PNNL

Bill Nelson has more than 20 years of experience analyzing microbial genomic data. He worked at the Institute for Genomic Research, participating in pioneering work on genome analysis and helping develop tools and techniques that are still used widely today. The team’s goal was to provide the most accurate functional predictions possible through a combination of high-confidence, automated methods and intensive manual curation where automated methods failed. Nelson also has extensive experience analyzing metagenomic data for functional gene distribution and genome binning. He was involved in some of the earliest metagenomic sequencing projects, including Sargasso Sea. Since joining PNNL, he’s been working on large, collaborative projects investigating mechanisms by which metabolic interactions contribute to community and ecological function. This work has included processing and analysis of multi-omics data (16S rRNA-based taxonomy, metagenomics, transcriptomics, and proteomics), metabolic reconstruction, and correlative network analysis—all of which allow projects to develop an integrated, systems biology approach to examining microbial ecology in complex communities.

• Bioinformatics
• Biological Databases
• Genomics
• Metabolic Reconstruction
• Metadata Management
• Molecular Microbiology
• Transcriptomics

• PhD in Biology, University of North Carolina, Chapel Hill, 1996
• BA in Biology, Bucknell University, 1990
• BA in Chemistry, Bucknell University, 1990

• American Association for the Advancement of Science
• American Geophysical Union
• American Society for Microbiology

2020

• Nelson, W.C., L.N. Anderson, R. Wu, J.E. McDermott, S.L. Bell, A. Jumpponnen, S.J. Fansler, K.J. Tyrell, Y. Farris, K.S. Hofmockel, J.K. Jansson. 2020. “Terabase Metagenome Sequencing of Grassland Soil Microbiomes.” Microbiology Resource Announcements 9(32). doi: 10.1128/MRA.00718-20
• 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

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 of the United States of America 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