Computational Scientist
Computational Scientist

Biography

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.

Education

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

Publications

2025

  • Ast H., M.J. Hammer, S. Zhang, A.M. Bruton, I. Hatsu, B. Leung, and R.S. McClure, et al. 2025. "Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study." Gut Microbes 17, no. 1:Art. No. 2463570. PNNL-SA-200316. doi:10.1080/19490976.2025.2463570

2024

  • George A.D., W.E. Anthony, A.D. McNaughton, T.T. Lin, V. Torres-Rodriguez, S.M. Mahserejian, and S.L. Altus, et al. 2024. Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities. PNNL-36693. Richland, WA: Pacific Northwest National Laboratory. Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities
  • Graham E.B., V.A. Garayburu-Caruso, R. Wu, J. Zheng, R.S. McClure, and G. Jones. 2024. "Genomic fingerprints of the world's soil ecosystems." mSystems 9, no. 6:Art. No. e01112-23. PNNL-SA-191207. doi:10.1128/msystems.01112-23
  • McDermott J.E., J.M. Jacobs, N.J. Merrill, H.D. Mitchell, O.A. Arshad, R.S. McClure, and J.G. Teeguarden, et al. 2024. "Molecular-Level Dysregulation of Insulin Pathways and Inflammatory Processes in Peripheral Blood Mononuclear Cells by Circadian Misalignment." Journal of Proteome Research 23, no. 5:1547-1558. PNNL-SA-186735. doi:10.1021/acs.jproteome.3c00418
  • Rericha Y., L. St. Mary, L. Truong, R.S. McClure, K. Martin, S. Leonard, and P. Thunga, et al. 2024. "Diverse PFAS produce unique transcriptomic changes linked to developmental toxicity in zebrafish." Frontiers in Toxicology 6, no. _:Art. No. 1425537. PNNL-SA-197332. doi:10.3389/ftox.2024.1425537

2023

  • Couvillion S.P., R.E. Danczak, X. Cao, Q. Yang, T.P. Keerthisinghe, R.S. McClure, and D. Bitounis, et al. 2023. "Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model." NanoImpact 30. PNNL-SA-177384. doi:10.1016/j.impact.2023.100463
  • Ferrocino I., K. Rantsiou, R.S. McClure, T. Kostic, R. Soares Correa De Souza, L. Lange, and J. Fitzgerald, et al. 2023. "The need for an integrated multi-OMICs approach in microbiome science in the food system." Comprehensive Reviews in Food Science and Food Safety 22, no. 2:1082-1103. PNNL-SA-176734. doi:10.1111/1541-4337.13103
  • Jansson J.K., R.S. McClure, and R.G. Egbert. 2023. "Soil microbiome engineering for sustainability in a changing environment." Nature Biotechnology 41, no. 12:1716-1728. PNNL-SA-188763. doi:10.1038/s41587-023-01932-3
  • McClure R.S. 2023. "Editorial for Special Issue "Advances in Soil Microbiome"." Microorganisms 11, no. 8:Art. No. 2026. PNNL-SA-189586. doi:10.3390/microorganisms11082026
  • McClure R.S., Y. Rericha, K.M. Waters, and R.L. Tanguay. 2023. "3’ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior with respect to identifying toxicity pathways in a model organism." Frontiers in Bioinformatics 3, no. 2023:1234218. PNNL-SA-178190. doi:10.3389/fbinf.2023.1234218
  • Okemo P., I. Njaci, Y. Kim, R.S. McClure, M.J. Peterson, A.S. Beliaev, and K.K. Hixson, et al. 2023. "Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying." Scientific Reports 13. PNNL-SA-177979. doi:10.1038/s41598-023-47456-3
  • Wu R., M.R. Davison, W.C. Nelson, M.L. Smith, M.S. Lipton, J.K. Jansson, and R.S. McClure, et al. 2023. "Hi-C metagenome sequencing reveals soil phage-host interactions." Nature Communications 14. PNNL-SA-181374. doi:10.1038/s41467-023-42967-z

2022

  • McClure R.S., Y. Farris, R.E. Danczak, W.C. Nelson, H. Song, A. Kessler, and J. Lee, et al. 2022. "Interaction Networks are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes." mSystems 7, no. 5:Art. No. e00372-22. PNNL-SA-169189. doi:10.1128/msystems.00372-22
  • Naylor D., R.S. McClure, and J.K. Jansson. 2022. "Trends in microbial community composition and function by soil depth." Microorganisms 10, no. 3:Art. No. 540. PNNL-SA-170986. doi:10.3390/microorganisms10030540
  • Sunkavalli A., R.S. McClure, and C. Genco. 2022. "Molecular Regulatory Mechanisms Drive Emergent Pathogenetic Properties of Neisseria gonorrhoeae." Microorganisms 10, no. 5:Art. No. 922. PNNL-SA-172593. doi:10.3390/microorganisms10050922
  • Wilson L.B., R.S. McClure, K.M. Waters, M. Simonich, and R.L. Tanguay. 2022. "Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene." Frontiers in Toxicology 4. PNNL-SA-173226. doi:10.3389/ftox.2022.950503

2021

  • Oliver A., S. Podell, A. Pinowska, J. Traller, S.R. Smith, R.S. McClure, and A.S. Beliaev, et al. 2021. "Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom." Scientific Reports 11. PNNL-SA-161367. doi:10.1038/s41598-021-95106-3
  • Shankar P., R.S. McClure, K.M. Waters, and R.L. Tanguay. 2021. "Gene Co-Expression Network Analysis in Zebrafish Reveals Chemical Class Specific Modules." BMC Genomics 22, no. 1:658. PNNL-SA-160902. doi:10.1186/s12864-021-07940-4

2020

  • 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

2019

  • 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

2018

  • 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

2017

  • 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

2016

  • 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

2015

  • 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

2014

  • 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

2013

  • 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

2010

  • 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