List of works by Karen E. Nelson

387 Restoration of Intestinal Metabolic Homeostasis Results in Eubiosis and Protects Mice From Alcoholic Liver Disease

scientific article published on 02 May 2014

A Metagenomic Interrogation of Primates

scientific article

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation.

scientific article

A catalog of reference genomes from the human microbiome

scientific article

A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes

scientific article published on 11 November 2005

A guild of forty-five CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes

scientific article published on 06 October 2005

A multi-omic systems-based approach reveals metabolic markers of bacterial vaginosis and insight into the disease

scientific article published in 2013

A new antibiotic selectively kills Gram-negative pathogens

scientific article published on 20 November 2019

A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus

scientific article published on February 2000

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome

scientific article

An Update on the Status of Current Research on the Mammalian Microbiome

scientific article (publication date: 2015)

An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome

scientific article published on 02 October 2013

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data

scientific article published on 10 January 2020

Antimicrobial resistance of the coral pathogen Vibrio coralliilyticus and Caribbean sister phylotypes isolated from a diseased octocoral

scientific article published on 23 March 2010

Applications of weighted association networks applied to compositional data in biology

scientific article published on 20 May 2020

Author Correction: A new antibiotic selectively kills Gram-negative pathogens

scientific article published on 01 April 2020

Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

scientific article published on 16 June 2020

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques

scientific article

Bacterial diversity in the oral cavity of 10 healthy individuals

scientific article

Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease

scientific article

Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen

scientific article

Champions of versatility

scientific article published on 01 March 2004

Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections

scientific article

Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities

scientific article

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance

scientific article published on 21 May 2020

Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences

scientific article

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

scientific article

Co-occurrence of Anaerobes in Human Chronic Wounds

scientific article published on 23 August 2018

Comparative analysis of the vaginal microbiome in health and disease

scientific article published on 19 September 2011

Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche.

scientific article

Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus

scientific article

Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential

scientific article

Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome

scientific article

Complete Genome Sequence of Neisseria meningitidis Serogroup B Strain MC58

scientific article

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

scientific article published in January 2004

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

scientific article

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

article by K. E. Nelson et al published July 2003 in Environmental Microbiology

Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae

scientific article

Complete genome sequence of Caulobacter crescentus

scientific article

Complete genome sequence of the Q-fever pathogen Coxiella burnetii

scientific article

Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83

scientific article

Comprehensive Metaproteomic Analyses of Urine in the Presence and Absence of Neutrophil-Associated Inflammation in the Urinary Tract

scientific article published on January 2017

Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma

scientific article published on 20 November 2020

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

scientific article

DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae

scientific article

Diagnosing inflammation and infection in the urinary system via proteomics.

scientific article

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy

scientific article

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes.

scientific article

Diversity of 16S rRNA genes within individual prokaryotic genomes.

scientific article

Diversity of cervicovaginal microbiota associated with female lower genital tract infections

scientific article published on 2 February 2011

Diversity of the human intestinal microbial flora

scientific article

Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces

scientific article published on January 2013

Draft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces

scientific article published on 6 February 2014

Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period

scientific article published on 16 May 2013

Draft genome sequence of Bacteroides vulgatus PC510, a strain isolated from human feces

scientific article published on 27 May 2011

Draft genome sequence of Turicibacter sanguinis PC909, isolated from human feces

scientific article published on 23 December 2010

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla).

scientific article

Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.

scientific article published on 4 November 2016

Enteric dysbiosis associated with a mouse model of alcoholic liver disease

scientific article

Environmental genome shotgun sequencing of the Sargasso Sea

scientific article (publication date: 2 April 2004)

Environmental microbial ecology in an "omics" era: summary report of MicroEnGen-II (Shanghai, June 12-15, 2006).

scientific article published in April 2007

Erratum: The complete genome sequence of the gastric pathogen Helicobacter pylori

scientific article published in Nature

Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

scientific article published in Nature

Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

scientific article

Evolution of catabolic pathways: Genomic insights into microbial s-triazine metabolism

scientific article

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

scientific article published on 11 July 2018

Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy

scientific article (publication date: October 2008)

Foregut Microbiome, Development of Esophageal Adenocarcinoma, Project

Foregut Microbiome, Development of Esophageal Adenocarcinoma, Project

article

Foregut microbiome in development of esophageal adenocarcinoma

Functional metagenomic profiling of nine biomes

scientific article (publication date: 3 April 2008)

Functional metagenomic profiling of nine biomes

scientific article published in Nature

Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtus.

scientific article

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus.

scientific article published on 16 October 2017

Gastro-intestinal and oral microbiome signatures associated with healthy aging

scientific article published on 16 October 2019

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.

scientific article

Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species

scientific article published on July 2005

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

scientific article

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease

scientific article published on 18 January 2018

Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes

scientific article

Genome Sequence of the Radioresistant Bacterium Deinococcus radiodurans R1

scientific article

Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments

scientific article

Genome of Thermotoga maritima MSB8.

scientific article published on January 2001

Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores

scientific article

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

scientific article

Genome sequence of the human malaria parasite Plasmodium falciparum

scientific article

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

scientific article published in August 2014

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)

scientific article

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

scientific article published on 9 February 2016

Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns

scientific article

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease

scientific article published on May 2017

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease

scientific article published on 01 September 2019

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology

scientific article published on May 2015

Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors

scientific article published on 25 April 2019

HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences

scientific article published on 13 October 2016

Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes

scientific article

Heritability of Hepatic Fibrosis and Steatosis Based on a Prospective Twin Study

scientific article

High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae

scientific article

Host Genetic Control of the Oral Microbiome in Health and Disease

scientific article

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta).

scientific article

Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets

scientific article

Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus.

scientific article published on 5 September 2008

Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants

scientific article published on 23 July 2019

Impact of stress on the gut microbiome of free-ranging western lowland gorillas

scientific article

Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus

scientific article published on 13 June 2008

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

scientific article

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.

scientific article

Integrating the microbiome as a resource in the forensics toolkit

scientific article published on 27 June 2017

Interplay between the human gut microbiome and host metabolism

scientific article published on 03 October 2019

It's a cold world out there (but the prospects are hot).

scientific article

Library preparation methodology can influence genomic and functional predictions in human microbiome research

scientific article published on 28 October 2015

Longitudinal Study of Oral Microbiome Variation in Twins

scientific article published on 14 May 2020

Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species

scientific article published in January 2005

Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling

scientific article published on 21 February 2020

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism

scientific article published on 29 May 2015

Metagenomic analysis of the human distal gut microbiome

scientific article

Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime

scientific article published on 07 January 2021

Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species

scientific article

Microbial diversity in individuals and their household contacts following typical antibiotic courses.

scientific article published on 30 July 2016

Microbial environmental genomics

scientific article published on 01 April 2007

Microbial fuel cells and microbial ecology: applications in ruminant health and production research

scientific article

Microbial metagenome of urinary tract infection.

scientific article

Microbial metagenomics

scientific article

Microbiome analysis of stool samples from African Americans with colon polyps.

scientific article

Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

scientific article published on 21 May 2020

Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in analog hosts

article

Microbiome in human health and disease.

scientific article published in January 2013

Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications

Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery.

scientific article published on 14 September 2015

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Molecular analysis of the bacterial microbiota in the human stomach

scientific article

Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis ⬇️

scientific article published on September 7, 2010

Nasopharyngeal Lactobacillus is Associated with Childhood Wheezing Illnesses Following Acute Respiratory Syncytial Virus Infection in Infancy

scientific article published on 9 January 2018

Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk

scientific article published on May 2016

Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen

scientific article (publication date: 2012)

Novel diversity of bacterial communities associated with bottlenose dolphin upper respiratory tracts

scientific article

Novel molecular features of the fibrolytic intestinal bacterium Fibrobacter intestinalis not shared with Fibrobacter succinogenes as determined by suppressive subtractive hybridization

scientific article

OMeta: an ontology-based, data-driven metadata tracking system

scientific article published on 07 January 2019

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

scientific article

Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma

scientific article published on 06 November 2020

Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

scientific article

Papio spp. Colon microbiome and its link to obesity in pregnancy

scientific article published on 24 July 2018

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate

scientific article published on 26 January 2017

Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy

scientific article published on 21 November 2019

Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored niche

scientific article

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species

scientific article published on 24 November 2015

Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice

scientific article

Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements

scientific article

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints

scientific article published on 31 July 2019

Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy

scientific article

Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach

scientific article published on 29 March 2021

Predictive signatures of 19 antibiotics-induced Escherichia coli proteomes

scientific article published on 16 July 2020

Pregnancy's stronghold on the vaginal microbiome

scientific article

Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013.

scientific article published on 30 July 2013

Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort

scientific article published on 24 September 2020

Publisher Correction: Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus

scientific article published on 12 December 2017

Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates

scientific article

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.

scientific article

Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes

scientific article published on 22 July 2015

Reducing the Bottleneck in Discovery of Novel Antibiotics.

scientific article published on 28 November 2016

Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system

scientific article

Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas.

scientific article

Robust computational analysis of rRNA hypervariable tag datasets

scientific article (publication date: 31 December 2010)

Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1.

scientific article

Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery

scientific article published on 21 March 2019

Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities

scientific article

Shared genetic effects between hepatic steatosis and fibrosis: A prospective twin study ⬇️

scientific article published on 17 June 2016

Similar Neutrophil-Driven Inflammatory and Antibacterial Responses in Elderly Patients with Symptomatic and Asymptomatic Bacteriuria

scientific article

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality

scientific article published on 5 December 2017

Spatial and Environmental Variation of the Human Hair Microbiota.

scientific article published on 13 June 2018

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection

scientific article published on 22 August 2015

Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization

scientific article published in April 2004

Structural flexibility in the Burkholderia mallei genome

scientific article

Sugar metabolism by Brucellae

scientific article

Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice

scientific article

Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease

article

Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.

scientific article published on 28 August 2015

Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.

scientific article published on February 2016

The Airplane Cabin Microbiome

scientific article published on 06 June 2018

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

scientific article

The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology

scientific article

The Human Microbiome Project: a community resource for the healthy human microbiome

scientific article

The Human Microbiome and Cancer

scientific article published on 17 January 2017

The Montastraea faveolata microbiome: ecological and temporal influences on a Caribbean reef-building coral in decline

scientific article

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health

scientific article published on 14 September 2016

The Threat of Antimicrobial Resistance on the Human Microbiome.

scientific article published on 11 May 2017

The blood DNA virome in 8,000 humans

scientific article

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

scientific article

The complete genome sequence of the gastric pathogen Helicobacter pylori

scientific article

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

scientific article

The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea

scientific article

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

scientific article

The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra).

scientific article published on 19 December 2014

The minimum information about a genome sequence (MIGS) specification

scientific article

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

scientific article

The restoration of the vaginal microbiota after treatment for bacterial vaginosis with metronidazole or probiotics.

scientific article published on 19 December 2012

The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra).

scientific article

The vaginal microbiome in health and disease

scientific article

The value of complete microbial genome sequencing (you get what you pay for).

scientific article

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils

scientific article

Towards an Evolutionary Model of Animal-Associated Microbiomes

article

Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function

scientific article published on 7 July 2017

Urine sample preparation in 96-well filter plates for quantitative clinical proteomics.

scientific article

Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities

scientific article

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies

scientific article

Variable responses of human and non-human primate gut microbiomes to a Western diet

scientific article published on 16 November 2015

Vertical transmission of gut microbiome and antimicrobial resistance genes in infants exposed to antibiotics at birth

scientific article published on 02 April 2020

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

scientific article published on 18 February 2016

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

scientific article

Whole-genome expression profiling of Thermotoga maritima in response to growth on sugars in a chemostat

scientific article

Xylitol and sorbitol effects on the microbiome of saliva and plaque

scientific article published on 23 October 2018

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