Karen E Nelson

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. pmc Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species
    Derrick E Fouts
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 3:e15. 2005
  2. pmc Microbial metagenomics
    Emmanuel F Mongodin
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome Biol 6:347. 2005
  3. pmc Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy
    James R White
    University of Maryland, College Park, Maryland, USA
    Appl Environ Microbiol 74:6447-51. 2008
  4. ncbi request reprint Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored niche
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Environ Microbiol 5:1212-20. 2003
  5. pmc Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
    Karen E Nelson
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 185:5591-601. 2003
  6. pmc 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
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:2386-95. 2004
  7. ncbi request reprint The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 423:81-6. 2003
  8. ncbi request reprint Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
  9. pmc Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1
    Emmanuel F Mongodin
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Genet 2:e214. 2006
  10. pmc Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils
    Naomi L Ward
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Appl Environ Microbiol 75:2046-56. 2009

Detail Information

Publications56

  1. pmc Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species
    Derrick E Fouts
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 3:e15. 2005
    ....
  2. pmc Microbial metagenomics
    Emmanuel F Mongodin
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Genome Biol 6:347. 2005
  3. pmc Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy
    James R White
    University of Maryland, College Park, Maryland, USA
    Appl Environ Microbiol 74:6447-51. 2008
    ..The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties...
  4. ncbi request reprint Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored niche
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Environ Microbiol 5:1212-20. 2003
    ....
  5. pmc Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
    Karen E Nelson
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 185:5591-601. 2003
    ..gingivalis can metabolize a range of amino acids and generate a number of metabolic end products that are toxic to the human host or human gingival tissue and contribute to the development of periodontal disease...
  6. pmc 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
    Karen E Nelson
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:2386-95. 2004
    ..Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs...
  7. ncbi request reprint The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 423:81-6. 2003
    ..The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis...
  8. ncbi request reprint Environmental genome shotgun sequencing of the Sargasso Sea
    J Craig Venter
    Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA
    Science 304:66-74. 2004
    ..2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity...
  9. pmc Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1
    Emmanuel F Mongodin
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Genet 2:e214. 2006
    ..The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals...
  10. pmc Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils
    Naomi L Ward
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Appl Environ Microbiol 75:2046-56. 2009
    ....
  11. pmc The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses
    Barbara A Methe
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 102:10913-8. 2005
    ..Comparative genome analyses suggest that the psychrophilic lifestyle is most likely conferred not by a unique set of genes but by a collection of synergistic changes in overall genome content and amino acid composition...
  12. pmc Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus
    Robert T Deboy
    J Craig Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    J Bacteriol 190:5455-63. 2008
    ..Approximately 50% of the predicted C. japonicus plant-degradative apparatus appears to be shared with S. degradans, consistent with the utilization of plant-derived complex carbohydrates as a major substrate by both organisms...
  13. ncbi request reprint Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes
    Rekha Seshadri
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:105-8. 2005
    ..Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph...
  14. ncbi request reprint Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
    John F Heidelberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nat Biotechnol 20:1118-23. 2002
    ....
  15. pmc Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain
    Steven R Gill
    Microbial Genomics, The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Bacteriol 187:2426-38. 2005
    ..Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis...
  16. pmc Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)
    Naomi Ward
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:e303. 2004
    ..We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential...
  17. pmc Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements
    Martin Wu
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E69. 2004
    ..With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections...
  18. pmc Structural flexibility in the Burkholderia mallei genome
    William C Nierman
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:14246-51. 2004
    ..Variation in simple sequence repeats in key genes can provide a mechanism for generating antigenic variation that may account for the mammalian host's inability to mount a durable adaptive immune response to a B. mallei infection...
  19. pmc The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
    Ian T Paulsen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:13148-53. 2002
    ..A limited repertoire of genes homologous to known bacterial virulence factors were identified...
  20. pmc Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences
    Robert T Deboy
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    J Bacteriol 188:2364-74. 2006
    ....
  21. pmc Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species
    Emmanuel F Mongodin
    The Institute for Genomic Research, Rockville, MD 20850, USA
    J Bacteriol 187:4935-44. 2005
    ..Although the mechanism for gene transfer in this lineage remains to be elucidated, this analysis suggests possible associations with repetitive elements and highlights the possible benefits of rampant genetic exchange to these species...
  22. pmc A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
    Daniel H Haft
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Comput Biol 1:e60. 2005
    ..It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated...
  23. pmc Complete genome sequence of the Q-fever pathogen Coxiella burnetii
    Rekha Seshadri
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 100:5455-60. 2003
    ..burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation...
  24. pmc Metagenomic analysis of the human distal gut microbiome
    Steven R Gill
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 312:1355-9. 2006
    ..Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes...
  25. pmc Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae
    Herve Tettelin
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:12391-6. 2002
    ..agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms...
  26. ncbi request reprint It's a cold world out there (but the prospects are hot)
    Barbara Methe
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Trends Microbiol 12:532-4. 2004
  27. pmc Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus
    Jonathan H Badger
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    J Bacteriol 188:6841-50. 2006
    ..neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging...
  28. pmc The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium
    Jonathan A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:9509-14. 2002
    ..tepidum and many Archaeal species...
  29. doi request reprint Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche
    Janaki Purushe
    Department of Human Genomic Medicine, The J Craig Venter Institute JCVI, Rockville, MD 20850, USA
    Microb Ecol 60:721-9. 2010
    ..Our analysis demonstrates the diversity of this genus. The results from these analyses highlight their role in the gastrointestinal tract, and provide a template for additional work on genetic characterization of these species...
  30. pmc The value of complete microbial genome sequencing (you get what you pay for)
    Claire M Fraser
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 184:6403-5; discusion 6405. 2002
  31. ncbi request reprint Genomics for applied microbiology
    William C Nierman
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Adv Appl Microbiol 51:201-45. 2002
  32. ncbi request reprint Urine sample preparation in 96-well filter plates for quantitative clinical proteomics
    Yanbao Yu
    The J Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
    Anal Chem 86:5470-7. 2014
    ..This 96FASP method has potential to become a gold standard for high-throughput quantitative clinical proteomics. ..
  33. doi request reprint Microbiomes
    Karen E Nelson
    J Craig Venter Institute JCVI, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Microb Ecol 65:916-9. 2013
    ..In this review, we get a perspective on where the science is headed and what we expect to learn as additional studies unfold...
  34. pmc Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury
    Derrick E Fouts
    J Craig Venter Institute, Rockville, MD 20850, USA
    J Transl Med 10:174. 2012
    ....
  35. pmc Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
    Konstantinos Krampis
    J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Bioinformatics 13:42. 2012
    ..Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure...
  36. pmc Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease
    Derrick E Fouts
    J Craig Venter Institute, Rockville, MD, USA
    J Hepatol 56:1283-92. 2012
    ..The aims of our study were to investigate dynamics of bacterial translocation and changes in the enteric microbiome in early stages of liver disease...
  37. ncbi request reprint Champions of versatility
    Karen E Nelson
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Trends Microbiol 12:111-2. 2004
  38. pmc Genome sequence of the human malaria parasite Plasmodium falciparum
    Malcolm J Gardner
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:498-511. 2002
    ..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria...
  39. doi request reprint Novel diversity of bacterial communities associated with bottlenose dolphin upper respiratory tracts
    Wesley R Johnson
    Department of Biology, College of Charleston, Charleston, SC 29401, USA Hollings Marine Laboratory, 331 Ft Johnson Rd, Charleston, SC 29412, USA J Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA Center for Coastal Environmental Health and Biomolecular Research, NOAA National Ocean Service, 219 Fort Johnson Rd Charleston, SC 29412, USA Georgia Aquarium, 225 Baker St, NW, Atlanta, GA 30313, USA
    Environ Microbiol Rep 1:555-62. 2009
    ....
  40. pmc Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima
    Camilla L Nesbø
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    J Bacteriol 184:4475-88. 2002
    ....
  41. ncbi request reprint A novel family of carbohydrate-binding modules identified with Ruminococcus albus proteins
    Qi Xu
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
    FEBS Lett 566:11-6. 2004
    ..The evidence supports a distinctive carbohydrate-binding role of broad specificity for this type of domain, and we propose a novel family (designated family 37) of carbohydrate-binding modules that appear to be peculiar to R. albus...
  42. doi request reprint Functional metagenomic profiling of nine biomes
    Elizabeth A Dinsdale
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:629-32. 2008
    ....
  43. pmc Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy
    Malene Bek-Thomsen
    Institute of Medical Microbiology and Immunology, The Bartholin Building, Aarhus University, DK 8000 Aarhus C, Denmark
    Infect Immun 76:1889-96. 2008
    ..These findings provide a platform for understanding the mechanisms that govern the balance within the complex microbiota at mucosal sites and between the microbiota and the mucosal immune system of the host...
  44. pmc Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities
    Matthew N Ashby
    Taxon Biosciences, Inc, Tiburon, CA 94920, USA
    Appl Environ Microbiol 73:4532-42. 2007
    ..SARD may provide a means to explore the ecological roles of these rare members of microbial communities in qualitative and quantitative terms...
  45. pmc Whole-genome expression profiling of Thermotoga maritima in response to growth on sugars in a chemostat
    Tu N Nguyen
    Department of Molecular and Cell Biology, University of Connecticut, U 3125, 91 N Eagleville Rd, Storrs, CT 06269 3125, USA
    J Bacteriol 186:4824-8. 2004
    ..Genes involved in iron and sulfur metabolism were differentially expressed in response to lactose. These data help define the sets of coregulated genes and suggest possible functions for their encoded products...
  46. pmc Diversity of the human intestinal microbial flora
    Paul B Eckburg
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Room S 169, 300 Pasteur Drive, Stanford CA 94305 5107, USA
    Science 308:1635-8. 2005
    ..We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease...
  47. pmc Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridization
    Meng Qi
    Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
    J Bacteriol 187:3739-51. 2005
    ..It also documents substantive changes in the genome from that of F. succinogenes, which may be related to the introduction of the array of transposase and restriction-modification genes...
  48. ncbi request reprint Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization
    Dionysios A Antonopoulos
    Department of Animal Sciences, University of Illinois at Urbana Champaign, 1207 West Gregory Dr, Urbana, IL 61801, USA
    Environ Microbiol 6:335-46. 2004
    ..Subtracted sequences were then supplemented with the draft (2 x coverage) genome sequence of R. flavefaciens FD-1 to indicate potential regions of rearrangement within the genome, including a novel insertion sequence...
  49. pmc Ruminococcus albus 8 mutants defective in cellulose degradation are deficient in two processive endocellulases, Cel48A and Cel9B, both of which possess a novel modular architecture
    Estelle Devillard
    The MAPLE Research Initiative, Department of Animal Sciences, The Ohio State University, Columbus 43210, USA
    J Bacteriol 186:136-45. 2004
    ..Such X modules are also present in several other R. albus glycoside hydrolases and are phylogentically distinct from the fibronectin III-like and X modules identified so far in other cellulolytic bacteria...
  50. pmc Molecular analysis of the bacterial microbiota in the human stomach
    Elisabeth M Bik
    Department of Microbiology and Immunology, Stanford University School of Medicine, Fairchild Science Building, 299 Campus Drive, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:732-7. 2006
    ..The gastric microbiota may play important, as-yet-undiscovered roles in human health and disease...
  51. ncbi request reprint The future of microbial genomics
    Karen E Nelson
    Environ Microbiol 5:1223-5. 2003
  52. ncbi request reprint The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis
    Diana Stjepandic
    Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D 69120 Heidelberg, Germany
    Environ Microbiol 4:819-23. 2002
    ..A tiling path of clones was selected, from the shotgun clones used for sequencing, for the production of DNA microarrays that represent the entire genome including its non-coding portions...
  53. ncbi request reprint Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtus
    Maria S J Centeno
    CIISA Faculdade de Medicina Veterinaria, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
    FEMS Microbiol Lett 261:123-32. 2006
    ..The role of the identified enzymes in the hydrolysis of galactomannan by aerobic bacteria is discussed...
  54. ncbi request reprint Global features of the Pseudomonas putida KT2440 genome sequence
    Christian Weinel
    Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl Neuberg Str 1, D 30623 Hannover, Germany
    Environ Microbiol 4:809-18. 2002
    ....
  55. ncbi request reprint Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    Shannon B Conners
    Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 7905, USA
    FEMS Microbiol Rev 30:872-905. 2006
    ..The information gained from genomics studies will be particularly useful for developing new biotechnology applications for T. maritima enzymes...
  56. ncbi request reprint Microbial environmental genomics
    Karen E Nelson
    Howard University, Washington, DC, USA
    Microb Ecol 53:367-8. 2007