Related papers: Robust identification of noncoding RNA from transc…
Interpreting gene clusters from RNA sequencing (RNA-seq) remains challenging, especially in antimicrobial resistance studies where mechanistic insight is important for hypothesis generation. Existing pathway enrichment methods can summarize…
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
To develop an integrated transcriptome-proteome framework for identifying concurrent biomarkers predictive of radiation response, as measured by survival fraction at 2 Gy (SF2), in non-small cell lung cancer (NSCLC) cell lines. RNA…
Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames and which have been termed long non-coding RNAs (lncRNAs). Despite the existence of several well-characterized…
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
In the past decade, transcriptome data have become an important component of many phylogenetic studies. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and…
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…
RNA molecules follow a succession of enzyme-mediated processing steps from transcription until maturation. The participating enzymes, for example the spliceosome for mRNAs and Drosha and Dicer for microRNAs, are also produced in the cell…
Objectives: The vast and complex nature of human genomic sequencing data presents challenges for effective analysis. This review aims to investigate the application of Natural Language Processing (NLP) techniques, particularly Large…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
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…
The discovery of nucleic acids and the structure of DNA have brought considerable advances in the understanding of life. The development of next-generation sequencing technologies has led to a large-scale generation of data, for which…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved…
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…
Motivation: Assigning RNA-seq reads to their transcript of origin is a fundamental task in transcript expression estimation. Where ambiguities in assignments exist due to transcripts sharing sequence, e.g. alternative isoforms or alleles,…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…