Related papers: High-resolution transcriptome analysis with long-r…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Identification and quantification of condition-specific transcripts using RNA-Seq is vital in transcriptomics research. While initial efforts using mathematical or statistical modeling of read counts or per-base exonic signal have been…
Current popular methods in literature of RNA sequencing normalisation do not account for gene length when compared across samples, whilst adjusting for count biases in the data. This creates a gap in the normalisation as bigger genes in RNA…
The ability to measure the transcriptomes of single cells has only been feasible for a few years, and is becoming an extremely popular assay. While many types of analysis and questions can be answered using single cell RNA-sequencing, a…
Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…
Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in…
High-throughput sequencing of RNA transcripts (RNA-seq) has become the method of choice for detection of differential expression (DE). Concurrent with the growing popularity of this technology there has been a significant research effort…
Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Most human protein-coding genes can be transcribed into multiple possible distinct mRNA isoforms. These alternative splicing patterns encourage molecular diversity and dysregulation of isoform expression plays an important role in disease…
High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read count variability. These estimates are…
Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining the sequences for a large number of genes from an organism with no reference genome. With the rapidly increasing throughputs and…
In the face of rapidly accumulating genomic data, our understanding of the RNA regulatory code remains incomplete. Recent self-supervised methods in other domains have demonstrated the ability to learn rules underlying the data-generating…
Background and Objective: The massive parallel sequencing technology facilitates new discoveries in terms of transcript differential analysis; however, all the new findings must be validated, since the diversity of transcript expression may…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
High-throughput transcriptomics experiments have reached the stage where the count of the number of reads alignable to a given position can be treated as an almost-continuous signal. This allows to ask questions of biophysical/biotechnical…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce…