AIMC Topic: INDEL Mutation

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Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning.

Nature communications Sep 19, 2019
Highly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA acti...
Mice CRISPR-Cas Systems Internet HeLa Cells Humans Animals Deep Learning Cell Line, Tumor RNA, Guide, CRISPR-Cas Systems HEK293 Cells Gene Editing Base Sequence Promoter Regions, Genetic Clustered Regularly Interspaced Short Palindromic Repeats Endonucleases INDEL Mutation
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.

Scientific reports Jul 17, 2019
Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machin...
Alleles Nonlinear Dynamics Genotyping Techniques INDEL Mutation Decision Trees Area Under Curve Crohn Disease Genome-Wide Association Study ROC Curve Genetic Predisposition to Disease Polymorphism, Single Nucleotide Genotype Logistic Models Neural Networks, Computer Models, Genetic Female Male Deep Learning Humans
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A multi-task convolutional deep neural network for variant calling in single molecule sequencing.

Nature communications Mar 1, 2019
The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5-15%. Meeting this demand, we developed Cl...
INDEL Mutation Nanopores Polymorphism, Single Nucleotide DNA Mutational Analysis Neural Networks, Computer Humans Base Sequence Genotype Software Computational Biology Genome, Human Genome-Wide Association Study Sequence Analysis, DNA Genotyping Techniques Genomics
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A universal SNP and small-indel variant caller using deep neural networks.

Nature biotechnology Sep 24, 2018
Despite rapid advances in sequencing technologies, accurately calling genetic variants present in an individual genome from billions of short, errorful sequence reads remains challenging. Here we show that a deep convolutional neural network can call...
DNA Mutational Analysis Genome, Human INDEL Mutation Genotype Sequence Analysis, DNA Humans Mammals Neural Networks, Computer High-Throughput Nucleotide Sequencing Animals Software Genomics Polymorphism, Single Nucleotide
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An ensemble approach to accurately detect somatic mutations using SomaticSeq.

Genome biology Sep 17, 2015
SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions and deletions. The workflow currentl...
INDEL Mutation Humans Machine Learning Neoplasms DNA Mutational Analysis
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Do protein language models learn phylogeny?

Briefings in bioinformatics Nov 22, 2024
Deep machine learning demonstrates a capacity to uncover evolutionary relationships directly from protein sequences, in effect internalising notions inherent to classical phylogenetic tree inference. We connect these two paradigms by assessing the ca...
Deep Learning Evolution, Molecular Humans Proteins Machine Learning INDEL Mutation Phylogeny
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SICaRiO: short indel call filtering with boosting.

Briefings in bioinformatics Jul 20, 2021
Despite impressive improvement in the next-generation sequencing technology, reliable detection of indels is still a difficult endeavour. Recognition of true indels is of prime importance in many applications, such as personalized health care, diseas...
Machine Learning Software High-Throughput Nucleotide Sequencing Databases, Nucleic Acid INDEL Mutation
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Ensemble-Based Somatic Mutation Calling in Cancer Genomes.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2020
Identification of somatic mutations in tumor tissue is challenged by both technical artifacts, diverse somatic mutational processes, and genetic heterogeneity in the tumors. Indeed, recent independent benchmark studies have revealed low concordance b...
Genome, Human INDEL Mutation Humans Point Mutation Software Genomics Polymorphism, Single Nucleotide Neoplasms Mutation Supervised Machine Learning
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GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS.

Bioinformatics (Oxford, England) Sep 1, 2018
SUMMARY: Exome sequencing approach is extensively used in research and diagnostic laboratories to discover pathological variants and study genetic architecture of human diseases. However, a significant proportion of identified genetic variants are ac...
Deep Learning Genomics Polymorphism, Single Nucleotide Sequence Analysis, DNA High-Throughput Nucleotide Sequencing INDEL Mutation
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[GENES ALLELE STATUS OF ANGIOTENSINCONVERTING ENZYME (I/D) AND ENDOTHELIAL NITRIC OXIDE SYNTHASE (894 G > T) IN PATIENTS WITH ACUTE CORONARY SYNDROME].

Likars'ka sprava Jan 1, 2015
The association of genes polymorphism of angiotensin-converting enzyme ACE (I/D) and endothelial nitric oxide synthase eNOS (894 G > T) with acute myocardial infarction (MI) among residents of North Bukovina region was evaluated. II/GG and ID/GG hapl...
Gene Frequency Peptidyl-Dipeptidase A Nitric Oxide Synthase Type III INDEL Mutation Haplotypes Male Acute Coronary Syndrome Risk Factors Middle Aged Coronary Vessels Humans Polymorphism, Single Nucleotide Aged Prospective Studies Case-Control Studies Gene Expression Aged, 80 and over Female Adult Myocardial Infarction Alleles
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