AIMC Topic: Mutation

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SCONES: Self-Consistent Neural Network for Protein Stability Prediction Upon Mutation.

The journal of physical chemistry. B Sep 21, 2021
Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protei...
Neural Networks, Computer Proteins Mutation Protein Stability Thermodynamics
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Genetic dissection of complex traits using hierarchical biological knowledge.

PLoS computational biology Sep 17, 2021
Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical bio...
Metabolic Networks and Pathways Copper Mutation Glucose Glycine Polymorphism, Single Nucleotide Computational Biology Systems Biology Models, Genetic Multifactorial Inheritance Benomyl Nucleotidyltransferases Knowledge Bases Saccharomyces cerevisiae Gene Ontology Hydroxyurea Chromosome Mapping Neural Networks, Computer Machine Learning Phenotype Genome-Wide Association Study
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Weakly supervised learning on unannotated H&E-stained slides predicts BRAF mutation in thyroid cancer with high accuracy.

The Journal of pathology Sep 14, 2021
Deep neural networks (DNNs) that predict mutational status from H&E slides of cancers can enable inexpensive and timely precision oncology. Although expert knowledge is reliable for annotating regions informative of malignancy and other known histolo...
Humans Middle Aged Thyroid Neoplasms Staining and Labeling Mutation Proto-Oncogene Proteins B-raf Neural Networks, Computer Female Aged Adult Male
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Deep learning detects acute myeloid leukemia and predicts NPM1 mutation status from bone marrow smears.

Leukemia Sep 8, 2021
The evaluation of bone marrow morphology by experienced hematopathologists is essential in the diagnosis of acute myeloid leukemia (AML); however, it suffers from a lack of standardization and inter-observer variability. Deep learning (DL) can proces...
Humans Prognosis Deep Learning Follow-Up Studies Mutation Bone Marrow Nucleophosmin Biomarkers, Tumor Retrospective Studies Leukemia, Myeloid, Acute Female Male Aged Middle Aged Adult Case-Control Studies
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ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.

PLoS computational biology Sep 7, 2021
Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understan...
Enhancer Elements, Genetic Genes, Reporter Regulatory Sequences, Nucleic Acid Transcription Initiation, Genetic Mutation Gene Expression Regulation Genome, Human Promoter Regions, Genetic Humans Molecular Sequence Annotation Deep Learning Genome-Wide Association Study Computational Biology Models, Genetic
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NGS and phenotypic ontology-based approaches increase the diagnostic yield in syndromic retinal diseases.

Human genetics Aug 26, 2021
Syndromic retinal diseases (SRDs) are a group of complex inherited systemic disorders, with challenging molecular underpinnings and clinical management. Our main goal is to improve clinical and molecular SRDs diagnosis, by applying a structured pheno...
Gene Ontology Eye Diseases, Hereditary Ciliopathies Syndrome Genetic Testing High-Throughput Nucleotide Sequencing Retinal Diseases Male Humans Cohort Studies Phenotype Genetic Association Studies Prospective Studies Molecular Diagnostic Techniques Retrospective Studies Mutation Female
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Machine Learning-Based Radiomics Signatures for EGFR and KRAS Mutations Prediction in Non-Small-Cell Lung Cancer.

International journal of molecular sciences Aug 26, 2021
Early identification of epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations is crucial for selecting a therapeutic strategy for patients with non-small-cell lung cancer (NSCLC). We proposed a machin...
Humans Machine Learning Algorithms Biomarkers Middle Aged Neoplasm Staging Tomography, X-Ray Computed Female Mutation ROC Curve Reproducibility of Results Supervised Machine Learning Lung Neoplasms Aged ErbB Receptors Carcinoma, Non-Small-Cell Lung Aged, 80 and over Proto-Oncogene Proteins p21(ras) Male
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Using machine learning and big data to explore the drug resistance landscape in HIV.

PLoS computational biology Aug 26, 2021
Drug resistance mutations (DRMs) appear in HIV under treatment pressure. DRMs are commonly transmitted to naive patients. The standard approach to reveal new DRMs is to test for significant frequency differences of mutations between treated and naive...
Genes, Viral HIV-1 Drug Resistance, Viral United Kingdom Epistasis, Genetic HIV Reverse Transcriptase Humans Decision Trees Africa Bayes Theorem Big Data Mutation Anti-HIV Agents HIV Infections Supervised Machine Learning Computational Biology Logistic Models Models, Genetic Databases, Genetic
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Rosetta:MSF:NN: Boosting performance of multi-state computational protein design with a neural network.

PloS one Aug 26, 2021
Rational protein design aims at the targeted modification of existing proteins. To reach this goal, software suites like Rosetta propose sequences to introduce the desired properties. Challenging design problems necessitate the representation of a pr...
Databases, Protein Neural Networks, Computer Mutation Algorithms Amino Acid Sequence Computational Biology Thermodynamics Proteins Epistasis, Genetic
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Diagnosis of Wilson Disease and Its Phenotypes by Using Artificial Intelligence.

Biomolecules Aug 20, 2021
WD is caused by variants disrupting copper efflux resulting in excessive copper accumulation mainly in liver and brain. The diagnosis of WD is challenged by its variable clinical course, onset, morbidity, and variant type. Currently it is diagnosed...
Artificial Intelligence Algorithms Ceruloplasmin Phenotype Brain Female Adult Male Middle Aged DNA, Mitochondrial Diagnosis, Computer-Assisted Medical Informatics Fuzzy Logic Glutamic Acid Liver Copper-Transporting ATPases Humans Hepatolenticular Degeneration Principal Component Analysis Copper Neural Networks, Computer Mutation
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