Rifkin, Riaan F. Vikram, Surendra Ramond, Jean-Baptiste Rey-Iglesia, Alba Brand, Tina B. Porraz, Guillaume Val, Aurore Hall, Grant Woodborne, Stephan Le Bailly, Matthieu
...
Published in
Microbiome
BackgroundThe archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.MethodsFollowing the rec...
Tan, Zheng Hao, Yu-Hua Zheng, Ke-Wei
Published in
Biochemical and biophysical research communications
The particular enrichment of G-quadruplex-forming sequences near transcription start sites signifies the involvement of G-quadruplexes in the regulation of transcription. The characterization of G-quadruplex formation, which holds the key to understand the function it plays in physiological and pathological processes, is mostly performed under simp...
Cajigas, Sebastian Alzate, Daniel Orozco, Jahir
Published in
Microchimica Acta
The development of a stable nanobioconjugate based on gold nanoparticles (AuNPs) linked to single-strand DNA (ssDNA) is reported for amplification of the electrochemical signal of a Zika virus (ZIKV) genetic material-based bioassay, with high sensitivity. The genosensor was assembled either at a screen-printed gold electrode (SPAuE) or a screen-pri...
Vermond, Lukas (author)
In an effort to make DNA sequencing more accessible and affordable, Oxford Nanopore Technologies developed the MinION: A portable cellphone sized DNA sequencing device. Translating the information from this device to a nucleotide sequence is called basecalling, and is done with the aid of artificial neural networks. In this thesis, we accelerate a ...
Bangalore, Disha M. Heil, Hannah S. Mehringer, Christian F. Hirsch, Lisa Hemmen, Katherina Heinze, Katrin G. Tessmer, Ingrid
Published in
Scientific Reports
Base excision repair is the dominant DNA repair pathway of chemical modifications such as deamination, oxidation, or alkylation of DNA bases, which endanger genome integrity due to their high mutagenic potential. Detection and excision of these base lesions is achieved by DNA glycosylases. To investigate the remarkably high efficiency in target sit...
Gilson, Timra D. Gibson, Ryan T. Androphy, Elliot J.
Published in
Scientific Reports
Human papillomavirus (HPV) L1 and L2 capsid proteins self-assemble into virions capable of efficiently packaging either its 8 kilobase genome or non-viral DNA. The ability of HPV capsids to package non-viral DNA makes these a useful tool for delivering plasmids to study proteins of interest in a variety of cell types. We describe optimization of cu...
Bailey, Matthew H Meyerson, William U Dursi, Lewis Jonathan Wang, Liang-Bo Dong, Guanlan Liang, Wen-Wei Weerasinghe, Amila Li, Shantao Kelso, Sean group, mc3 working
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The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658...
Scotoni, Manuela Koch, Julian Julian, Timothy R. Clack, Lauren Pitol, Ana K. Wolfensberger, Aline Grass, Robert N. Sax, Hugo
Published in
Antimicrobial Resistance & Infection Control
BackgroundThe increase in antimicrobial resistance is of worldwide concern. Surrogate tracers attempt to simulate microbial transmission by avoiding the infectious risks associated with live organisms. We evaluated silica nanoparticles with encapsulated DNA (SPED) as a new promising surrogate tracer in healthcare.MethodsSPED and Escherichia coli we...
Awan, Muaaz G. Deslippe, Jack Buluc, Aydin Selvitopi, Oguz Hofmeyr, Steven Oliker, Leonid Yelick, Katherine
Published in
BMC Bioinformatics
BackgroundBioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming b...
Nguyen, Huynh Quoc Nguyen, Van Dan Van Nguyen, Hau Seo, Tae Seok
Published in
Scientific Reports
The increasing risk of infectious pathogens, especially in the under-developed countries, is demanding the development of point-of-care (POC) nucleic acid testing in the low-resource setting conditions. Here, we describe a methodology for colorimetric quantitative analysis of nucleic acid using an easy-to-build smartphone-based platform, offering l...
