AIMC Topic: Transcription, Genetic
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Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks.
Briefings in bioinformatics
Jul 20, 2021
A promoter is a region in the DNA sequence that defines where the transcription of a gene by RNA polymerase initiates, which is typically located proximal to the transcription start site (TSS). How to correctly identify the gene TSS and the core prom...
Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework.
Briefings in bioinformatics
Jul 20, 2021
Origins of replication sites (ORIs), which refers to the initiative locations of genomic DNA replication, play essential roles in DNA replication process. Detection of ORIs' distribution in genome scale is one of key steps to in-depth understanding t...
Deep representation learning improves prediction of LacI-mediated transcriptional repression.
Proceedings of the National Academy of Sciences of the United States of America
Jul 6, 2021
Recent progress in DNA synthesis and sequencing technology has enabled systematic studies of protein function at a massive scale. We explore a deep mutational scanning study that measured the transcriptional repression function of 43,669 variants of ...
SilencerDB: a comprehensive database of silencers.
Nucleic acids research
Jan 8, 2021
Gene regulatory elements, including promoters, enhancers, silencers, etc., control transcriptional programs in a spatiotemporal manner. Though these elements are known to be able to induce either positive or negative transcriptional control, the comm...
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.
Nucleic acids research
Jan 8, 2021
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their ass...
Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
As the interest in genetic resequencing increases, so does the need for effective mathematical, computational, and statistical approaches. One of the difficult problems in genome annotation is determination of precise positions of transcription start...
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