AIMC Topic: Transcription, Genetic

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Similarity corpus on microbial transcriptional regulation.

Journal of biomedical semantics May 22, 2019
BACKGROUND: The ability to express the same meaning in different ways is a well-known property of natural language. This amazing property is the source of major difficulties in natural language processing. Given the constant increase in published lit...
Natural Language Processing Gene Expression Regulation Transcription, Genetic Microbiology
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Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence.

Proceedings of the National Academy of Sciences of the United States of America Mar 6, 2019
Deep learning methodologies have revolutionized prediction in many fields and show potential to do the same in molecular biology and genetics. However, applying these methods in their current forms ignores evolutionary dependencies within biological ...
Deep Learning Models, Theoretical Sequence Analysis, DNA Evolution, Molecular DNA Gene Expression Regulation Base Sequence Transcription, Genetic
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Hispaglabridin B, a constituent of liquorice identified by a bioinformatics and machine learning approach, relieves protein-energy wasting by inhibiting forkhead box O1.

British journal of pharmacology Dec 4, 2018
BACKGROUND AND PURPOSE: Liquorice is the root of Glycyrrhiza glabra, which is a popular food in Europe and China that has previously shown benefits for skeletal fatigue and nutrient metabolism. However, the mechanism and active ingredients remain lar...
Machine Learning Transcription, Genetic Muscular Atrophy Forkhead Box Protein O1 Muscle, Skeletal Structure-Activity Relationship Plant Roots Models, Molecular Molecular Structure Benzopyrans Glycyrrhiza Animals Male Mice Computational Biology Plant Extracts Mice, Inbred C57BL Dose-Response Relationship, Drug
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RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes.

BMC genomics Jul 20, 2018
BACKGROUND: Although different quality controls have been applied at different stages of the sample preparation and data analysis to ensure both reproducibility and reliability of RNA-seq results, there are still limitations and bias on the detectabi...
Humans Machine Learning Transcription, Genetic Arabidopsis Histone Code Gene Expression Profiling Sequence Analysis, RNA Epigenesis, Genetic
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Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies.

IEEE/ACM transactions on computational biology and bioinformatics Mar 15, 2018
Sigma factor, as a unit of RNA polymerase holoenzyme, is a critical factor in the process of gene transcriptional regulation. It recognizes the specific DNA sites and brings the core enzyme of RNA polymerase to the upstream regions of target genes. T...
DNA-Directed RNA Polymerases RNA Polymerase Sigma 54 Transcription, Genetic Genome, Bacterial Amino Acid Motifs Computational Biology Escherichia coli Models, Statistical Escherichia coli Proteins Base Sequence False Positive Reactions Promoter Regions, Genetic Machine Learning Software Reproducibility of Results
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Candida albicans-derived mannoproteins activate NF-κB in reporter cells expressing TLR4, MD2 and CD14.

PloS one Dec 27, 2017
The ability of soluble C. albicans 20A (serotype A) mannoprotein (CMP) to serve as a ligand for toll-like receptor 4 (TLR4) and its co-receptors was examined using commercially available and stably-transfected HEK293 cells that express human TLR4, MD...
Humans Lymphocyte Antigen 96 Tumor Necrosis Factor-alpha Interleukin-8 Glycosylation Lipopolysaccharide Receptors NF-kappa B Candida albicans Toll-Like Receptor 4 HEK293 Cells Lipopolysaccharides Cyclooxygenase 2 Membrane Glycoproteins Transcription, Genetic
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Classifying cancer genome aberrations by their mutually exclusive effects on transcription.

BMC medical genomics Dec 21, 2017
BACKGROUND: Malignant tumors are typically caused by a conglomeration of genomic aberrations-including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemotherapies and targeted drug trea...
Transcription, Genetic Lung Neoplasms Humans Adenocarcinoma Machine Learning Mutation Neoplasms Genome, Human
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Identification of transcription factors that may reprogram lung adenocarcinoma.

Artificial intelligence in medicine Apr 1, 2017
BACKGROUND: Lung adenocarcinoma is one of most threatening disease to human health. Although many efforts have been devoted to its genetic study, few researches have been focused on the transcription factors which regulate tumor initiation and progre...
Adenocarcinoma of Lung Databases, Genetic Cell Transformation, Neoplastic Transcription, Genetic Gene Regulatory Networks Lung Neoplasms Computational Biology Epigenesis, Genetic Gene Expression Regulation, Neoplastic Signal Transduction Transcription Factors Humans Adenocarcinoma Artificial Intelligence
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Network stratification analysis for identifying function-specific network layers.

Molecular bioSystems Feb 16, 2016
A major challenge of systems biology is to capture the rewiring of biological functions (e.g. signaling pathways) in a molecular network. To address this problem, we proposed a novel computational framework, namely network stratification analysis (Ne...
Gene Expression Profiling Liver Neoplasms Carcinoma, Hepatocellular Protein Interaction Maps Gene Regulatory Networks Computational Biology Gene Expression Regulation, Neoplastic Humans Neural Networks, Computer Algorithms Disease Progression Gene Expression Regulation, Fungal Transcription, Genetic Signal Transduction Cluster Analysis Models, Biological
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A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems.

BMC systems biology Aug 28, 2015
BACKGROUND: There are increasing efforts to bring high-throughput systems biology techniques to bear on complex animal model systems, often with a goal of learning about underlying regulatory network structures (e.g., gene regulatory networks). Howev...
Malaria Transcription, Genetic Animals Macaca mulatta Machine Learning Gene Expression Profiling Systems Biology Bayes Theorem Algorithms
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