The ability to quantify cellular heterogeneity is a major advantage of single-cell technologies. Although understanding such heterogeneity is of primary interest in a number of studies, for convenience, statistical methods often treat cellular heterogeneity as a nuisance factor. A team ...
Read More »Identify, quantify and annotate SNPs without any reference genome, using RNA-seq data only
SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot ...
Read More »WheatExp – an RNA-seq expression database for polyploid wheat
For functional genomics studies, it is important to understand the dynamic expression profiles of transcribed genes in different tissues, stages of development and in response to environmental stimuli. The proliferation in the use of next-generation sequencing technologies by the plant ...
Read More »Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy Reveals Human Proteomic Variation
Mass spectrometry-based proteomic analysis underestimates proteomic variation due to the absence of variant peptides and posttranslational modifications (PTMs) from standard protein databases. Each individual carries thousands of missense mutations that lead to single amino acid variants, but these are missed ...
Read More »Net-RSTQ – Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, researchers at the University of Minnesota Twin Cities ...
Read More »Generating Sample-Specific Databases for Mass Spectrometry-Based Proteomic Analysis by Using RNA Sequencing
Mass spectrometry-based methods allow for the direct, comprehensive analysis of expressed proteins and their quantification among different conditions. However, in general identification of proteins by assigning experimental mass spectra to peptide sequences of proteins relies on matching mass spectra to ...
Read More »Transcriptome Sequencing for the Detection of Chimeric Transcripts
The occurrence of chimeric transcripts has been reported in many cancer cells and seen as potential biomarkers and therapeutic targets. Modern high-throughput sequencing technologies offer a way to investigate individual chimeric transcripts and the systematic information of associated gene expressions ...
Read More »SpliceJumper – a classification-based approach for calling splicing junctions from RNA-seq data
Next-generation RNA sequencing technologies have been widely applied in transcriptome profiling. This facilitates further studies of gene structure and expression on the genome wide scale. It is an important step to align reads to the reference genome and call out ...
Read More »Fine-mapping cellular QTLs with RASQUAL and ATAC-seq
When cellular traits are measured using high-throughput DNA sequencing, quantitative trait loci (QTLs) manifest as fragment count differences between individuals and allelic differences within individuals. Researchers from the Wellcome Trust Sanger Institute have developed RASQUAL (Robust Allele-Specific Quantitation and Quality Control), ...
Read More »FuMa – reporting overlap in RNA-seq detected fusion genes
A new generation of tools that identify fusion genes in RNA-seq data is limited in either sensitivity and or specificity. To allow further downstream analysis and to estimate performance, predicted fusion genes from different tools have to be compared. However, ...
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