Results 11 to 20 of about 700,365 (275)

An Illumina metabarcoding pipeline for fungi [PDF]

Ecology and Evolution, 2014
AbstractHigh‐throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired‐end reads on ...
Bálint, Miklós, Schmidt, Philipp-André, Sharma, Rahul, Thines, Marco, Schmitt, Imke   +4 more
openaire   +4 more sources

Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes

BMC Microbiology, 2023
The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time.
Asako Tan, Senthil Murugapiran, Alaya Mikalauskas, Jeff Koble, Drew Kennedy, Fred Hyde, Victor Ruotti, Emily Law, Jordan Jensen, Gary P. Schroth, Jean M. Macklaim, Scott Kuersten, Brice LeFrançois, Daryl M. Gohl   +13 more
doaj   +1 more source

Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion [PDF]

, 2018
The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades.
De Vrieze, Jo, Ijaz, Umer Z., Saunders, Aaron M., Theuerl, Susanne   +3 more
core   +6 more sources

The diagnostic trajectory of infants and children with clinical features of genetic disease

npj Genomic Medicine, 2021
We characterized US pediatric patients with clinical indicators of genetic diseases, focusing on the burden of disease, utilization of genetic testing, and cost of care.
Brock E. Schroeder, Nina Gonzaludo, Katie Everson, Kyi-Sin Than, Jeff Sullivan, Ryan J. Taft, John W. Belmont   +6 more
doaj   +1 more source

A High-Throughput Method for Illumina RNA-Seq Library Preparation. [PDF]

, 2012
With the introduction of cost effective, rapid, and superior quality next generation sequencing techniques, gene expression analysis has become viable for labs conducting small projects as well as large-scale gene expression analysis experiments. However,
Daniel H Chitwood, Jie ePeng, Julin N Maloof, Lauren R Headland, Neelima R Sinha, Ravi eKumar, Seisuke eKimura, Seisuke eKimura, Yasunori eIchihashi   +8 more
core   +2 more sources

Reactive gene curation to support interpretation and reporting of a clinical genome test for rare disease: Experience from over 1,000 cases

Cell Genomics, 2023
Summary: Current standards in clinical genetics recognize the need to establish the validity of gene-disease relationships as a first step in the interpretation of sequence variants.
Amanda R. Clause, Julie P. Taylor, Revathi Rajkumar, Krista Bluske, Maren Bennett, Laura M. Amendola, David R. Bentley, Ryan J. Taft, Denise L. Perry, Alison J. Coffey, Carolyn Brown, Matthew P. Brown, Amanda Buchanan, Brendan Burns, Nicole J. Burns, Anjana Chandrasekhar, Aditi Chawla, Katie Golden-Grant, Akanchha Kesari, Alka Malhotra, Becky Milewski, Samin A. Sajan, Zinayida Schlachetzki, Sarah Schmidt, Brittany Thomas, Erin Thorpe   +25 more
doaj   +1 more source

Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination [PDF]

, 2011
Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3-5-kb DNA fragment are not easy to identify and pose ...
Deforce, Dieter, Gaasterland, Terry, Head, Steven R, Ledesma, Jessica, Ordoukhanian, Phillip, Thompson, Ryan C, Van Nieuwerburgh, Filip   +6 more
core   +2 more sources

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. [PDF]

, 2017
Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles.
Honda, Shozo, Kirino, Yohei, Loher, Phillipe, Rigoutsos, Isidore, Shigematsu, Megumi, Telonis, Aristeidis G.   +5 more
core   +2 more sources

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing [PDF]

, 2016
Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors
Decock, Anneleen, Ongenaert, Maté, Speleman, Franki, Van Criekinge, Wim, Vandesompele, Jo   +4 more
core   +1 more source

Simulating Illumina metagenomic data with InSilicoSeq [PDF]

Bioinformatics, 2018
Abstract Motivation The accurate in silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation ...
Gourlé, Hadrien, Karlsson-Lindsjö, Oskar, Hayer, Juliette, Bongcam-Rudloff, Erik   +3 more
openaire   +2 more sources