AIMC Journal:
Nucleic acids research

Showing 171 to 180 of 228 articles

Uncovering the key dimensions of high-throughput biomolecular data using deep learning.

Nucleic acids research Jun 4, 2020
Recent advances in high-throughput single-cell RNA-seq have enabled us to measure thousands of gene expression levels at single-cell resolution. However, the transcriptomic profiles are high-dimensional and sparse in nature. To address it, a deep lea...
Humans RNA-Seq Mice Metabolomics Data Compression Animals Deep Learning Single-Cell Analysis
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Machine learning predicts new anti-CRISPR proteins.

Nucleic acids research May 21, 2020
The increasing use of CRISPR-Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR-Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that...
CRISPR-Associated Protein 9 Prophages Machine Learning Bacterial Proteins Proteome Streptococcus Sequence Analysis, Protein
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Uncovering tissue-specific binding features from differential deep learning.

Nucleic acids research Mar 18, 2020
Transcription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expres...
Mice Computational Biology Models, Genetic Poisson Distribution Animals Deep Learning Protein Binding Homeodomain Proteins Gene Expression Regulation, Developmental Chromatin Immunoprecipitation Organ Specificity RNA Branchial Region Protein Isoforms High-Throughput Nucleotide Sequencing Myeloid Ecotropic Viral Integration Site 1 Protein Binding Sites Embryo, Mammalian
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The neXtProt knowledgebase in 2020: data, tools and usability improvements.

Nucleic acids research Jan 8, 2020
The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describ...
Protein Kinases Knowledge Bases Trypsin User-Computer Interface Sequence Analysis, RNA Mass Spectrometry Humans Databases, Protein Software Internet Peptides Protein Processing, Post-Translational Proteins
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BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Nucleic acids research Jan 8, 2020
The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detai...
User-Computer Interface Models, Biological Knowledge Bases Software Genome Reproducibility of Results Phylogeny
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The reactome pathway knowledgebase.

Nucleic acids research Jan 8, 2020
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data mo...
Databases, Chemical Genome, Human Databases, Pharmaceutical Signal Transduction Metabolic Networks and Pathways Knowledge Bases Software Protein Interaction Maps Humans
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Convolutional neural network model to predict causal risk factors that share complex regulatory features.

Nucleic acids research Dec 16, 2019
Major progress in disease genetics has been made through genome-wide association studies (GWASs). One of the key tasks for post-GWAS analyses is to identify causal noncoding variants with regulatory function. Here, on the basis of >2000 functional fe...
Humans Neural Networks, Computer Mental Disorders Genetic Predisposition to Disease Polymorphism, Single Nucleotide Risk Factors Genome-Wide Association Study Autoimmune Diseases Quantitative Trait Loci Regulatory Sequences, Nucleic Acid
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Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification.

Nucleic acids research Nov 18, 2019
Identifying functional variants underlying disease risk and adoption of personalized medicine are currently limited by the challenge of interpreting the functional consequences of genetic variants. Predicting the functional effects of disease-associa...
Epigenesis, Genetic Sequence Analysis, DNA Polymorphism, Genetic Humans Deep Learning Chromatin Assembly and Disassembly Genome-Wide Association Study Histone Code
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Machine learning-based chemical binding similarity using evolutionary relationships of target genes.

Nucleic acids research Nov 18, 2019
Chemical similarity searching is a basic research tool that can be used to find small molecules which are similar in shape to known active molecules. Despite its popularity, the retrieval of local molecular features that are critical to functional ac...
Machine Learning Animals Small Molecule Libraries Protein Binding Sequence Analysis, Protein Humans Protein Kinases Evolution, Molecular Genes Quantitative Structure-Activity Relationship Protein Kinase Inhibitors
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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...
Markov Chains Datasets as Topic DNA Genome, Human Histones Humans Supervised Machine Learning Nucleosomes Software High-Throughput Nucleotide Sequencing Transposases Sequence Analysis, DNA
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