AIMC Journal:
Nucleic acids research

Showing 191 to 200 of 228 articles

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.

Nucleic acids research Jun 4, 2019
Interactions between regulatory elements are of crucial importance for the understanding of transcriptional regulation and the interpretation of disease mechanisms. Hi-C technique has been developed for genome-wide detection of chromatin contacts. Ho...
Humans Algorithms Cells, Cultured Gene Expression Regulation Promoter Regions, Genetic Regulatory Sequences, Nucleic Acid Chromatin Deep Learning Genome-Wide Association Study Computational Biology High-Throughput Nucleotide Sequencing
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SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles.

Nucleic acids research May 7, 2019
Characterization of individual cell types is fundamental to the study of multicellular samples. Single-cell RNAseq techniques, which allow high-throughput expression profiling of individual cells, have significantly advanced our ability of this task....
Humans Software Animals Gene Expression Profiling Gene Expression Regulation, Neoplastic Cluster Analysis Pancreatic Neoplasms Supervised Machine Learning Transcriptome Single-Cell Analysis Mice Sequence Analysis, RNA RNA, Small Cytoplasmic High-Throughput Nucleotide Sequencing Datasets as Topic Cell Lineage
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DriverML: a machine learning algorithm for identifying driver genes in cancer sequencing studies.

Nucleic acids research May 7, 2019
Although rapid progress has been made in computational approaches for prioritizing cancer driver genes, research is far from achieving the ultimate goal of discovering a complete catalog of genes truly associated with cancer. Driver gene lists predic...
Oncogenes Datasets as Topic Monte Carlo Method Cell Cycle Proteins Atlases as Topic Neoplasms Humans Cell Line, Tumor Nuclear Proteins Machine Learning Gene Expression Regulation, Neoplastic Cell Proliferation Cell Movement Software Neoplasm Proteins Mutation
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WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach.

Nucleic acids research Apr 23, 2019
N 6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotes, and plays a pivotal role in various biological processes, such as splicing, RNA degradation and RNA-protein interaction. We report here a prediction fram...
High-Throughput Nucleotide Sequencing Methylation Adenosine Sequence Analysis, RNA Epigenesis, Genetic Internet RNA Machine Learning Transcriptome Protein Interaction Maps Humans
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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...
Datasets as Topic Genome, Human Genotyping Techniques Humans Machine Learning Polymorphism, Single Nucleotide DNA Copy Number Variations Quality Control
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ME-Class2 reveals context dependent regulatory roles for 5-hydroxymethylcytosine.

Nucleic acids research Mar 18, 2019
Since the discovery of 5-hydroxymethylcytosine (5hmC) as a prominent DNA modification found in mammalian genomes, an emergent question has been what role this mark plays in gene regulation. 5hmC is hypothesized to function as an intermediate in the d...
Humans Datasets as Topic Mice Methylation Sequence Analysis, RNA Promoter Regions, Genetic Databases, Genetic Organ Specificity Sulfites Machine Learning Genome Brain Genes Animals 5-Methylcytosine
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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...
Base Sequence Drosophila melanogaster Histones Sequence Alignment Computer Heuristics Tandem Repeat Sequences Consensus Sequence Machine Learning Animals Sequence Analysis, DNA Genetic Variation Neural Networks, Computer
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canSAR: update to the cancer translational research and drug discovery knowledgebase.

Nucleic acids research Jan 8, 2019
canSAR (http://cansar.icr.ac.uk) is a public, freely available, integrative translational research and drug discovery knowlegebase. canSAR informs researchers to help solve key bottlenecks in cancer translation and drug discovery. It integrates genom...
Protein Conformation Protein Interaction Mapping Databases, Pharmaceutical Antineoplastic Agents Humans User-Computer Interface Neoplasms Translational Research, Biomedical Drug Discovery Knowledge Bases
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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...
Genetic Variation Biological Ontologies Rare Diseases Congenital Abnormalities Internet Phenotype Humans Whole Genome Sequencing Genetic Predisposition to Disease Computational Biology Databases, Genetic Knowledge Bases
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ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

Nucleic acids research Jan 8, 2019
The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product...
Gene Ontology Sequence Analysis, Protein Databases, Genetic Humans Proteins Animals Internet User-Computer Interface Information Storage and Retrieval Computational Biology
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