Staff information

PNNL Publications

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., D. Rybakova, D. Fischer, T. Cernava, M. Champomier-Vergès, T. Charles, and X. Chen, et al. 2020. "Microbiome definition re-visited: old concepts and new challenges." Microbiome 8, no. 1:103. PNNL-SA-151555. doi:10.1186/s40168-020-00875-0
• Bhattacharjee A., A.M. Thompson, K.C. Schwarz, M.C. Burnet, Y. Kim, J. Nunez, and S.J. Fansler, et al. 2020. "Soil microbial EPS resiliency is influenced by carbon source accessibility." Soil Biology and Biochemistry 151. PNNL-SA-153321. doi:10.1016/j.soilbio.2020.108037
• 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. PNNL-SA-144073. doi:10.1128/mSystems.00729-19
• McClure R.S., D.T. Naylor, Y. Farris, M.R. Davison, S.J. Fansler, K.S. Hofmockel, and J.K. Jansson. 2020. "Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome." Frontiers in Microbiology 11. PNNL-SA-153634. doi:10.3389/fmicb.2020.01987
• McClure R.S., J. Lee, T. Chowdhury, E.M. Bottos, R.A. White, Y. Kim, and C.D. Nicora, et al. 2020. "Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations." Scientific Reports 10, no. 1:Article Number 10882. PNNL-SA-153633. doi:10.1038/s41598-020-67878-7
• Naylor D.T., N.C. Sadler, A. Bhattacharjee, E.B. Graham, C.R. Anderton, R.S. McClure, and M.S. Lipton, et al. 2020. "Soil Microbiomes under Climate Change and Implications for Carbon Cycling." Annual Review of Environment and Resources 45. PNNL-SA-150059. doi:10.1146/annurev-environ-012320-082720
• Naylor D.T., S.J. Fansler, C.J. Brislawn, W.C. Nelson, K.S. Hofmockel, J.K. Jansson, and R.S. McClure. 2020. "Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules." mBio 11, no. 4:e01349-20. PNNL-SA-153705. doi:10.1128/mBio.01349-20

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. 2019. "Computational Analysis of Interactions of the Oral Microbiota." Current Oral Health Reports 6, no. 2:138-144. PNNL-SA-140880. doi:10.1007/s40496-019-0214-6
• McClure R.S. 2019. "Toward a Better Understanding of Species Interactions Through Network Biology." mSystems 4, no. 3:e00114-19. PNNL-SA-141234. doi:10.1128/mSystems.00114-19
• McClure R.S., A. Ahkami, and A.S. Beliaev. 2019. Programming Metabolite Exchange to Understand and Control Plant-Microbe Interactions. PNNL-29251. Richland, WA: Pacific Northwest National Laboratory. Programming Metabolite Exchange to Understand and Control Plant-Microbe Interactions
• 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
• Zegeye E. 2019. "Selection, Succession, and Stabilization of Soil Microbial Consortia." mSystems 4, no. 4:Article Number e00055-19. PNNL-SA-146173. doi:10.1128/mSystems.00055-19
• Zegeye E., C.J. Brislawn, Y. Farris, S.J. Fansler, K.S. Hofmockel, J.K. Jansson, and A.T. Wright, et al. 2019. "Selection, succession and stabilization of soil microbial consortia." mSystems 4, no. 4:e00055-19. PNNL-SA-138630. doi:10.1128/mSystems.00055-19
• Zegeye E., C.J. Brislawn, Y. Farris, S.J. Fansler, K.S. Hofmockel, J.K. Jansson, and A.T. Wright, et al. 2019. "Selection, Succession, and Stabilization of Soil Microbial Consortia." mSystems 4, no. 4:Article Number e00055-19. PNNL-SA-146173. doi:10.1128/mSystems.00055-19
• 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

2018

• 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
• McClure R.S., C.C. Overall, E.A. Hill, H. Song, M.A. Charania, H.C. Bernstein, and J.E. McDermott, et al. 2018. "SPECIES-SPECIFIC TRANSCRIPTOMIC NETWORK INFERENCE OF INTERSPECIES INTERACTIONS." The ISME Journal 12, no. 8:2011-2023. PNNL-SA-124736. doi:10.1038/s41396-018-0145-6
• 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-127453. doi:10.1128/mSphereDirect.00312-18
• 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

• 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