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Dr. Fouts is a Professor at the Rockville Campus of the JCVI. Dr. Fouts has extensive experience in viral and bacteriophage genomics, bacterial genomics, comparative genomics, and metagenomics of bacterial and viral communities. Since joining Dr. Karen Nelson's group at TIGR/JCVI in 2001, Dr. Fouts has led several microbial sequencing projects, including animal, plant and human pathogens. Many of these projects were among the first to compare multiple strains. In addition to leading projects, Dr. Fouts has developed various software tools, including applications to perform multi-genome comparisons and heuristic software (Phage Finder) to identify prophage regions in bacterial genomes. Dr. Fouts is currently leading the JCVI effort to sequence the human virome and reference viral and bacteriophage genomes under the Human Microbiome Project.

Dr. Fouts received his B.S. degree (1992) in Biology with honors from Indiana University, Bloomington, and his M.S. (1994) and Ph.D. (1997) degrees in Microbiology from the University of Illinois Urbana/Champaign Department of Microbiology. In 1997, he began postdoctoral work in Dr. Alan Collmer's lab at Cornell University.




CRACKLE: Carbapenems in Klebsiella pneumoniae and Other Enterobacteriaceae

Multidrug-Resistant Klebsiella pneumoniae from Pediatric Sepsis Patients in Nigeria



Synthetic Engineering of Bacteriophage for Treatment of Wound Infections

Leptospira Genomics and Human Health

Signature Infiltration and Maintenance on Plasmid Elements creating a Forensic Microbial System (SIMPLE-FMS)

Bacterial Translocation and Changes in the Intestinal Microbiome in Mouse Models of Liver Disease

Genomic Analysis of Multidrug Resistance in Esbl-Positive and Carbapenem-Resistant Bacterial Pathogens

Understanding the Influence of Genetic Variation and AMR in Enterobacter and Escherichia coli Bloodstream Infections (BSI) by Comparative Genomics and Association with Clinical Outcome Metadata

Genome Sequencing of Atypical Disease-associated and Emerging Infectious Disease Isolates of the Biodefense Category B Food and Water Borne Priority Pathogen Campylobacter Jejuni, and Related Species

Vibrio Genome Project

Genomic Sequencing of a Diversity of US Military Acinetobacter baumannii-calcoaceticus Complex Isolates

Viral Synthetic Genomics to Engineer Large dsDNA Viruses

Characterization and Expression of Drug Resistance Genes in Multidrug Resistance Organisms (MDROs) Originating from Combat Wound Infections

Asymptomatic Bacteriuria: Microbiome and Metaproteome

A Metagenomics Approach to Understanding the Relationship Between the Vaginal Microbiome, Bacterial Vaginosis, Vaginal Health and Preterm Birth

Enteric Dysbiosis Associated with a Mouse Model of Alcoholic Liver Disease

Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen

Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease.
Journal of hepatology. 2012-06-01; 56.6: 1283-92.
PMID: 22326468
Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice.
PLoS genetics. 2008-07-25; 4.7: e1000141.
PMID: 18654632
Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1.
Journal of bacteriology. 2007-01-01; 189.1: 52-64.
PMID: 17041058
Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry.
Journal of bacteriology. 2006-05-01; 188.9: 3402-8.
PMID: 16621835
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences.
Nucleic acids research. 2006-01-01; 34.3: 5839-51.
PMID: 17062630
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.
Journal of bacteriology. 2005-04-01; 187.7: 2426-38.
PMID: 15774886
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.
PLoS biology. 2005-01-01; 3.1: e15.
PMID: 15660156
A pseudomonas syringae pv. tomato DC3000 Hrp (Type III secretion) deletion mutant expressing the Hrp system of bean pathogen P. syringae pv. syringae 61 retains normal host specificity for tomato.
Molecular plant-microbe interactions : MPMI. 2003-01-01; 16.1: 43-52.
PMID: 12580281
Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor.
Proceedings of the National Academy of Sciences of the United States of America. 2002-02-19; 99.4: 2275-80.
PMID: 11854524
Translationally repressive RNA structures monitored in vivo using temperate DNA bacteriophages.
Gene. 1998-03-27; 210.1: 135-42.
PMID: 9524249
Functional recognition of fragmented operator sites by R17/MS2 coat protein, a translational repressor.
Nucleic acids research. 1997-11-15; 25.22: 4464-73.
PMID: 9358153
Site-specific phosphorylation of the human immunodeficiency virus type-1 Rev protein accelerates formation of an efficient RNA-binding conformation.
Biochemistry. 1997-10-28; 36.43: 13256-62.
PMID: 9341215
Improved method for selecting RNA-binding activities in vivo.
Nucleic acids research. 1996-04-15; 24.8: 1582-4.
PMID: 8628698