Search
Search Results
-
Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq
Pseudouridine, a modified RNA residue formed by the isomerization of its parental U nucleotide, is prevalent in a majority of cellular RNAs; its...
-
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data
BackgroundExtrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several...
-
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
BackgroundRNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice,...
-
Cloud Computing for Metagenomics: Building a Personalized Computational Platform for Pipeline Analyses
Cloud Computing services such as Microsoft Azure, Amazon Web Services, and Google Cloud provide a range of tools and services that enable scientists...
-
DeSP: a systematic DNA storage error simulation pipeline
BackgroundUsing DNA as a storage medium is appealing due to the information density and longevity of DNA, especially in the era of data explosion. A...
-
Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing
BackgroundReliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA...
-
A robust pipeline for efficient knock-in of point mutations and epitope tags in zebrafish using fluorescent PCR based screening
BackgroundGenome editing using CRISPR/Cas9 has become a powerful tool in zebrafish to generate targeted gene knockouts models. However, its use for...
-
A MATLAB Pipeline for Spatiotemporal Quantification of Monolayer Cell Migration
In this chapter we present a MATLAB-based computational pipeline for the quantification of monolayer migration assays. Wound healing assay (or...
-
COMPILE: a GWAS computational pipeline for gene discovery in complex genomes
BackgroundGenome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and...
-
SpykProps: an imaging pipeline to quantify architecture in unilateral grass inflorescences
BackgroundInflorescence properties such length, spikelet number, and their spatial distribution across the rachis, are fundamental indicators of seed...
-
MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis
BackgroundThe possibility of recovering metagenome-assembled genomes (MAGs) from sequence reads allows for further insights into microbial...
-
Streamlined Data Analysis Pipeline for Deep Sequence-Coupled Biopanning Identification of Pathogen-Specific Antibody Responses in Serum
Deep sequence-coupled biopanning (DSCB) is a powerful tool that couples affinity selection of a bacteriophage MS2 virus-like particle peptide display...
-
Biosynthetic Gene Cluster Analysis in Micromonospora Species Using ANTISMASH: Secondary Metabolite Genome Mining Pipeline
Micromonospora is a prolific producer of antibiotics. Producing more than about 700 antibiotic compounds, Micromonospora has received much attention...
-
Bioinformatics Methods for Transcriptome Analysis on Teratogenesis Testing
Teratogenesis testing can be challenging due to the limitations of both in vitro and in vivo models. Test-systems, based especially on human...
-
Lysate-based pipeline to characterize microtubule-associated proteins uncovers unique microtubule behaviours
The microtubule cytoskeleton forms complex macromolecular assemblies with a range of microtubule-associated proteins (MAPs) that have fundamental...
-
Genome-Wide Analysis of Planarian piRNAs
In planarian flatworms, the piRNA pathway is operated by three PIWI proteins, termed SMEDWI-1, SMEDWI-2, and SMEDWI-3 (SMEDWI = Schmidtea...
-
The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline
Aside from the well-known role in protein synthesis, RNA can perform catalytic, regulatory, and other essential biological functions which are...
-
Identification of Microcystin, Nodularin Synthatase Gene Clusters in Toxic Cyanobacteria Using AntiSMASH Pipeline
A wide variety of toxins produced by cyanobacteria can cause severe health problems or even death in both people and animals. These cyanotoxins...
-
VascuViz: a multimodality and multiscale imaging and visualization pipeline for vascular systems biology
Despite advances in imaging, image-based vascular systems biology has remained challenging because blood vessel data are often available only from a...
-
Development of an optimization pipeline of asymmetric PCR towards the generation of DNA aptamers: a guide for beginners
AbstractAsymmetric PCR is one of the most utilized strategies in ssDNA generation towards DNA aptamer generation due to its low cost, robustness and...
