AIMC Journal:
Nucleic acids research

Showing 221 to 228 of 228 articles

Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision.

Nucleic acids research Dec 1, 2017
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety...
Humans Neural Networks, Computer Tumor Suppressor Proteins Ubiquitin-Protein Ligases Cell Lineage Histone Code Alternative Splicing Embryonic Stem Cells Cell Line Cell Differentiation High-Throughput Nucleotide Sequencing Machine Learning Sequence Analysis, RNA Epigenesis, Genetic
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Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.

Nucleic acids research Dec 1, 2017
The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large n...
Animals Gene Expression Profiling Single-Cell Analysis Mice Machine Learning Software Humans Algorithms High-Throughput Nucleotide Sequencing RNA, Small Untranslated Ribonuclease III RNA, Plant Genomics Sequence Analysis, RNA MicroRNAs
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Using neural networks for reducing the dimensions of single-cell RNA-Seq data.

Nucleic acids research Sep 29, 2017
While only recently developed, the ability to profile expression data in single cells (scRNA-Seq) has already led to several important studies and findings. However, this technology has also raised several new computational challenges. These include ...
Computational Biology Sequence Analysis, RNA Databases, Genetic Cluster Analysis Software Gene Expression Profiling Single-Cell Analysis Protein Interaction Mapping Multifactor Dimensionality Reduction RNA Datasets as Topic Gene Expression Regulation Humans Neural Networks, Computer
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A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data.

Nucleic acids research Aug 21, 2017
Characterizing the binding behaviors of RNA-binding proteins (RBPs) is important for understanding their functional roles in gene expression regulation. However, current high-throughput experimental methods for identifying RBP targets, such as CLIP-s...
Base Sequence Binding Sites Nucleotide Motifs Binding, Competitive 3' Untranslated Regions Internet High-Throughput Nucleotide Sequencing Gene Expression Regulation Computational Biology RNA-Binding Proteins Mutation Humans Reproducibility of Results Protein Binding Machine Learning Algorithms
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agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update.

Nucleic acids research Jul 3, 2017
The agriGO platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (GO) enrichment analyses of plant and agricultural species. We continuously maintain and update the databases and accommodate th...
Software Animals Birds Insecta Vegetables Crops, Agricultural Agriculture Gene Ontology Internet Molecular Sequence Annotation Arabidopsis Fishes
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NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.

Nucleic acids research Jul 3, 2017
Peptides are extensively used to characterize functional or (linear) structural aspects of receptor-ligand interactions in biological systems, e.g. SH2, SH3, PDZ peptide-recognition domains, the MHC membrane receptors and enzymes such as kinases and ...
Peptides Protein Binding Databases, Protein Forkhead Transcription Factors Amino Acid Sequence Basic Helix-Loop-Helix Leucine Zipper Transcription Factors Internet Neural Networks, Computer Software Algorithms Humans HLA-B8 Antigen HLA-DRB1 Chains Ligands Trans-Activators HLA-A1 Antigen Cell Cycle Proteins Sequence Alignment HLA-B7 Antigen Binding Sites
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TSSPlant: a new tool for prediction of plant Pol II promoters.

Nucleic acids research May 5, 2017
Our current knowledge of eukaryotic promoters indicates their complex architecture that is often composed of numerous functional motifs. Most of known promoters include multiple and in some cases mutually exclusive transcription start sites (TSSs). M...
Transcription Initiation Site Neural Networks, Computer Gene Expression RNA Polymerase II Plant Proteins Software Oryza Genome, Plant Promoter Regions, Genetic Sequence Analysis, DNA Arabidopsis
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FARNA: knowledgebase of inferred functions of non-coding RNA transcripts.

Nucleic acids research Mar 17, 2017
Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/...
RNA, Long Noncoding Knowledge Bases Humans Databases, Nucleic Acid Transcription Factors MicroRNAs
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