Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Nucleic acid tests (NATs) are considered as gold standard in molecular diagnosis. To meet the demand for onsite, point-of-care, specific and sensitive, trace and genotype detection of pathogens and pathogenic variants, various types of NATs have been...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
In this chapter, we discuss the potential application of Restricted Boltzmann machines (RBM) to model sequence families of structured RNA molecules. RBMs are a simple two-layer machine learning model able to capture intricate sequence dependencies in...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Fundamental to the diverse biological functions of RNA are its 3D structure and conformational flexibility, which enable single sequences to adopt a variety of distinct 3D states. Currently, computational RNA design tasks are often posed as inverse p...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Machine learning algorithms, and in particular deep learning approaches, have recently garnered attention in the field of molecular biology due to remarkable results. In this chapter, we describe machine learning approaches specifically developed for...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Three-dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, topologically associating domains (TADs), and A/B compartments, play critical roles in a wide range of cellular processes by regulating gene expressi...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
One of the main challenges in food microbiology is to prevent the risk of outbreaks by avoiding the distribution of food contaminated by bacteria. This requires constant monitoring of the circulating strains throughout the food production chain. Bact...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Although MALDI-TOF mass spectrometry (MS) is considered as the gold standard for rapid and cost-effective identification of microorganisms in routine laboratory practices, its capability for antimicrobial resistance (AMR) detection has received limit...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2024
Digital reconstruction of neuronal structures from 3D neuron microscopy images is critical for the quantitative investigation of brain circuits and functions. Currently, neuron reconstructions are mainly obtained by manual or semiautomatic methods. H...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2024
A generative adversarial network (GAN) is a generative model that consists of two adversarial networks, a discriminator and a generator, usually in the form of neural networks. One of the useful things about applying GANs is that they can synthesize ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2024
Promoters are the genomic regions upstream of genes that RNA polymerase binds in order to initiate gene transcription. Understanding the regulation of gene expression depends on being able to identify promoters, because they are the most important co...