AIMC Topic: Gene Expression Regulation
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PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain.
Theoretical biology & medical modelling
Sep 22, 2015
BACKGROUND: Despite the unprecedented and increasing amount of data, relatively little progress has been made in molecular characterization of mechanisms underlying Parkinson's disease. In the area of Parkinson's research, there is a pressing need to...
Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task.
BMC bioinformatics
Jul 13, 2015
BACKGROUND: The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating system...
A tuberculosis ontology for host systems biology.
Tuberculosis (Edinburgh, Scotland)
Jun 30, 2015
A major hurdle facing tuberculosis (TB) investigators who want to utilize a rapidly growing body of data from both systems biology approaches and omics technologies is the lack of a standard vocabulary for data annotation and reporting. Lacking a mea...
Clustering high throughput biological data with B-MST, a minimum spanning tree based heuristic.
Computers in biology and medicine
Apr 14, 2015
To address important challenges in bioinformatics, high throughput data technologies are needed to interpret biological data efficiently and reliably. Clustering is widely used as a first step to interpreting high dimensional biological data, such as...
Identification of active transcriptional regulatory elements from GRO-seq data.
Nature methods
Mar 23, 2015
Modifications to the global run-on and sequencing (GRO-seq) protocol that enrich for 5'-capped RNAs can be used to reveal active transcriptional regulatory elements (TREs) with high accuracy. Here, we introduce discriminative regulatory-element detec...
Multifactor dimensionality reduction analysis to elucidate the cross-talk between one-carbon and xenobiotic metabolic pathways in multi-disease models.
Molecular biology reports
Feb 4, 2015
Putatively functional polymorphisms of one-carbon and xenobiotic metabolic pathways influence susceptibility for wide spectrum of diseases. The current study was aimed to explore gene-gene interactions among these two metabolic pathways in four disea...
Metabolic Networks and Pathways
Factor Analysis, Statistical
Lupus Erythematosus, Systemic
Coronary Artery Disease
Oxidoreductases
Genetic Predisposition to Disease
Sex Factors
Female
Humans
Transferases
Datasets as Topic
Polymorphism, Single Nucleotide
Breast Neoplasms
Carbon
Multifactor Dimensionality Reduction
Male
Gene Expression Regulation
Parkinson Disease
Case-Control Studies
Xenobiotics
Epistasis, Genetic
Inter-species pathway perturbation prediction via data-driven detection of functional homology.
Bioinformatics (Oxford, England)
Aug 22, 2014
MOTIVATION: Experiments in animal models are often conducted to infer how humans will respond to stimuli by assuming that the same biological pathways will be affected in both organisms. The limitations of this assumption were tested in the IMPROVER ...
Gene Expression Profiling
Systems Biology
Rats
Signal Transduction
Epithelial Cells
Phosphorylation
Translational Research, Biomedical
Phosphoproteins
Cells, Cultured
Cytokines
Databases, Factual
Animals
Humans
Artificial Intelligence
Software
Algorithms
Bronchi
Gene Expression Regulation
Models, Animal
Species Specificity
Oligonucleotide Array Sequence Analysis
CDKN1A and EGR1 are key genes for endoplasmic reticulum stress-induced ferroptosis in MASH.
Free radical biology & medicine
Aug 16, 2025
Metabolic dysfunction-associated steatohepatitis (MASH) is a complex liver disease whose pathogenesis involving endoplasmic reticulum (ER) stress and ferroptosis. However, key regulatory genes remain poorly understood, hindering the development of ef...
Gene Expression Regulation
Endoplasmic Reticulum Stress
Phenylenediamines
Early Growth Response Protein 1
Disease Models, Animal
Hep G2 Cells
Cyclin-Dependent Kinase Inhibitor p21
Mice, Inbred C57BL
Liver
Animals
Diet, High-Fat
Humans
Male
Ferroptosis
Mice
Non-alcoholic Fatty Liver Disease
Fatty Liver
Machine learning Reveals ATM and CNOT6L as critical factors in Cataract pathogenesis.
Experimental eye research
Aug 1, 2025
OBJECTIVE: Cataract, a common age-related blinding eye disease, has a complex pathogenesis. This study aims to identify key genes and potential mechanisms associated with cataracts, offering new targets and insights for its prevention and treatment.
Screening and preliminary analysis of antimicrobial peptide genes in Octopussinensis.
Fish & shellfish immunology
Aug 1, 2025
Antimicrobial peptides (AMPs) are small molecular peptides that widely exist in organisms to resist external microbial invasion and play a crucial role in the host's immune defense system. Owing to their functions of efficient broad-spectrum killing ...
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