Research Topics
Genomes and GenesSpecies | Karen E NelsonSummaryAffiliation: The Institute for Genomic Research Country: USA Publications
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Detail Information
Publications
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter speciesDerrick E Fouts
The Institute for Genomic Research, Rockville, Maryland, United States of America
PLoS Biol 3:e15. 2005....- Microbial metagenomicsEmmanuel F Mongodin
The Institute for Genomic Research, Rockville, MD 20850, USA
Genome Biol 6:347. 2005 - Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, ItalyJames 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... - Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83Karen 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... 
Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored nicheKaren E Nelson
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Environ Microbiol 5:1212-20. 2003....- 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 speciesKaren 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... - Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elementsMartin 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... - Environmental genome shotgun sequencing of the Sargasso SeaJ 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... - Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soilsNaomi L Ward
The Institute for Genomic Research, Rockville, Maryland 20850, USA
Appl Environ Microbiol 75:2046-56. 2009.... - Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1Emmanuel 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... - The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteriaTimothy 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... - The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analysesBarbara 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... - Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicusRobert 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... - 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 strainSteven 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... - Structural flexibility in the Burkholderia mallei genomeWilliam 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... - Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenesRekha 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... - Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensisJohn F Heidelberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nat Biotechnol 20:1118-23. 2002.... - Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic speciesEmmanuel 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... - 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... - A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomesDaniel 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... - Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequencesRobert T Deboy
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
J Bacteriol 188:2364-74. 2006.... - Complete genome sequence of the Q-fever pathogen Coxiella burnetiiRekha 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... - Metagenomic analysis of the human distal gut microbiomeSteven 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... - The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbiontsIan 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... - Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentusJonathan 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... 
Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental nicheJanaki 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...- The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacteriumJonathan 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... - 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 - 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 - Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiaeHerve 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... - Genomics for applied microbiologyWilliam C Nierman
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Adv Appl Microbiol 51:201-45. 2002 - Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injuryDerrick E Fouts
J Craig Venter Institute, Rockville, MD 20850, USA
J Transl Med 10:174. 2012.... - Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics communityKonstantinos 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... - Bacterial translocation and changes in the intestinal microbiome in mouse models of liver diseaseDerrick 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... - Champions of versatilityKaren E Nelson
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Trends Microbiol 12:111-2. 2004 - Genome sequence of the human malaria parasite Plasmodium falciparumMalcolm 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... - Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communitiesMatthew 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... - Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategyMalene 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... - Functional metagenomic profiling of nine biomesElizabeth A Dinsdale
Department of Biology, San Diego State University, San Diego, California 92182, USA
Nature 452:629-32. 2008.... - Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritimaCamilla L Nesbø
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
J Bacteriol 184:4475-88. 2002.... - Global features of the Pseudomonas putida KT2440 genome sequenceChristian Weinel
Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl Neuberg Str 1, D 30623 Hannover, Germany
Environ Microbiol 4:809-18. 2002.... - Whole-genome expression profiling of Thermotoga maritima in response to growth on sugars in a chemostatTu 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... - A novel family of carbohydrate-binding modules identified with Ruminococcus albus proteinsQi 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... - Diversity of the human intestinal microbial floraPaul 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... - Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridizationMeng 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... - Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridizationDionysios 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... - Ruminococcus albus 8 mutants defective in cellulose degradation are deficient in two processive endocellulases, Cel48A and Cel9B, both of which possess a novel modular architectureEstelle 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... - The future of microbial genomicsKaren E Nelson
Environ Microbiol 5:1223-5. 2003 - Molecular analysis of the bacterial microbiota in the human stomachElisabeth 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... - The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysisDiana 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... - Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtusMaria 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... - Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga speciesShannon 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... - Microbial environmental genomicsKaren E Nelson
Howard University, Washington, DC, USA
Microb Ecol 53:367-8. 2007