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Hongyu Gao
Washington University in St. Louis
10Publications
9H-index
6,313Citations
Publications 10
Newest
#2Patrick G. HoganH-Index: 10
Last.Stephanie A. FritzH-Index: 15
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Historically, a number of typing methods have been evaluated for Staphylococcus aureus strain characterization. The emergence of contemporary strains of community-associated S. aureus, and the ensuing epidemic with a predominant strain type (USA300), necessitates re-evaluation of the discriminatory power of these typing methods for discerning molecular epidemiology and transmission dynamics, essential to investigations of hospital and community outbreaks. We compared the discriminatory index of ...
15 CitationsSource
#1George TurabelidzeH-Index: 1
#2Steven J. Lawrence (WashU: Washington University in St. Louis)H-Index: 15
Last.Phillip I. Tarr (WashU: Washington University in St. Louis)H-Index: 65
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The current pathogen-typing methods have suboptimal sensitivities and specificities. DNA sequencing offers an opportunity to type pathogens with greater degrees of discrimination using single nucleotide polymorphisms (SNPs) than with pulsed-field gel electrophoresis (PFGE) and other methodologies. In a recent cluster of Escherichia coli O157:H7 infections attributed to salad bar exposures and romaine lettuce, a subset of cases denied exposure to either source, although PFGE and multiple-locus va...
27 CitationsSource
#1Truc T. TranH-Index: 17
#2Diana Panesso (El Bosque University)H-Index: 24
Last.Cesar A. Arias (El Bosque University)H-Index: 40
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Development of daptomycin (DAP) resistance in Enterococcus faecalis has recently been associated with mutations in genes encoding proteins with two main functions: (i) control of the cell envelope stress response to antibiotics and antimicrobial peptides (LiaFSR system) and (ii) cell membrane phospholipid metabolism (glycerophosphoryl diester phosphodiesterase and cardiolipin synthase [cls]). However, the genetic bases for DAP resistance in Enterococcus faecium are unclear. We performed whole-ge...
63 CitationsSource
#1Yanhua Zhou (WashU: Washington University in St. Louis)H-Index: 35
#2Hongyu Gao (WashU: Washington University in St. Louis)H-Index: 9
Last.George M. Weinstock (WashU: Washington University in St. Louis)H-Index: 99
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Background Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans.
199 CitationsSource
#1Barbara A. Methé (JCVI: J. Craig Venter Institute)H-Index: 7
#2Karen E. Nelson (JCVI: J. Craig Venter Institute)H-Index: 76
Last.Owen White (UMB: University of Maryland, Baltimore)H-Index: 88
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The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources.
1,252 CitationsSource
#1Curtis Huttenhower (Broad Institute)H-Index: 74
#2Dirk Gevers (Broad Institute)H-Index: 68
Last.Owen White (UMB: University of Maryland, Baltimore)H-Index: 88
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The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.
4,441 CitationsSource
#1Doyle V. Ward (Broad Institute)H-Index: 29
#2Dirk Gevers (Broad Institute)H-Index: 68
Last.Bruce W. Birren (Broad Institute)H-Index: 95
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200 CitationsSource
#1Kristine M. Wylie (WashU: Washington University in St. Louis)H-Index: 25
#2Rebecca M. Truty (UCSF: University of California, San Francisco)H-Index: 7
Last.Katherine S. Pollard (UCSF: University of California, San Francisco)H-Index: 54
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The human gut harbors thousands of bacterial taxa. A profusion of metagenomic sequence data has been generated from human stool samples in the last few years, raising the question of whether more taxa remain to be identified. We assessed metagenomic data generated by the Human Microbiome Project Consortium to determine if novel taxa remain to be discovered in stool samples from healthy individuals. To do this, we established a rigorous bioinformatics pipeline that uses sequence data from multipl...
63 CitationsSource
#1Curtis HuttenhowerH-Index: 74
#2Dirk GeversH-Index: 68
Last.Owen WhiteH-Index: 88
view all 248 authors...
8 Citations
#1Guohui Yao (WashU: Washington University in St. Louis)H-Index: 2
#2Liang Ye (WashU: Washington University in St. Louis)H-Index: 6
Last.George M. Weinstock (WashU: Washington University in St. Louis)H-Index: 99
view all 6 authors...
Motivation: No individual assembly algorithm addresses all the known limitations of assembling short-length sequences. Overall reduced sequence contig length is the major problem that challenges the usage of these assemblies. We describe an algorithm to take advantages of different assembly algorithms or sequencing platforms to improve the quality of next-generation sequence (NGS) assemblies. Results: The algorithm is implemented as a graph accordance assembly (GAA) program. The algorithm constr...
45 CitationsSource
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