Bioinformatics (Oxford, England)
Nov 28, 2024
MOTIVATION: For more than 25 years, learning-based eukaryotic gene predictors were driven by hidden Markov models (HMMs), which were directly inputted a DNA sequence. Recently, Holst et al. demonstrated with their program Helixer that the accuracy of...
Bioinformatics (Oxford, England)
Nov 28, 2024
MOTIVATION: RNA is implicated in numerous aberrant cellular functions and disease progressions, highlighting the crucial importance of RNA-targeted drugs. To accelerate the discovery of such drugs, it is essential to develop an effective computationa...
Bioinformatics (Oxford, England)
Nov 28, 2024
MOTIVATION: The advent of AlphaFold and other protein Artificial Intelligence (AI) models has transformed protein design, necessitating efficient handling of large-scale data and complex workflows. Using existing programming packages that predate rec...
Bioinformatics (Oxford, England)
Nov 1, 2024
MOTIVATION: Extracellular miRNAs (exmiRs) and intracellular mRNAs both can serve as promising biomarkers and therapeutic targets for various diseases. However, exmiR expression data is often noisy, and obtaining intracellular mRNA expression data usu...
Bioinformatics (Oxford, England)
Nov 1, 2024
MOTIVATION: Protein-protein interactions are essential for a variety of biological phenomena including mediating biochemical reactions, cell signaling, and the immune response. Proteins seek to form interfaces which reduce overall system energy. Alth...
Bioinformatics (Oxford, England)
Nov 1, 2024
MOTIVATION: Automated cell lineage tracing throughout embryogenesis plays a key role in the study of regulatory control of cell fate differentiation, morphogenesis and organogenesis in the development of animals, including nematode Caenorhabditis ele...
Bioinformatics (Oxford, England)
Nov 1, 2024
MOTIVATION: The modification of N4-acetylcytidine (ac4C) in RNA is a conserved epigenetic mark that plays a crucial role in post-transcriptional regulation, mRNA stability, and translation efficiency. Traditional methods for detecting ac4C modificati...
Bioinformatics (Oxford, England)
Nov 1, 2024
MOTIVATION: Recent brain mapping efforts are producing large-scale whole-brain images using different imaging modalities. Accurate alignment and delineation of anatomical structures in these images are essential for numerous studies. These requiremen...
Bioinformatics (Oxford, England)
Nov 1, 2024
MOTIVATION: Post-translational modifications (PTMs) increase the diversity of the proteome and are vital to organismal life and therapeutic strategies. Deep learning has been used to predict PTM locations. Still, limitations in datasets and their ana...
Bioinformatics (Oxford, England)
Oct 1, 2024
SUMMARY: The vast generation of genetic data poses a significant challenge in efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven chat framework that tackles this challenge by bridging the gap between genetic data generation ...