AIMC Topic: Gene Expression Regulation

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Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task.

BMC bioinformatics
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)
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
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
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...

Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Bioinformatics (Oxford, England)
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 ...

FASTK post-transcriptional regulators - a 'FAST-tracK' in mitochondrial gene expression.

Biochemical Society transactions
Fas-activated serine/threonine kinase (FASTK) proteins comprise one of the largest families of mitochondrial post-transcriptional regulators. Members are classified based on their conserved C-terminus, which shows homology with the PD-(D/E)XK superfa...

[Synthetic promoters: theory, design, and prospects].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Synthetic promoters are novel promoters artificially designed and do not exist in nature. They can initiate the expression of target genes with specific regulatory modes, offering advantages such as high expression efficiency, precise regulation, and...

Discovery of protein lactylation-associated biomarkers and their potential pathogenic mechanisms in recurrent spontaneous abortion.

International journal of biological macromolecules
Protein lactylation plays a critical regulatory role in various human diseases; however, its function in recurrent spontaneous abortion (RSA) remains unclear. In this study, we integrated scRNA-seq (GSE214607), bulk RNA-seq (GSE26787 and GSE165004) d...

CDKN1A and EGR1 are key genes for endoplasmic reticulum stress-induced ferroptosis in MASH.

Free radical biology & medicine
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...