AIMC Topic: Genetic Variation

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Machine-learned analysis of the association of next-generation sequencing-based genotypes with persistent pain after breast cancer surgery.

Pain Oct 1, 2019
Cancer and its surgical treatment are among the most important triggering events for persistent pain, but additional factors need to be present for the clinical manifestation, such as variants in pain-relevant genes. In a cohort of 140 women undergoi...
Aged Adult Breast Neoplasms Middle Aged Case-Control Studies Humans Machine Learning Female Mastectomy Genetic Variation High-Throughput Nucleotide Sequencing Cancer Pain Reelin Protein Cohort Studies Genotype Pain Measurement Pain, Postoperative
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Avoiding common pitfalls in machine learning omic data science.

Nature materials May 1, 2019
Cell Biology Humans Machine Learning Algorithms Phenotype Genetic Variation Data Science Oligonucleotide Array Sequence Analysis Genomics Proteomics Medical Errors Computational Biology Models, Theoretical
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GOF/LOF knowledge inference with tensor decomposition in support of high order link discovery for gene, mutation and disease.

Mathematical biosciences and engineering : MBE Feb 20, 2019
For discovery of new usage of drugs, the function type of their target genes plays an important role, and the hypothesis of "Antagonist-GOF" and "Agonist-LOF" has laid a solid foundation for supporting drug repurposing. In this research, an active ge...
Genetic Variation Cost-Benefit Analysis Myelodysplastic Syndromes Molecular Sequence Annotation Interleukin-2 Lymphoma Drug Repositioning Mutation Genetic Diseases, Inborn Interleukin-2 Receptor alpha Subunit Humans Algorithms Recombinant Proteins Models, Genetic Machine Learning Software
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Deep repeat resolution-the assembly of the Drosophila Histone Complex.

Nucleic acids research Feb 20, 2019
Though the advent of long-read sequencing technologies has led to a leap in contiguity of de novo genome assemblies, current reference genomes of higher organisms still do not provide unbroken sequences of complete chromosomes. Despite reads in exces...
Animals Sequence Analysis, DNA Genetic Variation Base Sequence Drosophila melanogaster Neural Networks, Computer Machine Learning Consensus Sequence Histones Sequence Alignment Computer Heuristics Tandem Repeat Sequences
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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Nucleic acids research Jan 8, 2019
The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detaile...
Congenital Abnormalities Genetic Predisposition to Disease Computational Biology Humans Databases, Genetic Phenotype Internet Genetic Variation Whole Genome Sequencing Biological Ontologies Knowledge Bases Rare Diseases
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PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs.

Nucleic acids research Jan 8, 2019
One important aspect of precision medicine aims to deliver the right medicine to the right patient at the right dose at the right time based on the unique 'omics' features of each individual patient, thus maximizing drug efficacy and minimizing adver...
Genetic Variation Information Storage and Retrieval Disease Pharmacogenetics Computational Biology Internet Knowledge Bases Humans Precision Medicine Reproducibility of Results
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An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Database : the journal of biological databases and curation Jan 1, 2019
Personalized genomic medicine depends on integrated analyses that combine genetic and phenotypic data from individual patients with reference knowledge of the functional and clinical significance of sequence variants. Sources of this reference knowle...
Workflow Knowledge Bases Databases, Protein Genetic Variation Nerve Tissue Proteins Copper-Transporting ATPases Zinc Finger Protein Gli3
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Outgroup Machine Learning Approach Identifies Single Nucleotide Variants in Noncoding DNA Associated with Autism Spectrum Disorder.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2019
Autism spectrum disorder (ASD) is a heritable neurodevelopmental disorder affecting 1 in 59 children. While noncoding genetic variation has been shown to play a major role in many complex disorders, the contribution of these regions to ASD susceptibi...
Child Gene Regulatory Networks Genetic Predisposition to Disease Polymorphism, Single Nucleotide Logistic Models MicroRNAs DNA Genetic Association Studies Computational Biology Female Male Case-Control Studies Cohort Studies Humans Machine Learning Phenotype Autism Spectrum Disorder Microsatellite Repeats Supranuclear Palsy, Progressive Whole Genome Sequencing Genetic Variation CpG Islands RNA, Untranslated
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ARIADNA: machine learning method for ancient DNA variant discovery.

DNA research : an international journal for rapid publication of reports on genes and genomes Dec 1, 2018
Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time- or environment-related damage of aDNA. In the absence of validated datasets and desp...
Mutation Genetic Variation Genome DNA, Ancient Machine Learning Animals Mammoths Neanderthals
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Machine-Assisted Genotype Update System (MAGUS) for Inherited Cardiomyopathies.

Circulation. Cardiovascular quality and outcomes Oct 1, 2018
Cardiomyopathy, Hypertrophic, Familial Computational Biology Heredity Predictive Value of Tests Reproducibility of Results Genetic Testing Pedigree Humans Risk Factors Cardiomyopathy, Dilated Machine Learning Data Mining Genetic Variation Risk Assessment Arrhythmogenic Right Ventricular Dysplasia Phenotype High-Throughput Nucleotide Sequencing Prognosis Genetic Predisposition to Disease
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