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3,685 full-text articles. Page 6 of 143.

Draft Genome Sequence Of Streptococcus Anginosus Umb0839, Isolated From The Female Urinary Tract, Thomas Scott, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Streptococcus Anginosus Umb0839, Isolated From The Female Urinary Tract, Thomas Scott, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Here, we present the draft genome sequence of Streptococcus anginosus UMB0839, isolated from the female urinary tract. The total size of the genome is 2,104,786 bp assembled into 42 contigs with a GC content of 38.8% and 284× genome coverage.


Machine Learning With Digital Signal Processing For Rapid And Accurate Alignment-Free Genome Analysis: From Methodological Design To A Covid-19 Case Study, Gurjit Singh Randhawa 2020 The University of Western Ontario

Machine Learning With Digital Signal Processing For Rapid And Accurate Alignment-Free Genome Analysis: From Methodological Design To A Covid-19 Case Study, Gurjit Singh Randhawa

Electronic Thesis and Dissertation Repository

In the field of bioinformatics, taxonomic classification is the scientific practice of identifying, naming, and grouping of organisms based on their similarities and differences. The problem of taxonomic classification is of immense importance considering that nearly 86% of existing species on Earth and 91% of marine species remain unclassified. Due to the magnitude of the datasets, the need exists for an approach and software tool that is scalable enough to handle large datasets and can be used for rapid sequence comparison and analysis. We propose ML-DSP, a stand-alone alignment-free software tool that uses Machine Learning and Digital Signal Processing to ...


Dynamics Of The 4d Genome During In Vivo Lineage Specification And Differentiation, A. Marieke Oudelaar, Daniel Hidalgo, Merav Socolovsky, Douglas R. Higgs, Jim R. Hughes 2020 University of Oxford

Dynamics Of The 4d Genome During In Vivo Lineage Specification And Differentiation, A. Marieke Oudelaar, Daniel Hidalgo, Merav Socolovsky, Douglas R. Higgs, Jim R. Hughes

Open Access Publications by UMMS Authors

Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of ...


Draft Genome Sequence Of Corynebacterium Aurimucosum Umb7769, Isolated From The Female Urinary Tract, Samantha Eskandar, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Corynebacterium Aurimucosum Umb7769, Isolated From The Female Urinary Tract, Samantha Eskandar, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Here, we present the draft genome sequence of Corynebacterium aurimucosum UMB7769, isolated from the female urinary tract. The size of the genome is 2,731,818 bp, assembled in 50 contigs, with an observed GC content of 60.9% and an N50 score of 129,518 bp. Annotation revealed 31 antibiotic resistance genes.


Draft Genome Sequence Of Enterococcus Faecalis Umb1309, Isolated From Catheterized Urine, Adam Schwartz, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Enterococcus Faecalis Umb1309, Isolated From Catheterized Urine, Adam Schwartz, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

A strain of Enterococcus faecalis was isolated from catheterized urine. Here, we present the draft genome sequence of this isolate, E. faecalis UMB1309. Analysis of the genome revealed multiple genes coding for virulence factors, as well as genes associated with antibiotic resistance.


Draft Genome Sequence Of Enterococcus Faecalis Umb7780, Isolated From The Female Urinary Tract, Martin Kalski, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Enterococcus Faecalis Umb7780, Isolated From The Female Urinary Tract, Martin Kalski, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Here, we present the draft genome sequence of Enterococcus faecalis UMB7780, isolated from the female urinary tract. The genome size is 3,005,901 bp, with a GC content of 37.36%, genome coverage of 179×, and an N50 score of 169,627 bp. Genome analysis identified evidence of antibiotic resistance, as well as intact prophages.


Three Draft Genome Sequences Of Staphylococcus Species Isolated From The Urine Of Healthy Bovine Heifers (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, Catherine Putoni 2020 Loyola University Chicago

Three Draft Genome Sequences Of Staphylococcus Species Isolated From The Urine Of Healthy Bovine Heifers (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, Catherine Putoni

Bioinformatics Faculty Publications

Members of the Staphylococcus genus are known pathogens causing mastitis in dairy cows, which results in major economic losses. Here, we present Staphylococcus epidermidis UFMG-H7, Staphylococcus hominis UFMG-H7B, and Staphylococcus sciuri UFMG-H6, isolated from the urine of healthy purebred Gyr heifers.


Draft Genome Sequence Of Enterobacter Asburiae Ufmg-H9, Isolated From Urine From A Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Enterobacter Asburiae Ufmg-H9, Isolated From Urine From A Healthy Bovine Heifer (Gyr Breed), Silvia Giannattasio-Ferraz, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Enterobacter asburiae is part of the Enterobacter cloacae complex, related to nosocomial opportunistic infections in humans. Here, we report the draft genome of E. asburiae strain UFMG-H9, an isolate from urine from a healthy Gyr heifer.


Draft Genome Sequence Of Lactobacillus Jensenii Umb0836, Isolated From The Female Bladder, Isaac Rivera, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Lactobacillus Jensenii Umb0836, Isolated From The Female Bladder, Isaac Rivera, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Lactobacillus jensenii is a frequent member of both the vaginal and urinary microbiota. Here, we present the draft genome sequence for L. jensenii UMB0836, isolated from catheterized urine obtained from a pregnant female. The genome is 1,648,234 bp long, assembled in 40 contigs.


Draft Genome Sequence Of Lactobacillus Mulieris Umb7784, Isolated From The Female Urinary Tract, Oleksandra Tsibere, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Lactobacillus Mulieris Umb7784, Isolated From The Female Urinary Tract, Oleksandra Tsibere, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

We sequenced the genome of Lactobacillus mulieris UMB7784, isolated from the urinary tract. With a genome size of 1,695,489 bp and a GC content of 34.2%, the draft genome sequence presented here expands our understanding of lactobacilli in the female bladder.


Draft Genome Sequence Of Proteus Mirabilis Strain Umb0038, Isolated From The Female Bladder, Noreen Gallian, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Proteus Mirabilis Strain Umb0038, Isolated From The Female Bladder, Noreen Gallian, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Proteus mirabilis is a Gram-negative motile and rod-shaped bacterium that is a common pathogen of the urinary tract. Here, we report the draft genome sequence of P. mirabilis UMB0038, which was isolated from a woman without lower urinary tract symptoms.


Draft Genome Sequence Of Streptococcus Anginosus Umb7768, Isolated From A Woman With Recurrent Uti Symptoms, Sarah Miller, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Streptococcus Anginosus Umb7768, Isolated From A Woman With Recurrent Uti Symptoms, Sarah Miller, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Streptococcus anginosus recently was implicated as a pathogen involved in urinary tract infections. A strain of S. anginosus was isolated from the female urogenital tract. Here, we present the draft genome sequence of S. anginosus strain UMB7768.


Draft Genome Sequences Of Three Enterococcus Casseliflavus Strains Isolated From The Urine Of Healthy Bovine Heifers (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequences Of Three Enterococcus Casseliflavus Strains Isolated From The Urine Of Healthy Bovine Heifers (Gyr Breed), Silvia Giannattasio-Ferraz, Laura Maskeri, André P. Oliveira, Edel F. Barbosa-Stancioli, Catherine Putoni

Bioinformatics Faculty Publications

Enterococcus casseliflavus is a commensal bacterium present in the intestinal microbiota of different animals. Previous studies have found that strains isolated from livestock are often resistant to many different antibiotics. Here, we present three E. casseliflavus strains, UFMG-H7, UFMG-H8, and UFMG-H9, isolated from urine collected from healthy dairy heifers in Brazil.


A Cas9 With Pam Recognition For Adenine Dinucleotides, Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo 2020 Massachusetts Institute of Technology

A Cas9 With Pam Recognition For Adenine Dinucleotides, Pranam Chatterjee, Jooyoung Lee, Lisa Nip, Sabrina R. T. Koseki, Emma Tysinger, Erik J. Sontheimer, Joseph M. Jacobson, Noah Jakimo

Open Access Publications by UMMS Authors

CRISPR-associated (Cas) DNA-endonucleases are remarkably effective tools for genome engineering, but have limited target ranges due to their protospacer adjacent motif (PAM) requirements. We demonstrate a critical expansion of the targetable sequence space for a type II-A CRISPR-associated enzyme through identification of the natural 5[Formula: see text]-NAAN-3[Formula: see text] PAM preference of Streptococcus macacae Cas9 (SmacCas9). To achieve efficient editing activity, we graft the PAM-interacting domain of SmacCas9 to its well-established ortholog from Streptococcus pyogenes (SpyCas9), and further engineer an increased efficiency variant (iSpyMac) for robust genome editing activity. We establish that our hybrids can target all ...


Multi-Omics Integration For Gene Fusion Discovery And Somatic Mutation Haplotyping In Cancer, Steven Mason Foltz 2020 Washington University in St. Louis

Multi-Omics Integration For Gene Fusion Discovery And Somatic Mutation Haplotyping In Cancer, Steven Mason Foltz

Arts & Sciences Electronic Theses and Dissertations

Cancer is a disease caused by changes to the genome and dysregulation of gene expression. Among many types of mutations, including point mutations, small insertions and deletions, large scale structural variants, and copy number changes, gene fusions are another category of genomic and transcriptomic alteration that can lead to cancer and which can serve as therapeutic targets. We studied gene fusion events using data from The Cancer Genome Atlas, including over 9,000 patients from 33 cancer types, finding patterns of gene fusion events and dysregulation of gene expression within and across cancer types. With data from the CoMMpass study ...


Lymphatic Filariasis: Host And Parasite Factors And The Pathogenesis Of Systemic Adverse Events Following Treatment, Britt Juul Andersen 2020 Washington University in St. Louis

Lymphatic Filariasis: Host And Parasite Factors And The Pathogenesis Of Systemic Adverse Events Following Treatment, Britt Juul Andersen

Arts & Sciences Electronic Theses and Dissertations

Lymphatic filariasis (LF) is a neglected tropical disease caused by the nematode parasites Wuchereria bancrofti, Brugia malayi and B. timori. The primary tool used by the Global Program to Eliminate LF is mass drug administration (MDA), and some 500 million people take the medications each year. Mild to moderate adverse events (AEs) are common after LF treatment, and these pose a major challenge for the LF elimination program. To better understand the pathogenesis of AEs, we studied patients from LF treatment trials in Côte d’Ivoire and Papua New Guinea, where plasma and leucocytes were collected pre and post-treatment and ...


Draft Genome Sequence Of Antibiotic-Resistant Enterococcus Faecalis Strain Umb0843, Isolated From The Female Urinary Tract, Natalia Purta, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Antibiotic-Resistant Enterococcus Faecalis Strain Umb0843, Isolated From The Female Urinary Tract, Natalia Purta, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Here, we introduce the 2.8-Mbp draft genome of Enterococcus faecalis strain UMB0843, isolated from the female urinary tract. E. faecalis is a leading cause of nosocomial infections, and many strains are often resistant to multiple antibiotics. We focus our genome analysis on the multiple genes involved in antibiotic resistance in this strain.


Draft Genome Sequence Of Staphylococcus Epidermidis Umb7765, Isolated From The Urobiome Of A Woman With Recurrent Urinary Tract Infection, Lucy Kemper, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Staphylococcus Epidermidis Umb7765, Isolated From The Urobiome Of A Woman With Recurrent Urinary Tract Infection, Lucy Kemper, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Staphylococcus epidermidis is a Gram-positive bacterium that is resistant to many antibiotics. Here, we present the 2.5-Mb draft genome of S. epidermidis UMB7765, isolated from a voided urine sample from a female with recurrent urinary tract infections.


Draft Genome Sequence Of Klebsiella Pneumoniae Umb8492, Isolated From The Female Urinary Tract, Suma Gondi, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Klebsiella Pneumoniae Umb8492, Isolated From The Female Urinary Tract, Suma Gondi, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Here, we present the draft genome sequence for Klebsiella pneumoniae strain UMB8492, isolated from a urine sample from a female patient with overactive bladder (OAB) symptoms. The assembled genome has a length of 5,660,575 bp, a G+C content of 57.19%, and an N50 value of 136,315 bp.


Draft Genome Sequence Of Lactobacillus Jensenii Umb0847, Isolated From The Female Urinary Tract, Ella West-Pelak, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni 2020 Loyola University Chicago

Draft Genome Sequence Of Lactobacillus Jensenii Umb0847, Isolated From The Female Urinary Tract, Ella West-Pelak, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putoni

Bioinformatics Faculty Publications

Lactobacillus jensenii is a protective bacterium native to the female urinary tract. Here, we present the 1.6-Mbp draft genome for Lactobacillus jensenii UMB0847, isolated from a catheterized urine sample obtained from a pregnant female.


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