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- Bladder (2)
- Female urinary microbiota (2)
- Microbiome (2)
- Alpha satellite; chromosome 21; chromosome evolution; centromere; acrocentric chromosome (1)
- Bacteriophage; metagenomics; metaviromics; prophage; whole genome sequencing; virus. (1)
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- Bacteriophages (1)
- CRC TUmors (1)
- Chromosome mapping (1)
- Colorectal Cancer (1)
- Comparative genomics (1)
- Draft genome sequence (1)
- Enterobacteriaceae (1)
- Escherichia coli (1)
- Gene Expression Traits (1)
- Genetic Mutations (1)
- Genome sequence (1)
- Genomic DNA (1)
- Genomic databases (1)
- Heritability (1)
- Host genetics (1)
- Human Tissues (1)
- Lower urinary tract symptoms (1)
- Phylogenetic analysis (1)
- Sequence databases (1)
- Sparse Architecture (1)
- UPEC (1)
- Urinary isolate (1)
- Urinary tract infection (1)
- Viral genomics (1)
Articles 1 - 8 of 8
Full-Text Articles in Life Sciences
Discrete Mutations In Colorectal Cancer Correlate With Defined Microbial Communities In The Tumor Microenvironment, Michael B. Burns, Emmanuel Montassier, Juan Abrahante, Timothy K. Starr, Dan Knights, Ran Blekhman
Discrete Mutations In Colorectal Cancer Correlate With Defined Microbial Communities In The Tumor Microenvironment, Michael B. Burns, Emmanuel Montassier, Juan Abrahante, Timothy K. Starr, Dan Knights, Ran Blekhman
Biology: Faculty Publications and Other Works
Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetics. However, we do not know whether genetic mutations in CRC tumors interact with the structure and composition of the microbial communities surrounding the tumors, and if so, whether changes in the microbiome can be used as a predictor for tumor mutational status. Here, we characterized the association between CRC tumor mutational landscape and its proximal microbial communities by performing whole exome sequencing and microbiome profiling in tumors and normal colorectal tissue samples from the same patient. We find a significant association between …
Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti
Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti
Bioinformatics Faculty Publications
Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates …
Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, Alan J. Wolfe
Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, Alan J. Wolfe
Bioinformatics Faculty Publications
A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N50 of 109,831 bp.
Survey Of The Heritability And Sparse Architecture Of Gene Expression Traits Across Human Tissues., Heather E. Wheeler, Kaanan P. Shah, Jonathon Brenner, Tzintzuni Garcia, Keston Aquino-Michaels, Gtex-Consortium, Nancy J. Cox, Dan L. Nicolae, Hae Kyung Im
Survey Of The Heritability And Sparse Architecture Of Gene Expression Traits Across Human Tissues., Heather E. Wheeler, Kaanan P. Shah, Jonathon Brenner, Tzintzuni Garcia, Keston Aquino-Michaels, Gtex-Consortium, Nancy J. Cox, Dan L. Nicolae, Hae Kyung Im
Bioinformatics Faculty Publications
Understanding the genetic architecture of gene expression traits is key to elucidating the underlying mechanisms of complex traits. Here, for the first time, we perform a systematic survey of the heritability and the distribution of effect sizes across all representative tissues in the human body. We find that local h2 can be relatively well characterized with 59% of expressed genes showing significant h2 (FDR < 0.1) in the DGN whole blood cohort. However, current sample sizes (n ≤ 922) do not allow us to compute distal h2. Bayesian Sparse Linear Mixed Model (BSLMM) analysis provides strong evidence that the genetic contribution to local expression traits is dominated by …
Genome Sequences And Annotation Of Two Urinary Isolates Of E.Coli, Travis Kyle Price, Arya Mehtash, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe
Genome Sequences And Annotation Of Two Urinary Isolates Of E.Coli, Travis Kyle Price, Arya Mehtash, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe
Bioinformatics Faculty Publications
The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did …
Phagephisher: A Pipeline For The Discovery Of Covert Viral Sequences In Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti
Phagephisher: A Pipeline For The Discovery Of Covert Viral Sequences In Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti
Bioinformatics Faculty Publications
Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with …
Draft Genome For A Urinary Isolate Of Lactobacillus Crispatus, Travis Kyle Price, Majed Shaheen, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe
Draft Genome For A Urinary Isolate Of Lactobacillus Crispatus, Travis Kyle Price, Majed Shaheen, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe
Bioinformatics Faculty Publications
While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its role in urinary health remains unclear. As part of an on-going attempt to characterize the female urinary microbiota, we report the genome sequence of an L. crispatus strain isolated from a woman displaying no lower urinary tract symptoms.
Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering
Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering
Bioinformatics Faculty Publications
Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the …