AIMC Topic: Transcription Factors

Clear Filters Showing 141 to 150 of 206 articles

Correcting the impact of docking pose generation error on binding affinity prediction.

BMC bioinformatics Sep 22, 2016
BACKGROUND: Pose generation error is usually quantified as the difference between the geometry of the pose generated by the docking software and that of the same molecule co-crystallised with the considered protein. Surprisingly, the impact of this e...
Ligands Protein Binding Protein Conformation Nuclear Proteins Humans Software Transcription Factors Molecular Docking Simulation Pyrazines
View on PubMed DOI

DiscMLA: An Efficient Discriminative Motif Learning Algorithm over High-Throughput Datasets.

IEEE/ACM transactions on computational biology and bioinformatics May 3, 2016
The transcription factors (TFs) can activate or suppress gene expression by binding to specific sites, hence are crucial regulatory elements for transcription. Recently, series of discriminative motif finders have been tailored to offering promising ...
Machine Learning Algorithms Cell Line, Tumor Computational Biology Humans High-Throughput Nucleotide Sequencing Nucleotide Motifs Chromatin Immunoprecipitation Transcription Factors Databases, Genetic Sequence Analysis, DNA Area Under Curve
View on PubMed DOI

g:Profiler-a web server for functional interpretation of gene lists (2016 update).

Nucleic acids research Apr 20, 2016
Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene ...
Computer Graphics Vertebrates Plants Fungi Insecta Gene Expression Regulation Molecular Sequence Annotation Gene Ontology Binding Sites User-Computer Interface Protein Binding Transcription Factors Internet Humans Animals Gene Expression Profiling
View on PubMed DOI

Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.

BMC bioinformatics Jan 11, 2016
BACKGROUND: A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular responses, including a tightly con...
Computer Simulation Gene Expression Profiling Systems Biology Signal Transduction Models, Theoretical Neural Networks, Computer Saccharomyces cerevisiae Proteins Transcription Factors Saccharomyces cerevisiae Gene Expression Regulation, Fungal
View on PubMed DOI

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.

BMC bioinformatics Jan 11, 2016
BACKGROUND: Understanding the mechanisms by which transcription factors (TF) are recruited to their physiological target sites is crucial for understanding gene regulation. DNA sequence intrinsic features such as predicted binding affinity are often ...
Gene Expression Regulation Algorithms Genome, Human Humans Histones Transcription Factors Machine Learning Cell Lineage Binding Sites Protein Processing, Post-Translational Chromatin DNA Chromatin Immunoprecipitation Nucleosomes
View on PubMed DOI

Transcriptomes of lineage-specific Drosophila neuroblasts profiled by genetic targeting and robotic sorting.

Development (Cambridge, England) Dec 23, 2015
A brain consists of numerous distinct neurons arising from a limited number of progenitors, called neuroblasts in Drosophila. Each neuroblast produces a specific neuronal lineage. To unravel the transcriptional networks that underlie the development ...
Cell Lineage Gene Expression Regulation, Developmental Gene Targeting Animals, Genetically Modified Drosophila Proteins Drosophila melanogaster Sequence Analysis, RNA Transcription Factors Robotics Neurons Animals Transcriptome Single-Cell Analysis
View on PubMed DOI

Effect of sprint training on resting serum irisin concentration - Sprint training once daily vs. twice every other day.

Metabolism: clinical and experimental Dec 19, 2015
OBJECTIVE: Exercise twice every other day has been shown to lead to increasing peroxisome proliferator receptor γ coactivator-1α (PGC-1α) expression (up-stream factor of irisin) via lowered muscle glycogen level during second of exercise compared wit...
Physical Endurance Adiponectin Physical Education and Training Fibronectins Humans Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha Interleukin-6 Running Glycogen Young Adult Molecular Weight Male Transcription Factors
View on PubMed DOI

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.
Humans Machine Learning Animals Oxidative Stress Cataract Lens, Crystalline Gene Expression Regulation Ataxia Telangiectasia Mutated Proteins Cell Proliferation Transcription Factors Apoptosis Epithelial Cells
View on PubMed DOI

SCIG: Machine learning uncovers cell identity genes in single cells by genetic sequence codes.

Nucleic acids research May 22, 2025
Deciphering cell identity genes is pivotal to understanding cell differentiation, development, and cell identity dysregulation involving diseases. Here, we introduce SCIG, a machine-learning method to uncover cell identity genes in single cells. In a...
Humans Endothelial Cells Epigenesis, Genetic Machine Learning Transcription Factors Single-Cell Analysis Cell Differentiation Gene Regulatory Networks Gene Expression Regulation
View on PubMed DOI

Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.

The Plant cell May 9, 2025
Systems biology aims to uncover gene regulatory networks (GRNs) for agricultural traits, but validating them in crops is challenging. We addressed this challenge by learning and validating model-to-crop transcription factor (TF) regulons governing ni...
Gene Expression Regulation, Plant Arabidopsis Regulon Machine Learning Gene Regulatory Networks Transcription Factors Zea mays Nitrogen Crops, Agricultural Plant Proteins
View on PubMed DOI
Popular Topics
Recent Journals