Genetics

Deep learning in regulatory genomics: from identification to design.

Genomics and deep learning are a natural match since both are data-driven fields. Regulatory genomics refers to functional noncoding DNA regulating gene expression. In recent years, deep learning applications on regulatory genomics have achieved remarkable advances so-much-so that it has revolutionized the rules of the game of the computational methods in this field. Here, we review two emerging t...

Finding the sweet spot: a qualitative study exploring patients' acceptability of chatbots in genetic service delivery.

Chatbots, web-based artificial intelligence tools that simulate human conversation, are increasingly in use to support many areas of genomic medicine. However, patient preferences towards using chatbots across the range of clinical settings are unknown. We conducted a qualitative study with individuals who underwent genetic testing for themselves or their child. Participants were asked about their...

Deep learning prediction of pathological complete response, residual cancer burden, and progression-free survival in breast cancer patients.

The goal of this study was to employ novel deep-learning convolutional-neural-network (CNN) to predict pathological complete response (PCR), residual ...

Deep Learning With Radiogenomics Towards Personalized Management of Gliomas.

A state-of-the-art interdisciplinary survey on multi-modal radiogenomic approaches is presented involving applications to the diagnosis and personaliz...

Fused deep learning paradigm for the prediction of o6-methylguanine-DNA methyltransferase genotype in glioblastoma patients: A neuro-oncological investigation.

BACKGROUND: The O6-methylguanine-DNA methyltransferase (MGMT) is a deoxyribonucleic acid (DNA) repairing enzyme that has been established as an essent...

Artificial intelligence-based recognition for variant pathogenicity of BRCA1 using AlphaFold2-predicted structures.

With the surge of the high-throughput sequencing technologies, many genetic variants have been identified in the past decade. The vast majority of the...

Mateverse, the Future Materials Science Computation Platform Based on Metaverse.

Currently, computational materials science involves human-computer interaction through coding in software or neural networks. There is still no direct...

Prediction of designer-recombinases for DNA editing with generative deep learning.

Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeuti...

Predicting Genetic Disorder and Types of Disorder Using Chain Classifier Approach.

Genetic disorders are the result of mutation in the deoxyribonucleic acid (DNA) sequence which can be developed or inherited from parents. Such mutati...

Rapid Detection of SARS-CoV-2 RNA in Human Nasopharyngeal Specimens Using Surface-Enhanced Raman Spectroscopy and Deep Learning Algorithms.

A rapid and cost-effective method to detect the infection of SARS-CoV-2 is fundamental to mitigating the current COVID-19 pandemic. Herein, a surface-...

Application of machine learning on understanding biomolecule interactions in cellular machinery.

Machine learning (ML) applications have become ubiquitous in all fields of research including protein science and engineering. Apart from protein stru...

Mechano-fluorescence actuation in single synaptic vesicles with a DNA framework nanomachine.

Biomimetic machines that can convert mechanical actuation to adaptive coloration in a manner analogous to cephalopods have found widespread applicatio...

Dicentric chromosome assay using a deep learning-based automated system.

The dicentric chromosome assay is the "gold standard" in biodosimetry for estimating radiation exposure. However, its large-scale deployment is limite...

Water irradiation devoid pulses enhance the sensitivity of H,H nuclear Overhauser effects.

The nuclear Overhauser effect (NOE) is one of NMR spectroscopy's most important and versatile parameters. NOE is routinely utilized to determine the s...

Symphonizing pileup and full-alignment for deep learning-based long-read variant calling.

Deep learning-based variant callers are becoming the standard and have achieved superior single nucleotide polymorphisms calling performance using lon...

Calligraphy and Painting Identification 3D-CNN Model Based on Hyperspectral Image MNF Dimensionality Reduction.

As a kind of cultural art, calligraphy and painting are not only an important part of traditional culture but also has important value of art collecti...

Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network.

Cross-species comparative analyses of single-cell RNA sequencing (scRNA-seq) data allow us to explore, at single-cell resolution, the origins of the c...

Accuracy and data efficiency in deep learning models of protein expression.

Synthetic biology often involves engineering microbial strains to express high-value proteins. Thanks to progress in rapid DNA synthesis and sequencin...

Operon Finder: A Deep Learning-based Web Server for Accurate Prediction of Prokaryotic Operons.

Operons are groups of consecutive genes that transcribe together under the regulation of a common promoter. They influence protein regulation and vari...

Molecular modeling of C1-inhibitor as SARS-CoV-2 target identified from the immune signatures of multiple tissues: An integrated bioinformatics study.

The expeditious transmission of the severe acute respiratory coronavirus 2 (SARS-CoV-2), a strain of COVID-19, crumbled the global economic strength a...