AIMC Topic: High-Throughput Nucleotide Sequencing

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Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis.

Genetics in medicine : official journal of the American College of Medical Genetics Jan 24, 2019
PURPOSE: Despite the successful progress next-generation sequencing technologies has achieved in diagnosing the genetic cause of rare Mendelian diseases, the current diagnostic rate is still far from satisfactory because of heterogeneity, imprecision...
Genetic Variation High-Throughput Nucleotide Sequencing Rare Diseases Exome Computational Biology Mutation Genetic Testing Humans Machine Learning Software Phenotype Genomics Genotype
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GOTrapper: a tool to navigate through branches of gene ontology hierarchy.

BMC bioinformatics Jan 11, 2019
BACKGROUND: Gene Ontology (GO) is a useful resource of controlled vocabulary that provides information about annotated genes. Based on such resource, finding the biological function is useful for biologists to come up with different hypotheses and he...
Computational Biology Humans Software High-Throughput Nucleotide Sequencing Gene Expression Profiling Information Storage and Retrieval User-Computer Interface Gene Ontology
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Annotation of gene product function from high-throughput studies using the Gene Ontology.

Database : the journal of biological databases and curation Jan 1, 2019
High-throughput studies constitute an essential and valued source of information for researchers. However, high-throughput experimental workflows are often complex, with multiple data sets that may contain large numbers of false positives. The repres...
Molecular Sequence Annotation Gene Ontology Genomics Databases, Genetic Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Humans Animals
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Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations.

Proceedings of the National Academy of Sciences of the United States of America Dec 26, 2018
Biophysical interactions between proteins and peptides are key determinants of molecular recognition specificity landscapes. However, an understanding of how molecular structure and residue-level energetics at protein-peptide interfaces shape these l...
High-Throughput Nucleotide Sequencing Energy Metabolism Drug Resistance, Viral Serine Proteases Viral Nonstructural Proteins Substrate Specificity Peptide Hydrolases Structure-Activity Relationship Antiviral Agents Models, Molecular Metabolomics Supervised Machine Learning Hepacivirus
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PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data.

BMC bioinformatics Dec 17, 2018
BACKGROUND: Predicting prognosis in patients from large-scale genomic data is a fundamentally challenging problem in genomic medicine. However, the prognosis still remains poor in many diseases. The poor prognosis may be caused by high complexity of ...
High-Throughput Nucleotide Sequencing Biomarkers, Tumor Predictive Value of Tests Glioblastoma Humans Area Under Curve Neural Networks, Computer Software Prognosis
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Knowledge base toward understanding actionable alterations and realizing precision oncology.

International journal of clinical oncology Dec 12, 2018
In Japan, the National Cancer Center and university hospitals have initiated next-generation sequencing-based in vitro diagnostic testing for cancer patients as a method of clinical sequencing. Based on the molecular alterations detected, physicians ...
Japan Knowledge Bases High-Throughput Nucleotide Sequencing Humans Precision Medicine Biomarkers, Tumor Neoplasms Genomics Mutation
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Improving the calling of non-invasive prenatal testing on 13-/18-/21-trisomy by support vector machine discrimination.

PloS one Dec 5, 2018
With the advance of next-generation sequencing (NGS) technologies, non-invasive prenatal testing (NIPT) has been developed and employed in fetal aneuploidy screening on 13-/18-/21-trisomies through detecting cell-free fetal DNA (cffDNA) in maternal b...
Trisomy 13 Syndrome Trisomy 18 Syndrome Diagnosis, Computer-Assisted Support Vector Machine False Negative Reactions Pregnancy Sequence Analysis, DNA Humans False Positive Reactions Female Diagnosis, Differential Machine Learning Prenatal Diagnosis Young Adult Genetic Testing Retrospective Studies High-Throughput Nucleotide Sequencing Adult Down Syndrome
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Porcine single nucleotide polymorphisms and their functional effect: an update.

BMC research notes Dec 4, 2018
OBJECTIVE: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was publ...
Animals Male Swine Genome-Wide Association Study Molecular Sequence Annotation Gene Ontology Genome Tail Polymorphism, Single Nucleotide DNA Semen High-Throughput Nucleotide Sequencing Untranslated Regions
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Prediction of plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models.

BMC genomics Nov 26, 2018
BACKGROUND: An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective absorption of plant-derived xenom...
Humans Neural Networks, Computer Biomarkers Databases, Nucleic Acid MicroRNAs RNA, Plant Plants High-Throughput Nucleotide Sequencing
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Machine Learning Methods as a Tool for Predicting Risk of Illness Applying Next-Generation Sequencing Data.

Risk analysis : an official publication of the Society for Risk Analysis Nov 21, 2018
Next-generation sequencing (NGS) data present an untapped potential to improve microbial risk assessment (MRA) through increased specificity and redefinition of the hazard. Most of the MRA models do not account for differences in survivability and vi...
Listeria monocytogenes Virulence Genetic Variation High-Throughput Nucleotide Sequencing Humans Probability Machine Learning Linear Models Food Risk Assessment Algorithms Databases, Genetic Phenotype Listeriosis Food Microbiology Sensitivity and Specificity Foodborne Diseases
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