相关论文: DNA-MATRIX a tool for DNA motif discovery and weig…

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…

Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA.…

The problem of motif detection can be formulated as the construction of a discriminant function to separate sequences of a specific pattern from background. In computational biology, motif detection is used to predict DNA binding sites of a…

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…

Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through Position…

Scoring DNA sequences against Position Weight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools produce scores that can reflect the binding strength between…

We present ensemble methods in a machine learning (ML) framework combining predictions from five known motif/binding site exploration algorithms. For a given TF the ensemble starts with position weight matrices (PWM's) for the motif,…

Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…

We present a simple and efficient method for prediction of transcription factor binding sites from DNA sequence. Our method computes a random approximation of a convolutional kernel feature map from DNA sequence and then learns a linear…

Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…

The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…

When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently,…

The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…

We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…

The most common gene regulation mechanism is when a protein binds to a regulatory sequence to change RNA transcription. However, these sequences are short relative to the genome length, so finding them poses a challenging search problem.…

Genome-wide experiments to map the DNA-binding locations of transcription-associated factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of possible direct target genes. Distinguishing functional from…

Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…

Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…

The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we…

MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor…