tanguay. 2019. "Coupling Genome-wide Transcriptomics and Developmental Toxicity Profiles in Zebrafish to Characterize Polycyclic Aromatic Hydrocarbon (PAH) Hazard." International Journal of Molecular Sciences 20, no. 10:2570. PNNL-SA-143672. doi:10.3390/ijms20102570
  • Zhu T., R.S. McClure, O.B. Harrison, C. Genco, and P. Massari. 2019. "Integrated Bioinformatic Analyses and Immune Characterization of New Neisseria gonorrhoeae Vaccine Antigens Expressed during Natural Mucosal Infection." Vaccines 7, no. 4:Article No. 153. PNNL-SA-146316. doi:10.3390/vaccines7040153
  • Zegeye EK, Brislawn CJ, Farris Y, Fansler SJ, Hofmockel KS, Jansson JK, Wright AT, Graham EB, Naylor D, McClure RS, Bernstein HC. (2019).  Selection, Succession, and Stabilization of Soil Microbial Consortia. mSystems 4(4).  doi: 10.1128/mSystems.00055-19.  PNNL-SA-146173
  • McClure RS. (2019) Computational Analysis of Interactions of the Oral Microbiota. June 2019, Volume 6, Issue 2, pp 138–144.  doi:10.1007/s40496-019-0214-6.  PNNL-SA-140880
  • McClure RS. (2019) Toward a Better Understanding of Species Interactions through Network Biology. vol. 4, no. 3.  DOI: 10.1128/mSystems.00114-19.  PNNL-SA-141234.
  • McClure R and C Genco. 2019. “Strategies for Global RNA Sequencing of the Human Pathogen Neisseria gonorrhoeae.” Methods Mol Biol. 1997:163-183.  doi:10.1007/978-1-4939-9496-0_11.  PNNL-SA-138905


  • McClure, R.S., Overall, C.C., Overall, Hill, E.A., Charania, M., Bernstein, H.C., McDermott, J.E., Beliaev, A.S. (2018) Species-specific transcriptomic network inference of interspecies interactions in microbial communities. ISME 12(8):2011-2023.  PNNL-SA-124736.  doi: 10.1038/s41396-018-0145-6
  • Colby S.M., R.S. McClure, C.C. Overall, R.S. Renslow, and J.E. McDermott. 2018. "Improving network inference algorithms using resampling methods." BMC Bioinformatics 19. PNNL-SA-134995. doi:10.1186/s12859-018-2402-0
  • Khan N.E., Y. Maezato, R.S. McClure, C.J. Brislawn, J.M. Mobberley, N.G. Isern, and W.B. Chrisler, et al. 2018. "Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture." Scientific Reports 8. PNNL-SA-129337. doi:10.1038/s41598-017-18630-1
  • Nudel K., R.S. McClure, M. Moreau, E. Briars, A. Abrams, B. Tjaden, and X. Su, et al. 2018. "Transcriptome Analysis of Neisseria gonorrhoeae during Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants between Men and Women." mSphere 3, no. 3:Article No. e00312-18. PNNL-SA-138245. doi:10.1128/mSphereDirect.00312-18


  • Bernstein H.C., R.S. McClure, V. Thiel, N.C. Sadler, Y. Kim, W.B. Chrisler, and E.A. Hill, et al. 2017. "Indirect interspecies regulation; transcriptional and physiological responses of a cyanobacterium to heterotrophic partnership." mSystems 2, no. 2:Article No. e00181-16. PNNL-SA-113682. doi:10.1128/mSystems.00181-16


  • Yu, C., McClure, R., Nudel, K., Daou, N. and Genco, C.A. (2016) Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network. Journal of bacteriology, 198 (16).  doi: 10.1128/JB.00166-16
  • Bernstein H.C., R.S. McClure, E.A. Hill, L.M. Markillie, W.B. Chrisler, M.F. Romine, and J.E. McDermott, et al. 2016. "Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth." mBio 7, no. 4:Article No. e00949-16. PNNL-SA-112394. doi:10.1128/mBio.00949-16
  • McClure R.S., C.C. Overall, J.E. McDermott, E.A. Hill, L.M. Markillie, L.A. McCue, and R.C. Taylor, et al. 2016. "Network Analysis of Transcriptomics Expands Regulatory Landscapes in Synechococcus sp. PCC 7002." Nucleic Acids Research 44, no. 18:8810-8825. PNNL-SA-113421. doi:10.1093/nar/gkw737


  • Bernstein H.C., M.A. Charania, R.S. McClure, N.C. Sadler, M.R. Melnicki, E.A. Hill, and L.M. Markillie, et al. 2015. "Multi-omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-mediated H2 production in Cyanothece sp. ATCC 51142." Scientific Reports 5. PNNL-SA-111925. doi:10.1038/srep16004
  • Song H., R.S. McClure, H.C. Bernstein, C.C. Overall, E.A. Hill, and A.S. Beliaev. 2015. "Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality." Life 5, no. 2:1127-1140. PNNL-SA-109173. doi:10.3390/life5021127
  • McClure, R., Nudel, K., Massari, P., Tjaden, B., Su, X., Rice, P.A. and Genco, C.A. (2015) The Gonococcal Transcriptome during Infection of the Lower Genital Tract in Women. PloS one, 10, (8).  doi: 10.1371/journal.pone.0133982


  • McClure, R. and Massari, P. (2014) TLR-Dependent Human Mucosal Epithelial Cell Responses to Microbial Pathogens. Frontiers in immunology, 5, 386.  doi: 10.1099/mic.0.039040-0
  • McClure, R., Tjaden, B. and Genco, C. (2014) Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions. Frontiers in microbiology, 5, 456.  doi: 10.1099/mic.0.039040-0


  • Daou, N., Yu, C., McClure, R., Gudino, C., Reed, G.W. and Genco, C.A. (2013) Neisseria  prophage repressor implicated in gonococcal pathogenesis. Infection and immunity, 81 (10).  doi: 10.1099/mic.0.039040-0
  • McClure, R., Balasubramanian, D., Sun, Y., Bobrovskyy, M., Sumby, P., Genco, C.A., Vanderpool, C.K. and Tjaden, B. (2013) Computational analysis of bacterial RNA-Seq data. Nucleic acids research, 41 (14).  doi: 10.1099/mic.0.039040-0


  • Mellin, J.R., McClure, R., Lopez, D., Green, O., Reinhard, B. and Genco, C. (2010) Role of Hfq in iron-dependent and -independent gene regulation in Neisseria meningitidis. Microbiology, 156, 2316-2326.  doi: 10.1099/mic.0.039040-0