BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection
A promoter is a sequence of DNA that initializes the process of transcription and regulates
whenever and wherever genes are expressed in the organism. Because of its importance in …
whenever and wherever genes are expressed in the organism. Because of its importance in …
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction
Promoters are crucial regulatory DNA regions for gene transcriptional activation. Rapid
advances in next-generation sequencing technologies have accelerated the accumulation …
advances in next-generation sequencing technologies have accelerated the accumulation …
Role of DNA sequence based structural features of promoters in transcription initiation and gene expression
Highlights•We briefly review the status of sequence based promoter methods.•The role of
non-B-DNA motifs in promoters and their effect on transcription is discussed.•The DNA …
non-B-DNA motifs in promoters and their effect on transcription is discussed.•The DNA …
DeePromoter: robust promoter predictor using deep learning
The promoter region is located near the transcription start sites and regulates transcription
initiation of the gene by controlling the binding of RNA polymerase. Thus, promoter region …
initiation of the gene by controlling the binding of RNA polymerase. Thus, promoter region …
Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli
A Mendoza-Vargas, L Olvera, M Olvera, R Grande… - PloS one, 2009 - journals.plos.org
Despite almost 40 years of molecular genetics research in Escherichia coli a major fraction
of its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding …
of its Transcription Start Sites (TSSs) are still unknown, limiting therefore our understanding …
Explainability in transformer models for functional genomics
The effectiveness of deep learning methods can be largely attributed to the automated
extraction of relevant features from raw data. In the field of functional genomics, this …
extraction of relevant features from raw data. In the field of functional genomics, this …
The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting
We perform a genome-wide analysis of the transition between transcriptional initiation and
elongation in Escherichia coli by determining the association of core RNA polymerase …
elongation in Escherichia coli by determining the association of core RNA polymerase …
70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features
W He, C Jia, Y Duan, Q Zou - BMC systems biology, 2018 - Springer
Background Promoter is an important sequence regulation element, which is in charge of
gene transcription initiation. In prokaryotes, σ 70 promoters regulate the transcription of most …
gene transcription initiation. In prokaryotes, σ 70 promoters regulate the transcription of most …
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes
During the process of transcription, RNA polymerase can exactly locate a promoter
sequence in the complex maze of a genome. Several experimental studies and …
sequence in the complex maze of a genome. Several experimental studies and …
Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli
Antibiotic treatment kills a large portion of a population, while a small, tolerant subpopulation
survives. Tolerant bacteria disrupt antibiotic efficacy and increase the likelihood that a …
survives. Tolerant bacteria disrupt antibiotic efficacy and increase the likelihood that a …