Genetics

Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

Increasingly frequent marine heatwaves devastate coral reefs around the world, so there is great interest in finding warm-adapted coral populations that could be used as sources for assisted gene flow and restoration. Here, we evaluated the relative power of various environmental factors to explain coral genetic variation, suggestive of differential local adaptation to these factors, across the Fl...

Genetic Deconvolution of Embryonic and Maternal Cell-Free DNA in Spent Culture Medium of Human Preimplantation Embryo Through Deep Learning.

Noninvasive preimplantation genetic testing for aneuploidy based on embryonic cell-free DNA (cfDNA) released in spent embryo culture media (SECM) has brought hope in selecting embryos that are most likely to implant and grow into healthy babies during assisted reproduction. However, maternal DNA contamination in SECM significantly hampers the reliability of embryonic chromosome ploidy profiles, le...

DNA methylation as a diagnostic biomarker for rheumatoid arthritis: a validation study using targeted sequencing.

OBJECTIVES: To validate the potential of the serotonin receptor encoded by 5-hydroxytryptamine receptor 2A (HTR2A) cg15692052 DNA methylation as a dia...

Development and Validation of a Hierarchical Machine Learning Method using MALDI-TOF Mass Spectrometry for Rapid SCCmec Typing and PVL Detection in MRSA: A Multi-Center Study.

OBJECTIVES: Methicillin-resistant (MRSA) is a major public health concern because of its genotypic diversity and association with severe infections, ...

Development and validation of an interpretable machine learning model for predicting Philadelphia chromosome-positive acute lymphoblastic leukaemia using clinical and laboratory parameters: a single-centre retrospective study.

OBJECTIVE: To develop and validate a prediction model of Philadelphia chromosome-positive acute lymphoblastic leukaemia (Ph+ALL).

Generating and characterizing human telencephalic brain organoids from stem cell-derived single neural rosettes.

We have developed a method for generating human telencephalic organoids from stem cell-derived isolated single neural rosettes. The use of single neur...

Machine learning application to predict binding affinity between peptide containing non-canonical amino acids and HLA-A0201.

Class Ι major histocompatibility complexes (MHC-Ι), encoded by the highly polymorphic HLA-A, HLA-B, and HLA-C genes in humans, are expressed on all nu...

AffiGrapher: Contrastive Heterogeneous Graph Learning with Aromatic Virtual Nodes for RNA-Small Molecule Binding Affinity Prediction.

RNA molecules exhibit diverse structures and functions, making them promising drug targets. However, predicting RNA-small molecule binding affinity re...

Aptamer-directed siRNA delivery systems for triple-negative breast cancer therapy.

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by the absence of estrogen, progesterone, and HER2 recept...

Unraveling the role of perineural invasion in cancer progression across multiple tumor types.

Perineural invasion (PNI) refers to the infiltration of tumor cells into the connective tissue of nerves and is increasingly recognized as a pathologi...

Computer Vision Techniques for High-Speed Atomic Force Microscopy of DNA Molecules.

High- speed atomic force microscopy (HSAFM) can produce thousands of topographic, nanoscale images over a small area. One emerging application of this...

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing.

MOTIVATION: High-throughput sequencing is a modern sequencing technology used to profile microbiomes by sequencing thousands of short genomic fragment...

Programmable DNA-Based Molecular Neural Network Biocomputing Circuits for Solving Partial Differential Equations.

Partial differential equations, essential for modeling dynamic systems, persistently confront computational complexity bottlenecks in high-dimensional...

A composite universal DNA signature for the tree of life.

Species identification using DNA barcodes has revolutionized biodiversity sciences. However, conventional barcoding methods may lack power and univers...

Predicting IDH Mutation in Glioma Patients Using Deep Learning Algorithms with Conformal Prediction.

The World Health Organization glioma classification highlights genetic profiles, such as isocitrate dehydrogenase (IDH) mutation. This study developed...

Neural network prediction model based on Levy flight and natural biomimetic technology for its application in cancer prediction.

Precise forecasting of cancer outcomes is essential for medical professionals to assess the well-being of patients and develop customized therapeutic ...

Prognosis and prognostic factors for chronic fibrosing idiopathic interstitial pneumonias.

Progressive lung fibrosis is frequently observed in patients with idiopathic interstitial pneumonias (IIPs), especially in those with idiopathic pulmo...

Gaining insights into epigenetic memories through artificial intelligence and omics science in plants.

Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus-dependent decision-making circuits. Unlike animals, plant me...

Prime editor-based high-throughput screening reveals functional synonymous mutations in human cells.

Synonymous mutations are generally considered neutral, while their roles in the human genome remain largely unexplored. Here we use the PEmax system t...

RNA-ligand interaction scoring via data perturbation and augmentation modeling.

Despite recent advances in RNA-targeting drug discovery, the development of data-driven deep learning models remains challenging owing to limited vali...