Search
Search Results
-
Bulk and Single-Cell RNA-Seq Analyses for Studies of Spermatogonia
Robust methods have been developed that leverage next-generation sequencing (NGS) to measure abundance of all mRNAs (RNA-seq) in samples as small as...
-
Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data
Even though high-throughput transcriptome sequencing is routinely performed in many laboratories, computational analysis of such data remains a...
-
Exaggerated false positives by popular differential expression methods when analyzing human population samples
When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation...
-
A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses
BackgroundIn this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and...
-
Transcriptome software results show significant variation among different commercial pipelines
BackgroundWe have been documenting the biological responses to low levels of radiation (natural background) and very low level radiation (below...
-
Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures
The lack of benchmark data sets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and...
-
Differential Expression Analysis of Long Noncoding RNAs
Long noncoding RNA (lncRNA) expression data have been increasingly used in identifying diagnostic and prognostic biomarkers in clinical studies....
-
The Overexpression of Solanum nigrum Osmotin (SnOLP) Boosts Drought Response Pathways in Soybean
Environmental stresses are responsible for limiting soybean yield. To mitigate the impacts generated by water deficit, molecular biology tools are...
-
Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells
RNA sequencing (RNA-seq)RNA sequencing (RNA-seq) analysis of virus-infected host cells enables researchers to study a wide range of phenomena...
-
The influence of maternal unhealthy diet on maturation of offspring gut microbiota in rat
BackgroundDespite well-known effects of diet on gut microbiota diversity, relatively little is known about how maternal diet quality shapes the...
-
Transcriptomic Analysis During the Induction of Somatic Embryogenesis in Coffea canephora
Omic tools have changed the way of doing research in experimental biology. The somatic embryogenesis (SE) study has not been immune to this benefit....
-
Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis
Human microbiome studies have shown diversity to exist among different ethnic populations. However, studies pertaining to the microbial composition...
-
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density
Recent studies have shown that probiotic supplementation has beneficial effects on bone metabolism. In a randomized controlled trial (RCT) we...
-
Bioinformatics Analysis of miRNA Sequencing Data
The bioinformatics analysis of miRNA is a complicated task with multiple operations and steps involved from processing of raw sequence data to...
-
Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana ‘Xtreme Red’
BackgroundThe microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants...
-
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...
-
Differential Expression Feature Extraction (DEFE): A Case Study in Wheat FHB RNA-Seq Data Analysis
In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset in order to detect the...
-
Map** Transcription Regulation with Run-on and Sequencing Data Using the Web-Based tfTarget Gateway
Run-on and sequencing assays like GRO-seq, PRO-seq, and ChRO-seq allow for joint profiling of transcription activity of transcriptional regulatory...
-
A Workflow Guide to RNA-Seq Analysis of Chaperone Function and Beyond
RNA sequencing (RNA-seq) is a powerful method of transcriptional analysis that allows for the sequence identification and quantification of cellular...
-
Modeling Plant Transcription Factor Networks Using ConSReg
Plants have developed complex regulatory programs to respond to various environmental stress such as heat, drought, and cold. Systematic...