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GSCID White Papers

Since these sequencing projects are considered community resources and the data sets are valuable research resources to the community, centers anticipate making the white papers available to the scientific community through their websites. If necessary, we will work with white paper authors to make suitable versions of the white papers available through the centers’ websites. White papers will not undergo alteration if sequencing or analysis strategies change during the course of the project.

Sequence analysis of the genus Acinetobacter

Bacillus cereus
The pathogenomics and evolution of anthrax-like Bacillus cereus isolates and plasmid

Bartonella sp.
Characterization of pathogenicity and ecology of Bartonella species through whole genome sequence analysis

Brucella spp.
A continuation of the comparative genomics of the zoonotic genus Brucella and development of diagnostic resources for epidemiological tracking of potential bioweapons agents

Candida albicans
Using next generation sequencing to define strain variation and virulence in clinical isolates of Candida albicans

Carbapenem Resistant bacteria
Whole genome sequence analysis of carbapenem-resistant Enterobacteriaceae isolated from 3 Boston area medical institutions

Cryptococcus neoformans
RNASeq analysis to study determinants of poor outcome in cryptococcal disease

Dengue Surveillance 
Surveillance of dengue virus in Florida mosquitoes

Dengue Virus
Sequence analysis of mouse-passaged dengue virus strains that induce a non-paralytic, lethal disease in mouse

Dengue Virus
Comparative genomics of dengue virus: genome population structure, transmission, and understanding differential inflammatory disease responses

Diarrheal Dysbiosis and Treatment
Understanding the pathogenesis of diarrheal illness

Dimorphic Fungi
Comparative genomics of Coccidioides and other pathogenic dimorphic fungi

Scope of the diversity of emerging hospital pathogens Enterococcus faecalis and Enterococcus faecium

Escherichia coli UTI Bacteremia
E. coli as a human pathogen: Uncomplicated urinary tract infection (UTI) and UTI-induced bacteremia

Escherichia coli UTI Defensins
E. coli urinary tract infection: Importance of antimicrobial peptides and bacterial factors of the rectal flora and UTI pathogenic E. coli

Francisella tularensis
Genome sequencing of Francisella tularensis subsp. tularensis Schu S4 isolates

Infant gut Metagenomics
Assessing the impact of antibiotic administration on the establishment and development of infant gut flora

Influenza virus and SARS-CoV
Examination of differential occupancy in early innate immunity in an infection time course

Ixodes scapularis
Genome analysis of major tick and mite vectors of human pathogens

Microsporidia spp.
Comparative genomics of the phylum defining shared and specific genes in a phylum of emerging human pathogens

High Throughput Genomic Microbial Surveillance.

Mycobacterium tuberulosis - CDRC
To facilitate development of new diagnostic and therapeutic approaches to tuberculosis

Mycobacterium tuberulosis - Belarussia
Comparative sequence analysis of M. tuberculosis isolates from patients with multi and extensively drug resistant tuberculosis in Belarussia

Mycobacterium tuberculosis - K-RITH, South Africa
Characterization of M. tuberculosis resistance through whole genome sequence analysis to support diagnostic development, drug discovery, and molecular epidemiology 

Mycobacterium tuberculosis - Mali
A proposal to compare the genomes of MDR and susceptible M. africanum and M. tuberculosis

Mycobacterium tuberculosis - MRC, South Africa
PETTS (Preserving Effective TB Treatment Study) samples from the South African Medical Research Council for sequencing

Mycobacterium tuberculosis - Taiwan
Understanding resistance to fluoroquinolones in the treatment of MDR TB

Mustela putorius furo (Ferret)
Genomic and EST sequencing of the ferret

Persistence Genes
Bacterial persistence in E.coli, M. tuberculosis, P. aeruginosa and C. albicans

Plasmodium spp. Comparative Genomics
Comprehensive sequencing of malarial parasites: Plasmodium species

Plasmodium falciparum & RTS,S Vaccine
RTS,S Phase III malaria vaccine trial genotyping

Plasmodium vivax
Sequencing of Plasmodium vivax clinical malaria samples using hybrid selection

Pseudomonas aeruginosa
Whole genome sequence analysis of Pseudomonas aeruginosa clinical isolates

Respiratory Syncytial Virus (RSV)
Respiratory syncytial virus (RSV) intra-host sequence variation over the course of infection in immune competent and immunocompromised hosts

TraCS for Mycobacterium tuberculosis
Identification of novel drug target through genome-wide mapping of metabolic networks in Mycobacterium tuberculosis

Vibrio cholerea Transcriptome
Using next-generation sequencing technology to define the Vibrio cholerae transcriptome

Comparative genome analysis of vancomycin resistant Staphylococcus aureus and vancomycin resistant enterococci