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Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

Genome biology, 2009-01, Vol.10 (9), p.R91-R91

2009

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cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets

BMC bioinformatics, 2021-02, Vol.22 (1), p.70-70, Article 70

2021

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Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

Proceedings of the National Academy of Sciences - PNAS, 2017-09, Vol.114 (39), p.10467-10472

2017

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Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing

Science translational medicine, 2012-08, Vol.4 (148), p.148ra116

2012

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Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with UTIs

eLife, 2019-10, Vol.8

2019

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Application of Combined Genomic and Transfer Analyses to Identify Factors Mediating Regional Spread of Antibiotic-resistant Bacterial Lineages

Clinical infectious diseases, 2020-12, Vol.71 (10), p.e642-e649

2020

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Genomic epidemiology of multidrug‐resistant Gram‐negative organisms

Annals of the New York Academy of Sciences, 2019-01, Vol.1435 (1), p.39-56

2019

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Epistatic interaction maps relative to multiple metabolic phenotypes

PLoS genetics, 2011-02, Vol.7 (2), p.e1001294-e1001294

2011

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Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

Science translational medicine, 2014-09, Vol.6 (254), p.254ra126

2014

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Gut Microbiota Features on Nursing Home Admission Are Associated With Subsequent Acquisition of Antibiotic-resistant Organism Colonization

Clinical infectious diseases, 2020-12, Vol.71 (12), p.3244-3247

2020

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Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant Klebsiella pneumoniae in a regional outbreak

Science translational medicine, 2017-11, Vol.9 (417)

2017

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Whole Genome Sequencing—Implications for Infection Prevention and Outbreak Investigations

Current Infectious Disease Reports, 2017-04, Vol.19 (4), p.15-15, Article 15

2017

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MRSA Transmission in Intensive Care Units: Genomic Analysis of Patients, Their Environments, and Healthcare Workers

Clinical infectious diseases, 2021-06, Vol.72 (11), p.1879-1887

2021

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Regional Spread of blaNDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities

Clinical infectious diseases, 2021-10, Vol.73 (8), p.1431-1439

2021

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Hogwash: three methods for genome-wide association studies in bacteria

Microbial genomics, 2020-11, Vol.6 (11)

2020

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Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection

Nature communications, 2022-08, Vol.13 (1), p.4459-4459, Article 4459

2022

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Genomic Epidemiology Suggests Community Origins of Healthcare-Associated USA300 Methicillin-Resistant Staphylococcus aureus

The Journal of infectious diseases, 2022-08, Vol.226 (1), p.157-166

2022

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Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

Nature microbiology, 2020-09, Vol.5 (9), p.1170

2020

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Contamination of Hospital Plumbing: A Source or a Sink for Antibiotic-Resistant Organisms?

JAMA network open, 2019-02, Vol.2 (2), p.e187660-e187660

Snitkin, Evan S

2019

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Genomic and Epidemiological Evidence for Community Origins of Hospital-Onset Methicillin-Resistant Staphylococcus aureus Bloodstream Infections

The Journal of infectious diseases, 2017-06, Vol.215 (11), p.1640-1647

2017

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Ferric Citrate Uptake Is a Virulence Factor in Uropathogenic Escherichia coli

mBio, 2022-06, Vol.13 (3), p.e0103522-e0103522

2022

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Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit

Nature medicine, 2023-10, Vol.29 (10), p.2526-2534

2023

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Rapid Growth of Uropathogenic Escherichia coli during Human Urinary Tract Infection

mBio, 2018-03, Vol.9 (2)

2018

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Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota

eLife, 2018-10, Vol.7

2018

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Genomic Epidemiology of MRSA During Incarceration at a Large Inner-City Jail

Clinical infectious diseases, 2021-12, Vol.73 (11), p.e3708-e3717

2021

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Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing

Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with UTIs

Application of Combined Genomic and Transfer Analyses to Identify Factors Mediating Regional Spread of Antibiotic-resistant Bacterial Lineages

Genomic epidemiology of multidrug‐resistant Gram‐negative organisms

Epistatic interaction maps relative to multiple metabolic phenotypes

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

Gut Microbiota Features on Nursing Home Admission Are Associated With Subsequent Acquisition of Antibiotic-resistant Organism Colonization

Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant Klebsiella pneumoniae in a regional outbreak

Whole Genome Sequencing—Implications for Infection Prevention and Outbreak Investigations

MRSA Transmission in Intensive Care Units: Genomic Analysis of Patients, Their Environments, and Healthcare Workers

Regional Spread of blaNDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities

Hogwash: three methods for genome-wide association studies in bacteria

Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection

Genomic Epidemiology Suggests Community Origins of Healthcare-Associated USA300 Methicillin-Resistant Staphylococcus aureus

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

Contamination of Hospital Plumbing: A Source or a Sink for Antibiotic-Resistant Organisms?

Genomic and Epidemiological Evidence for Community Origins of Hospital-Onset Methicillin-Resistant Staphylococcus aureus Bloodstream Infections

Ferric Citrate Uptake Is a Virulence Factor in Uropathogenic Escherichia coli

Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit

Rapid Growth of Uropathogenic Escherichia coli during Human Urinary Tract Infection

Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota

Genomic Epidemiology of MRSA During Incarceration at a Large Inner-City Jail

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