相关论文: Whole genome mapping of 5' RNA ends in bacteria by…

This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…

In eukaryotes, DNA replication is initiated along each chromosome at multiple sites called replication origins. Locally, each replication origin is "licensed", or specified, at the end of the M and the beginning of G1 phases of the cell…

The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…

The regulAS software package is a bioinformatics tool designed to support computational biology researchers in investigating regulatory mechanisms of splicing alterations through integrative analysis of large-scale RNA-Seq data from cancer…

Recent advances in molecular biology allow the quantification of the transcriptome and scoring transcripts as differentially or equally expressed between two biological conditions. Although these two tasks are closely linked, the available…

The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…

Bacterial infections are responsible for high mortality worldwide. Antimicrobial resistance underlying the infection, and multifaceted patient's clinical status can hamper the correct choice of antibiotic treatment. Randomized clinical…

With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this…

During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…

How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to…

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…

Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…

We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to…

We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…

Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…

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…

By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…

Network motifs, the recurring regulatory structural patterns in networks, are able to self-organize to produce networks. Three major motifs, feedforward loop, single input modules and bi-fan are found in gene regulatory networks. The large…

Recently, there has been a lot of effort in understanding sRNA mediated regulation of gene expression and how this mode of regulation differs from transcriptional regulation.In E.coli, in the presence of oxidative stress, the synthesis of…

We propose a learning method well-suited to infer the presence of Tuberculosis (TB) manifestations on Computer Tomography (CT) scans mimicking the radiologist reports. Latent features are extracted from the CT volumes employing the V-Net…