AIMC Topic: Mutation

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Identification and segregation of genes with improved recurrent neural network trained with optimal gene level and mutation level features.

Computer methods in biomechanics and biomedical engineering
Even though many different approaches have been employed to address the complex mutational heterogeneity of cancer, finding driver genes is still problematic since other genomic factors cannot be fully integrated for combined analyses. This research ...

Protein design using structure-based residue preferences.

Nature communications
Recent developments in protein design rely on large neural networks with up to 100s of millions of parameters, yet it is unclear which residue dependencies are critical for determining protein function. Here, we show that amino acid preferences at in...

Inference of annealed protein fitness landscapes with AnnealDCA.

PLoS computational biology
The design of proteins with specific tasks is a major challenge in molecular biology with important diagnostic and therapeutic applications. High-throughput screening methods have been developed to systematically evaluate protein activity, but only a...

TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations.

BMC genomics
The most widely practiced strategy for constructing the deep learning (DL) prediction model for drug resistance of Mycobacterium tuberculosis (MTB) involves the adoption of ready-made and state-of-the-art architectures usually proposed for non-biolog...

Accurate top protein variant discovery via low-N pick-and-validate machine learning.

Cell systems
A strategy to obtain the greatest number of best-performing variants with least amount of experimental effort over the vast combinatorial mutational landscape would have enormous utility in boosting resource producibility for protein engineering. Tow...

A systematic analysis of deep learning in genomics and histopathology for precision oncology.

BMC medical genomics
BACKGROUND: Digitized histopathological tissue slides and genomics profiling data are available for many patients with solid tumors. In the last 5 years, Deep Learning (DL) has been broadly used to extract clinically actionable information and biolog...

Advances in next-generation sequencing and emerging technologies for hematologic malignancies.

Haematologica
Innovations in molecular diagnostics have often evolved through the study of hematologic malignancies. Examples include the pioneering characterization of the Philadelphia chromosome by cytogenetics in the 1970s, the implementation of polymerase chai...

Next generation phenotyping for diagnosis and phenotype-genotype correlations in Kabuki syndrome.

Scientific reports
The field of dysmorphology has been changed by the use Artificial Intelligence (AI) and the development of Next Generation Phenotyping (NGP). The aim of this study was to propose a new NGP model for predicting KS (Kabuki Syndrome) on 2D facial photog...

Using Vision Transformer for high robustness and generalization in predicting EGFR mutation status in lung adenocarcinoma.

Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico
BACKGROUND: Lung adenocarcinoma is a common cause of cancer-related deaths worldwide, and accurate EGFR genotyping is crucial for optimal treatment outcomes. Conventional methods for identifying the EGFR genotype have several limitations. Therefore, ...

Deep learning-radiomics integrated noninvasive detection of epidermal growth factor receptor mutations in non-small cell lung cancer patients.

Scientific reports
This study focused on a novel strategy that combines deep learning and radiomics to predict epidermal growth factor receptor (EGFR) mutations in patients with non-small cell lung cancer (NSCLC) using computed tomography (CT). A total of 1280 patients...