AIMC Topic: Drosophila Proteins
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A library of lineage-specific driver lines connects developing neuronal circuits to behavior in the ventral nerve cord.
eLife
Jun 10, 2025
Understanding developmental changes in neuronal lineages is crucial to elucidate how they assemble into functional neural networks. Studies investigating nervous system development in model systems have only focused on select regions of the CNS due t...
Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis.
Genome research
May 2, 2025
Understanding how genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F crosses with extensive genetic diversity...
Neural network conditioned to produce thermophilic protein sequences can increase thermal stability.
Scientific reports
Apr 23, 2025
This work presents Neural Optimization for Melting-temperature Enabled by Leveraging Translation (NOMELT), a novel approach for designing and ranking high-temperature stable proteins using neural machine translation. The model, trained on over 4 mill...
Deep learning reveals a damage signalling hierarchy that coordinates different cell behaviours driving wound re-epithelialisation.
Development (Cambridge, England)
Sep 24, 2024
One of the key tissue movements driving closure of a wound is re-epithelialisation. Earlier wound healing studies describe the dynamic cell behaviours that contribute to wound re-epithelialisation, including cell division, cell shape changes and cell...
Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.
Biophysical journal
Dec 30, 2023
Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions tha...
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 ...
Latent space of a small genetic network: Geometry of dynamics and information.
Proceedings of the National Academy of Sciences of the United States of America
Jun 22, 2022
The high-dimensional character of most biological systems presents genuine challenges for modeling and prediction. Here we propose a neural network-based approach for dimensionality reduction and analysis of biological gene expression data, using, as...
An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.
Genome biology
Nov 8, 2021
BACKGROUND: Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can predict the locations of enhan...
Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning.
International journal of molecular sciences
May 11, 2021
Experimental studies of and have contributed substantially to our understanding of molecular and cellular processes in metazoans at large. Since the publication of their genomes, functional genomic investigations have identified genes that are esse...
DeTerm: Software for automatic detection of neuronal dendritic branch terminals via an artificial neural network.
Genes to cells : devoted to molecular & cellular mechanisms
May 28, 2019
Dendrites of neurons receive and process synaptic or sensory inputs. The Drosophila class IV dendritic arborization (da) neuron is an established model system to explore molecular mechanisms of dendrite morphogenesis. The total number of dendritic br...
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