AIMC Topic: Transcription, Genetic
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Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer.
Nature communications
Jul 1, 2025
Investigating the temporal dynamics of gene expression is crucial for understanding gene regulation across various biological processes. Using the Fluorescent Timer protein, the Timer-of-cell-kinetics-and-activity system enables analysis of transcrip...
Machine learning-based identification of general transcriptional predictors for plant disease.
The New phytologist
Nov 21, 2024
This study investigated the generalizability of Arabidopsis thaliana immune responses across diverse pathogens, including Botrytis cinerea, Sclerotinia sclerotiorum, and Pseudomonas syringae, using a data-driven, machine learning approach. Machine le...
Deep Learning Sequence Models for Transcriptional Regulation.
Annual review of genomics and human genetics
Aug 6, 2024
Deciphering the regulatory code of gene expression and interpreting the transcriptional effects of genome variation are critical challenges in human genetics. Modern experimental technologies have resulted in an abundance of data, enabling the develo...
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design.
Journal of chemical information and modeling
Jul 24, 2024
Computational molecular generation methods that generate chemical structures from gene expression profiles have been actively developed for de novo drug design. However, most omics-based methods involve complex models consisting of multiple neural ne...
Fundamentals for predicting transcriptional regulations from DNA sequence patterns.
Journal of human genetics
May 10, 2024
Cell-type-specific regulatory elements, cataloged through extensive experiments and bioinformatics in large-scale consortiums, have enabled enrichment analyses of genetic associations that primarily utilize positional information of the regulatory el...
promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting DNA Promoter Sequences.
IEEE/ACM transactions on computational biology and bioinformatics
Feb 5, 2024
Accurate identification of DNA promoter sequences is of crucial importance in unraveling the underlying mechanisms that regulate gene transcription. Initiation of transcription is controlled through regulatory transcription factors binding to promote...
Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease.
Nature communications
Nov 15, 2023
The genomic distribution of cleavage and polyadenylation (polyA) sites should be co-evolutionally optimized with the local gene structure. Otherwise, spurious polyadenylation can cause premature transcription termination and generate aberrant protein...
Predicting transcriptional outcomes of novel multigene perturbations with GEARS.
Nature biotechnology
Aug 17, 2023
Understanding cellular responses to genetic perturbation is central to numerous biomedical applications, from identifying genetic interactions involved in cancer to developing methods for regenerative medicine. However, the combinatorial explosion in...
Designer genes courtesy of artificial intelligence.
Genes & development
May 30, 2023
The core promoter determines not only where gene transcription initiates but also the transcriptional activity in both basal and enhancer-induced conditions. Multiple short sequence elements within the core promoter have been identified in different ...
Exogenous Chemicals Impact Virus Receptor Gene Transcription: Insights from Deep Learning.
Environmental science & technology
May 15, 2023
Despite the fact that coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been disrupting human life and health worldwide since the outbreak in late 2019, the impact of exogenous substance ...
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