All Stories

  1. Proteome-informed interrogation of a methanogenic archaeon links stress response mechanisms with microbial performance and robustness during biomethanation

    Article • Engineering Microbiology, September 2026, Elsevier

    William Nelson

  2. Describing the persistence landscape for introducing microbes into complex communities

    Article • Applied and Environmental Microbiology, July 2026, ASM Journals

    William Nelson

  3. Carbon starvation of Mycobacterium abscessus induces a non-replicating state with extensive proteomic remodeling

    Article • May 2026, openRxiv

    William Nelson

  4. Chemoproteomic elucidation of β-lactam drug targets in Mycobacterium abscessus

    Article • December 2025, openRxiv

    William Nelson

  5. Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors

    Article • The ISME Journal, November 2025, Oxford University Press (OUP)

    William Nelson

  6. Comparisons of fractionation methods for DNA and RNA viruses unearths a multifaceted relationship between viruses and soil moisture

    Article • August 2025, Springer Science + Business Media

    William Nelson

  7. Correction for Van Fossen et al., “Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pittii ”

    Article • Applied and Environmental Microbiology, July 2025, ASM Journals

    William Nelson

  8. A Rhodopseudomonas strain with a substantially smaller genome retains the core metabolic versatility of its genus

    Article • Applied and Environmental Microbiology, April 2025, ASM Journals

    William Nelson

  9. Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

    Article • mSystems, March 2025, ASM Journals

    William Nelson

  10. ARhodopseudomonasstrain with a substantially smaller genome retains the core metabolic versatility of its genus

    Article • October 2024, Cold Spring Harbor Laboratory Press

    William Nelson

  11. Environmental matrix and moisture are key determinants of microbial phenotypes expressed in a reduced complexity soil-analog

    Article • October 2024, Cold Spring Harbor Laboratory Press

    William Nelson

  12. Improving the visualization of viruses in soil

    Article • September 2024, Cold Spring Harbor Laboratory Press

    William Nelson

  13. Hi-C metagenome sequencing reveals soil phage–host interactions

    Article • Nature Communications, November 2023, Springer Science + Business Media

    William Nelson

  14. Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders inAcinetobacter pittii

    Article • June 2023, Cold Spring Harbor Laboratory Press

    William Nelson

  15. Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes

    Article • mSystems, October 2022, ASM Journals

    William Nelson

  16. A Histoplasma capsulatum Lipid Metabolic Map Identifies Antifungal Targets

    Article • mBio, December 2021, ASM Journals

    William Nelson

  17. DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes

    Article • mBio, December 2021, ASM Journals

    William Nelson

  18. Draft Genome Sequence of Fusarium sp. Strain DS 682, a Novel Fungal Isolate from the Grass Rhizosphere

    Article • Microbiology Resource Announcements, January 2021, ASM Journals

    William Nelson

  19. The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn’s Disease: A Randomized Diet Controlled Trial

    Article • Nutrients, December 2020, MDPI AG

    William Nelson

  20. Biases in genome reconstruction from metagenomic data

    Article • PeerJ, October 2020, PeerJ

    William Nelson

  21. Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

    Article • mBio, August 2020, ASM Journals

    William Nelson

  22. Terabase Metagenome Sequencing of Grassland Soil Microbiomes

    Article • Microbiology Resource Announcements, August 2020, ASM Journals

    William Nelson

  23. Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome

    Article • PLOS One, January 2020, PLOS

    William Nelson

  24. Temporal dynamics of nitrogen cycle gene diversity in a hyporheic microbiome

    Article • August 2019, Cold Spring Harbor Laboratory Press

    William Nelson

  25. Correction for Christensen et al., “Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli”

    Article • mBio, April 2019, ASM Journals

    William Nelson

  26. Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli

    Article • mBio, October 2018, ASM Journals

    Dr Alan J Wolfe, William Nelson

  27. Identification of novel protein lysine acetyltransferases inEscherichia coli

    Article • September 2018, Cold Spring Harbor Laboratory Press

    William Nelson

  28. Publisher Correction: Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology

    Article • Nature Communications, March 2018, Springer Science + Business Media

    William Nelson

  29. Draft Genome Sequence of Cyanobacterium sp. Strain HL-69, Isolated from a Benthic Microbial Mat from a Magnesium Sulfate-Dominated Hypersaline Lake

    Article • Genome Announcements, February 2018, ASM Journals

    William Nelson

  30. Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology

    Article • Nature Communications, February 2018, Springer Science + Business Media

    William Nelson

  31. Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

    Article • Scientific Reports, January 2018, Springer Science + Business Media

    William Nelson

  32. Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

    Article • Scientific Reports, September 2017, Springer Science + Business Media

    Dr Timothy D Scheibe, William Nelson

  33. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

    Article • Nature Biotechnology, August 2017, Springer Science + Business Media

    Prof. Jonathan A. Eisen, Dr Susannah Green Tringe, Dr Nikos C Kyrpides, William Nelson

  34. Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach

    Article • Frontiers in Microbiology, June 2017, Frontiers

    William Nelson

  35. Biases in genome reconstruction from metagenomic data

    Article • April 2017, PeerJ

    William Nelson

  36. Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat

    Article • FEMS Microbiology Ecology, March 2017, Oxford University Press (OUP)

    William Nelson

  37. Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

    Article • Nature Communications, April 2016, Springer Science + Business Media

    William Nelson

  38. Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

    Article • Applied and Environmental Microbiology, October 2015, ASM Journals

    William Nelson

  39. The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

    Article • Frontiers in Microbiology, July 2015, Frontiers

    William Nelson

  40. Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

    Article • Proceedings of the National Academy of Sciences, March 2015, Proceedings of the National Academy of Sciences

    Dr Nikos C Kyrpides, William Nelson

  41. Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a

    Article • Genome Announcements, January 2014, ASM Journals

    Dr Sergey Stolyar, William Nelson

  42. Microbial secondary succession in soil microcosms of a desert oasis in the Cuatro Cienegas Basin, Mexico

    Article • PeerJ, March 2013, PeerJ

    William Nelson

  43. Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia

    Article • Frontiers in Microbiology, January 2013, Frontiers

    William Nelson

  44. Novel Miniature Transposable Elements in Thermophilic Synechococcus Strains and Their Impact on an Environmental Population

    Article • Journal of Bacteriology, May 2012, ASM Journals

    William Nelson

  45. Comparative Analysis of Eukaryotic Marine Microbial Assemblages from 18S rRNA Gene and Gene Transcript Clone Libraries by Using Different Methods of Extraction

    Article • Applied and Environmental Microbiology, March 2012, ASM Journals

    William Nelson

  46. Prospects for the study of evolution in the deep biosphere

    Article • Frontiers in Microbiology, January 2012, Frontiers

    William Nelson

  47. Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine

    Article • Environmental Microbiology, November 2011, Wiley

    William Nelson

  48. Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium

    Article • PLOS One, September 2011, PLOS

    William Nelson

  49. Analysis of Insertion Sequences in Thermophilic Cyanobacteria: Exploring the Mechanisms of Establishing, Maintaining, and Withstanding High Insertion Sequence Abundance

    Article • Applied and Environmental Microbiology, June 2011, ASM Journals

    William Nelson

  50. Genomic Potential of Marinobacter aquaeolei, a Biogeochemical “Opportunitroph”

    Article • Applied and Environmental Microbiology, February 2011, ASM Journals

    William Nelson

  51. Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche

    Article • Microbial Ecology, June 2010, Springer Science + Business Media

    William Nelson

  52. The FibRumBa Database: A Resource for Biologists with Interests in Gastrointestinal Microbial Ecology, Plant Biomass Degradation, and Anaerobic Microbiology

    Article • Microbial Ecology, July 2009, Springer Science + Business Media

    William Nelson

  53. Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism

    Article • PLOS One, May 2009, PLOS

    William Nelson, Dr Renato Lima Santos

  54. Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils

    Article • Applied and Environmental Microbiology, February 2009, ASM Journals

    William Nelson

  55. Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes

    Article • PLOS One, January 2009, PLOS

    William Nelson

  56. Genomic Differences between Fibrobacter succinogenes S85 and Fibrobacter intestinalis DR7, Identified by Suppression Subtractive Hybridization

    Article • Applied and Environmental Microbiology, December 2007, ASM Journals

    William Nelson

  57. Candidatus Chloracidobacterium thermophilum: An Aerobic Phototrophic Acidobacterium

    Article • Science, July 2007, American Association for the Advancement of Science

    William Nelson

  58. Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus

    Article • Nature Biotechnology, May 2007, Springer Science + Business Media

    William Nelson

  59. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

    Article • Nucleic Acids Research, January 2007, Oxford University Press (OUP)

    William Nelson

  60. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment

    Article • Proceedings of the National Academy of Sciences, September 2006, Proceedings of the National Academy of Sciences

    William Nelson

  61. Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens

    Article • Genome Research, July 2006, Cold Spring Harbor Laboratory Press

    William Nelson

  62. Correction: Corrigendum: Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

    Article • Nature Biotechnology, April 2006, Springer Science + Business Media

    William Nelson

  63. Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system

    Article • Proceedings of the National Academy of Sciences, January 2006, Proceedings of the National Academy of Sciences

    William Nelson

  64. Comparative Genomics of Emerging Human Ehrlichiosis Agents

    Article • PLoS Genetics, January 2006, PLOS

    Prof. Jonathan A. Eisen, William Nelson

  65. Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents

    Article • PLoS Genetics, January 2006, PLOS

    Prof. Jonathan A. Eisen, William Nelson

  66. Correction: Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

    Article • PLoS Genetics, January 2006, PLOS

    Prof. Jonathan A. Eisen, William Nelson

  67. Correction

    Article • Proceedings of the National Academy of Sciences, November 2005, Proceedings of the National Academy of Sciences

    William Nelson

  68. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial “pan-genome”

    Article • Proceedings of the National Academy of Sciences, September 2005, Proceedings of the National Academy of Sciences

    William Nelson

  69. Whole-Genome Sequence Analysis of Pseudomonas syringae pv. phaseolicola 1448A Reveals Divergence among Pathovars in Genes Involved in Virulence and Transposition

    Article • Journal of Bacteriology, September 2005, ASM Journals

    William Nelson

  70. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses

    Article • Proceedings of the National Academy of Sciences, July 2005, Proceedings of the National Academy of Sciences

    William Nelson

  71. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

    Article • Nature Biotechnology, July 2005, Springer Science + Business Media

    William Nelson

  72. Novel Molecular Features of the Fibrolytic Intestinal Bacterium Fibrobacter intestinalis Not Shared with Fibrobacter succinogenes as Determined by Suppressive Subtractive Hybridization

    Article • Journal of Bacteriology, June 2005, ASM Journals

    William Nelson

  73. Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes

    Article • Science, January 2005, American Association for the Advancement of Science

    Prof. Jonathan A. Eisen, William Nelson

  74. Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

    Article • PLoS Genetics, January 2005, PLOS

    Prof. Jonathan A. Eisen, William Nelson

  75. Article • Genome Biology, January 2005, Springer Science + Business Media

    William Nelson

  76. Article • Genome Biology, January 2005, Springer Science + Business Media

    William Nelson

  77. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

    Article • December 2004

    William Whitman, Prof. Jonathan A. Eisen, William Nelson

  78. Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)

    Article • PLoS Biology, September 2004, PLOS

    Prof. Jonathan A. Eisen, William Nelson

  79. Structural flexibility in the Burkholderia mallei genome

    Article • Proceedings of the National Academy of Sciences, September 2004, Proceedings of the National Academy of Sciences

    William Nelson

  80. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species

    Article • Nucleic Acids Research, April 2004, Oxford University Press (OUP)

    William Nelson

  81. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

    Article • Nature Biotechnology, April 2004, Nature

    Prof. Jonathan A. Eisen, William Nelson

  82. Environmental Genome Shotgun Sequencing of the Sargasso Sea

    Article • Science, April 2004, American Association for the Advancement of Science

    Prof. Jonathan A. Eisen, William Nelson

  83. Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements

    Article • PLoS Biology, March 2004, PLOS

    Prof. Jonathan A. Eisen, William Nelson

  84. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1

    Article • Nucleic Acids Research, February 2004, Oxford University Press (OUP)

    William Nelson

  85. Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments

    Article • Science, December 2003, American Association for the Advancement of Science

    Prof. Jonathan A. Eisen, William Nelson

  86. Complete Genome Sequence of the Oral Pathogenic Bacterium Porphyromonas gingivalis Strain W83

    Article • Journal of Bacteriology, September 2003, ASM Journals

    Prof. Jonathan A. Eisen, William Nelson

  87. Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

    Article • Journal of Bacteriology, September 2003, ASM Journals

    Prof. Jonathan A. Eisen, William Nelson

  88. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000

    Article • Proceedings of the National Academy of Sciences, August 2003, Proceedings of the National Academy of Sciences

    William Nelson

  89. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

    Article • Environmental Microbiology, July 2003, Wiley

    Prof. Jonathan A. Eisen, William Nelson

  90. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

    Article • Nature, May 2003, Springer Science + Business Media

    Roger D Plaut, Prof. Jonathan A. Eisen, William Nelson

  91. Complete genome sequence of the Q-fever pathogenCoxiellaburnetii

    Article • Proceedings of the National Academy of Sciences, April 2003, Proceedings of the National Academy of Sciences

    Prof. Jonathan A. Eisen, William Nelson

  92. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae

    Article • Nucleic Acids Research, April 2003, Oxford University Press (OUP)

    William Nelson

  93. Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis

    Article • Science, March 2003, American Association for the Advancement of Science

    Prof. Jonathan A. Eisen, William Nelson

  94. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

    Article • Environmental Microbiology, December 2002, Wiley

    Prof. Jonathan A. Eisen, William Nelson

  95. Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis

    Article • Nature Biotechnology, October 2002, Nature

    Prof. Jonathan A. Eisen, William Nelson

  96. Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains

    Article • Journal of Bacteriology, October 2002, ASM Journals

    Prof. Jonathan A. Eisen, William Nelson

  97. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts

    Article • Proceedings of the National Academy of Sciences, September 2002, Proceedings of the National Academy of Sciences

    Prof. Jonathan A. Eisen, William Nelson

  98. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium

    Article • Proceedings of the National Academy of Sciences, July 2002, Proceedings of the National Academy of Sciences

    Prof. Jonathan A. Eisen, William Nelson

  99. Unsuspected diversity among marine aerobic anoxygenic phototrophs

    Article • Nature, February 2002, Springer Science + Business Media

    Jonathan Eisen, Prof. Jonathan A. Eisen, William Nelson

  100. Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae

    Article • Science, July 2001, American Association for the Advancement of Science

    Prof. Jonathan A. Eisen, William Nelson

  101. Complete genome sequence of Caulobacter crescentus

    Article • Proceedings of the National Academy of Sciences, March 2001, Proceedings of the National Academy of Sciences

    Prof. Jonathan A. Eisen, William Nelson, Professor Craig M Stephens

  102. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39

    Article • Nucleic Acids Research, March 2000, Oxford University Press (OUP)

    Prof. Jonathan A. Eisen, William Nelson

  103. Complete Genome Sequence of Neisseria meningitidis Serogroup B Strain MC58

    Article • Science, March 2000, American Association for the Advancement of Science

    Prof. Jonathan A. Eisen, William Nelson

  104. Genome Sequence of the Radioresistant Bacterium Deinococcus radiodurans R1

    Article • Science, November 1999, American Association for the Advancement of Science

    Prof. Jonathan A. Eisen, William Nelson

  105. The F plasmid traY gene product binds DNA as a monomer or a dimer: structural and functional implications

    Article • Molecular Microbiology, June 1996, Wiley

    William Nelson