AIMC Topic: Genome, Human

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SomaticSeq: An Ensemble and Machine Learning Method to Detect Somatic Mutations.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2020
A standard strategy to discover somatic mutations in a cancer genome is to use next-generation sequencing (NGS) technologies to sequence the tumor tissue and its matched normal (commonly blood or adjacent normal tissue) for side-by-side comparison. H...
Mutation High-Throughput Nucleotide Sequencing Genome, Human Humans Neoplasms Genomics Machine Learning Software
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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...
Humans Software Neoplasms Supervised Machine Learning Genome, Human INDEL Mutation Point Mutation Genomics Polymorphism, Single Nucleotide Mutation
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DL-CNV: A deep learning method for identifying copy number variations based on next generation target sequencing.

Mathematical biosciences and engineering : MBE Sep 30, 2019
Copy number variations (CNVs) play an important role in many types of cancer. With the rapid development of next generation sequencing (NGS) techniques, many methods for detecting CNVs of a single sample have emerged: (i) require genome-wide data of ...
In Situ Hybridization, Fluorescence Receptor, ErbB-2 Genome, Human DNA Copy Number Variations Area Under Curve High-Throughput Nucleotide Sequencing False Positive Reactions Exons Proto-Oncogene Proteins c-met Reproducibility of Results Sensitivity and Specificity Deep Learning Lung Neoplasms Carcinoma, Non-Small-Cell Lung Genome-Wide Association Study Humans ROC Curve Algorithms Databases, Factual
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HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.

Nucleic acids research Sep 19, 2019
ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragm...
Humans Software Sequence Analysis, DNA DNA Nucleosomes Transposases Datasets as Topic Genome, Human Histones Supervised Machine Learning High-Throughput Nucleotide Sequencing Markov Chains
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Promoter analysis and prediction in the human genome using sequence-based deep learning models.

Bioinformatics (Oxford, England) Aug 15, 2019
MOTIVATION: Computational identification of promoters is notoriously difficult as human genes often have unique promoter sequences that provide regulation of transcription and interaction with transcription initiation complex. While there are many at...
Genome, Human Promoter Regions, Genetic Transcription Initiation Site Deep Learning Genomics Humans
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The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.

Nature biotechnology Jun 1, 2019
Genomics Whole Genome Sequencing Humans Genome, Human Machine Learning Gene Editing Databases, Factual
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EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.

Nucleic acids research Apr 23, 2019
The associations between diseases/traits and copy number variants (CNVs) have not been systematically investigated in genome-wide association studies (GWASs), primarily due to a lack of robust and accurate tools for CNV genotyping. Herein, we propose...
Humans DNA Copy Number Variations Quality Control Machine Learning Datasets as Topic Polymorphism, Single Nucleotide Genome, Human Genotyping Techniques
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Localizing and Classifying Adaptive Targets with Trend Filtered Regression.

Molecular biology and evolution Feb 1, 2019
Identifying genomic locations of natural selection from sequence data is an ongoing challenge in population genetics. Current methods utilizing information combined from several summary statistics typically assume no correlation of summary statistics...
Genetic Techniques Genetics, Population Humans Models, Genetic Machine Learning Regression Analysis Software Genome, Human Computer Simulation
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Machine learning spots natural selection at work in human genome.

Nature Nov 1, 2018
Deep Learning Europe Evolution, Molecular Humans Animals Selection, Genetic Milk History, Ancient Lactase DNA Mutational Analysis Genome, Human
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Gene multifunctionality scoring using gene ontology.

Journal of bioinformatics and computational biology Oct 1, 2018
Multifunctional genes are important genes because of their essential roles in human cells. Studying and analyzing multifunctional genes can help understand disease mechanisms and drug discovery. We propose a computational method for scoring gene mult...
Genetic Association Studies Gene Ontology Biomedical Research Proteins Computational Biology PubMed Protein Interaction Maps Evolution, Molecular Genome, Human Humans Genetic Predisposition to Disease Algorithms Reproducibility of Results
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