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Mutation

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Identification of a gene signature and prediction of overall survival of patients with stage IV colorectal cancer using a novel machine learning approach.

European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology
OBJECTIVE: We sought to characterize unique gene signature patterns associated with worse overall survival (OS) among patients with stage IV colorectal cancer (CRC) using a machine learning (ML) approach.

Deep learning-driven semi-rational design in phenylalanine ammonia-lyase for enhanced catalytic efficiency.

International journal of biological macromolecules
Phenylalanine ammonia-lyase (PAL) possesses significant potential in agriculture, industry, and the treatment of various diseases, including cancer. In particular, PAL derived from Anabaena variabilis (AvPAL) has been successfully utilized in clinica...

Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time.

Nucleic acids research
In infected individuals, viruses are present as a population consisting of dominant and minor variant genomes. Most databases contain information on the dominant genome sequence. Since the emergence of SARS-CoV-2 in late 2019, variants have been sele...

Deep learning prioritizes cancer mutations that alter protein nucleocytoplasmic shuttling to drive tumorigenesis.

Nature communications
Genetic variants can affect protein function by driving aberrant subcellular localization. However, comprehensive analysis of how mutations promote tumor progression by influencing nuclear localization is currently lacking. Here, we systematically ch...

Deep learning radiomics for the prediction of epidermal growth factor receptor mutation status based on MRI in brain metastasis from lung adenocarcinoma patients.

BMC cancer
BACKGROUND: Early and accurate identification of epidermal growth factor receptor (EGFR) mutation status in non-small cell lung cancer (NSCLC) patients with brain metastases is critical for guiding targeted therapy. This study aimed to develop a deep...

Identification of Novel Fourth-Generation Allosteric Inhibitors Targeting Inactive State of EGFR T790M/L858R/C797S and T790M/L858R Mutations: A Combined Machine Learning and Molecular Dynamics Approach.

The journal of physical chemistry. B
Targeted therapy with an allosteric inhibitor (AIs) is an important area of research in patients with epidermal growth factor receptor (EGFR) mutations. Current treatment of nonsmall cell lung cancer patients with EGFR mutations using orthosteric inh...

Deep mutational learning for the selection of therapeutic antibodies resistant to the evolution of Omicron variants of SARS-CoV-2.

Nature biomedical engineering
Most antibodies for treating COVID-19 rely on binding the receptor-binding domain (RBD) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). However, Omicron and its sub-lineages, as well as other heavily mutated variants, have rendered m...

Discovery of mutations predictive of survival benefit from immunotherapy in first-line NSCLC: A retrospective machine learning study of IMpower150 liquid biopsy data.

Computers in biology and medicine
Predictive biomarker identification in cancer treatment has traditionally relied on pre-defined analyses, limiting discoveries to expected biomarkers and potentially overlooking novel ones predictive of therapy response. In this work, we develop a no...

Machine learning identifies clinical tumor mutation landscape pathways of resistance to checkpoint inhibitor therapy in NSCLC.

Journal for immunotherapy of cancer
BACKGROUND: Immune checkpoint inhibitors (CPIs) have revolutionized cancer therapy for several tumor indications. However, a substantial fraction of patients treated with CPIs derive no benefit or have short-lived responses to CPI therapy. Identifyin...