Staff information
William Nelson
Computational Biology
Computational Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352
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PNNL Publications
2023
- Chang C.H., W.C. Nelson, A.R. Jerger, A.T. Wright, R.G. Egbert, and J.E. McDermott. 2023. "Snekmer: A scalable pipeline for protein sequence fingerprinting based on amino acid recoding." Bioinformatics Advances 3, no. 1:Art. No. vbad005. PNNL-SA-169271. doi:10.1039/d2cc01517j
2022
- Bhattacharjee A., O. Qafoku, J. Richardson, L.N. Anderson, K.C. Schwarz, L.M. Bramer, and G.X. Lomas, et al. 2022. "A Mineral-Doped Micromodel Platform Demonstrates Fungal Bridging of Carbon Hot Spots and Hyphal Transport of Mineral-Derived Nutrients." mSystems 7, no. 6:Art. No. e00913-22. PNNL-SA-167557. doi:10.1128/msystems.00913-22
- Krishnamoorthy S., A.K. Steiger, W.C. Nelson, R.G. Egbert, and A.T. Wright. 2022. "An activity-based probe targeting the streptococcal virulence factor C5a peptidase." Chemical Communications 58, no. 58:8113-8116. PNNL-SA-170832. doi:10.1039/d2cc01517j
- 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
2021
- 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
- Zamith-Miranda D., H.M. Heyman, M.C. Burnet, S.P. Couvillion, X. Zheng, N. Munoz Munoz, and W.C. Nelson, et al. 2021. "A Histoplasma capsulatum lipid metabolic map identifies antifungal targets." mBio 12, no. 6:e02972-21. PNNL-SA-152496. doi:10.1128/mBio.02972-21
2020
- 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
- Nelson W.C., B. Tully, and J.M. Mobberley. 2020. "Biases in Genome Reconstruction from Metagenomic Data." PeerJ 8. PNNL-SA-151193. doi:10.7717/peerj.10119
- Nelson W.C., E.B. Graham, A.R. Crump, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, and J.C. Stegen. 2020. "Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome." PLoS One 15, no. 1:Article No. e0228165. PNNL-SA-125632. doi:10.1371/journal.pone.0228165
- 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
- Song H., J.C. Stegen, E.B. Graham, J. Lee, V.A. Garayburu-Caruso, W.C. Nelson, and X. Chen, et al. 2020. "Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling." Frontiers in Microbiology 11. PNNL-SA-151734. doi:10.3389/fmicb.2020.531756
- Suskind D., D. Lee, Y. Kim, G. Wahbeh, N. Singh, K. Braly, and M. Nuding, et al. 2020. "The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn’s Disease: A Randomized Diet Controlled Trial." Nutrients 12, no. 12:3749. PNNL-SA-152828. doi:10.3390/nu12123749
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
- Song H., J. Lee, S. Haruta, W.C. Nelson, D. Lee, S.R. Lindemann, and J.K. Fredrickson, et al. 2019. "Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities." Frontiers in Microbiology 10. PNNL-SA-131990. doi:10.3389/fmicb.2019.01264
2018
- Christensen D.G., J.G. Meyer, J.T. Baumgartner, A.K. D'Souza, W.C. Nelson, S.H. Payne, and M.L. Kuhn, et al. 2018. "Identification of novel protein lysine acetyltransferases in Escherichia coli." mBio 9, no. 5:Article Number e01905-18. PNNL-SA-138542. doi:10.1128/mBio.01905-18
- Cole J.K., B.R. Morton, H.C. Cardamone, H.R. Lake, A. Dohnalkova, Y. Kim, and J.E. Kyle, et al. 2018. "Salinivirga fredricksonii gen. nov. , sp. nov., a heterotrophic halophile isolated from photosynthetic mat of a novel lineage (Salinivirgaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinivirgaceae." International Journal of Systematic and Evolutionary Microbiology 68, no. 5:1591-1598. PNNL-SA-118460. doi:10.1099/ijsem.0.002715
- Graham E.B., A.R. Crump, D.W. Kennedy, E.V. Arntzen, S.J. Fansler, S.O. Purvine, and C.D. Nicora, et al. 2018. "Multi ‘omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone." Science of the Total Environment 642. PNNL-SA-133671. doi:10.1016/j.scitotenv.2018.05.256
- 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
- Mobberley J.M., M.F. Romine, J.K. Cole, Y. Maezato, S.R. Lindemann, and W.C. Nelson. 2018. "Draft genome sequence of Cyanobacterium sp. strain HL-69, isolated from a benthic microbial mat from a magnesium sulfate-dominated hypersaline lake." Genome Announcements 6, no. 6:Article No. e01493-17. PNNL-SA-129362. doi:10.1128/genomeA.01583-17
- Song H., W.C. Nelson, J. Lee, R.C. Taylor, C.S. Henry, A.S. Beliaev, and D. Ramkrishna, et al. 2018. "Metabolic Network Modeling for Computer-Aided Design of Microbial Interactions." In Emerging Areas in Bioengineering, edited by HN Chang, et al. 793-801. Weinheim:Wiley-VCH Verlag GmbH & Co. PNNL-SA-115176. doi:10.1002/9783527803293.ch45
2017
- Bowers R.M., N. Kyrpides, R. Stepanauskas, M. Harmon-Smith, D. Doud, T. Reddy, and F. Schulz, et al. 2017. "Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea." Nature Biotechnology 35. PNNL-SA-125978. doi:10.1038/nbt.3893
- Graham E.B., J.C. Stegen, A.R. Crump, C.T. Resch, S.J. Fansler, E.V. Arntzen, and D.W. Kennedy, et al. 2017. "Organic carbon thermodynamics elucidate spatiotemporal mechanisms governing hyporheic zone biogeochemical cycling." In Proceedings of the Subsurface Biogeochemical Research and Terrestrial Ecosystem Science Joint Meeting April 25-26, 2017, Potomac, Maryland. Washington, District Of Columbia:US Department of Energy, Office of Biological and Environmental Research. PNNL-SA-125130.
- Hou Z., W.C. Nelson, J.C. Stegen, C.J. Murray, E.V. Arntzen, A.R. Crump, and D.W. Kennedy, et al. 2017. "Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies." Scientific Reports 7. PNNL-SA-121286. doi:10.1038/s41598-017-12275-w
- Li M., Y. Gao, W. Qian, L. Shi, Y. Liu, W.C. Nelson, and C.D. Nicora, et al. 2017. "Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes." Environmental Microbiology Reports 9, no. 5:512-521. PNNL-SA-120732. doi:10.1111/1758-2229.12558
- Lindemann S.R., J.M. Mobberley, J.K. Cole, L. Markillie, R.C. Taylor, E.L. Huang, and W.B. Chrisler, et al. 2017. "Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach." Frontiers in Microbiology 8. PNNL-SA-129376. doi:10.3389/fmicb.2017.01020
- Liu Y., C. Liu, W.C. Nelson, L. Shi, F. Xu, Y. Liu, and A. Yan, et al. 2017. "Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns." Environmental Science & Technology 51, no. 9:4877-4886. PNNL-SA-121316. doi:10.1021/acs.est.6b05018
- Mobberley J.M., S.R. Lindemann, H.C. Bernstein, J.J. Moran, R.S. Renslow, J.T. Babauta, and D. Hu, et al. 2017. "Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat." FEMS Microbiology Ecology 93, no. 4:Article No. fix028. PNNL-SA-124562. doi:10.1093/femsec/fix028
2016
- Nelson W.C., Y. Maezato, Y. Wu, M.F. Romine, and S.R. Lindemann. 2016. "Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia." Applied and Environmental Microbiology 82, no. 1:255-267. PNNL-SA-111129. doi:10.1128/AEM.02274-15
- Stegen J.C., J.K. Fredrickson, M.J. Wilkins, A. Konopka, W.C. Nelson, E.V. Arntzen, and W.B. Chrisler, et al. 2016. "Groundwater-Surface Water Mixing Shifts Ecological Assembly Processes and Stimulates Organic Carbon Turnover." Nature Communications 7. PNNL-SA-111962. doi:10.1038/ncomms11237
2015
- Nelson W.C., and J.C. Stegen. 2015. "The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle." Frontiers in Microbiology 6. PNNL-SA-112374. doi:10.3389/fmicb.2015.00713
- Walworth N.G., U. Pfreundt, W.C. Nelson, T. Mincer, J.F. Heidelberg, F. Fu, and J.B. Waterbury, et al. 2015. "Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle." Proceedings of the National Academy of Sciences (PNAS) 112, no. 4:4251-4256. PNNL-SA-108623. doi:10.1073/pnas.1422332112
2014
- Stolyar S., Z. Liu, V. Thiel, L.P. Tomsho, N. Pinel, W.C. Nelson, and S.R. Lindemann, et al. 2014. "Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a." Genome Announcements 2, no. 1:Article No. e01060-13. PNNL-SA-100453. doi:10.1128/genomeA.01060-13