AIMC Topic: DNA Replication
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Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.
Nature communications
Jul 1, 2025
DNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules. By combining high-resolution Atomic Force Micro...
Supervised and unsupervised deep learning-based approaches for studying DNA replication spatiotemporal dynamics.
Communications biology
Feb 26, 2025
In eukaryotic cells, DNA replication is organised both spatially and temporally, as evidenced by the stage-specific spatial distribution of replication foci in the nucleus. Despite the genetic association of aberrant DNA replication with numerous hum...
Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.
Nature communications
Feb 8, 2025
Genomic heterogeneity has largely been overlooked in single-cell replication timing (scRT) studies. Here, we develop MnM, an efficient machine learning-based tool that allows disentangling scRT profiles from heterogenous samples. We use single-cell c...
Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides.
Nature communications
Nov 8, 2023
Bioactive peptides are key molecules in health and medicine. Deep learning holds a big promise for the discovery and design of bioactive peptides. Yet, suitable experimental approaches are required to validate candidates in high throughput and at low...
CNN-Pred: Prediction of single-stranded and double-stranded DNA-binding protein using convolutional neural networks.
Gene
Nov 26, 2022
DNA-binding proteins play a vital role in biological activity including DNA replication, DNA packing, and DNA reparation. DNA-binding proteins can be classified into single-stranded DNA-binding proteins (SSBs) or double-stranded DNA-binding proteins ...
Machine learning classification of trajectories from molecular dynamics simulations of chromosome segregation.
PloS one
Jan 21, 2022
In contrast to the well characterized mitotic machinery in eukaryotes it seems as if there is no universal mechanism organizing chromosome segregation in all bacteria. Apparently, some bacteria even use combinations of different segregation mechanism...
A deep learning framework combined with word embedding to identify DNA replication origins.
Scientific reports
Jan 12, 2021
The DNA replication influences the inheritance of genetic information in the DNA life cycle. As the distribution of replication origins (ORIs) is the major determinant to precisely regulate the replication process, the correct identification of ORIs ...
A symbolic network-based nonlinear theory for dynamical systems observability.
Scientific reports
Feb 28, 2018
When the state of the whole reaction network can be inferred by just measuring the dynamics of a limited set of nodes the system is said to be fully observable. However, as the number of all possible combinations of measured variables and time deriva...
Immunohistochemistry and machine learning study of DNA replication-associated proteins in uterine epithelial tumors and precursor lesions.
Acta histochemica
Jun 1, 2025
Endometrioid adenocarcinoma (EA) has been on the increase in recent years in developed countries. Early detection of endometrioid adenocarcinoma in the endometrial corpus is crucial for patient prognosis and early treatment, although their distinctio...
Deep learning meets histones at the replication fork.
Cell
Sep 5, 2024
Epigenetic inheritance of heterochromatin requires transfer of parental H3-H4 tetramers to both daughter duplexes during replication. Three recent papers exploit yeast genetics coupled to inheritance assays and AlphaFold2-multimer predictions coupled...
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