AIMC Topic: Gene Expression Regulation

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Deep protein representations enable recombinant protein expression prediction.

Computational biology and chemistry Oct 27, 2021
A crucial process in the production of industrial enzymes is recombinant gene expression, which aims to induce enzyme overexpression of the genes in a host microbe. Current approaches for securing overexpression rely on molecular tools such as adjust...
Machine Learning Recombinant Proteins Bacillus subtilis Bacterial Proteins Gene Expression Regulation
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Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival.

International journal of molecular sciences Oct 5, 2021
Bisphenols are important environmental pollutants that are extensively studied due to different detrimental effects, while the molecular mechanisms behind these effects are less well understood. Like other environmental pollutants, bisphenols are bei...
Gene Expression Profiling Benzhydryl Compounds Mice Datasets as Topic Apoptosis Gene Expression Regulation Liver Air Pollutants, Occupational Cell Survival Models, Statistical Phenols Meta-Analysis as Topic Machine Learning Biomarkers Animals Male
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Effective gene expression prediction from sequence by integrating long-range interactions.

Nature methods Oct 4, 2021
How noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human genetics depend on improved solutions. Here, we report substantially improved gene expression prediction a...
Humans Machine Learning Animals Mice DNA Gene Expression Regulation Nerve Net Genome Quantitative Trait Loci Genomics Epigenesis, Genetic Databases, Genetic Cell Line
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Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies.

Nature communications Sep 10, 2021
Deep neural networks (DNNs) capture complex relationships among variables, however, because they require copious samples, their potential has yet to be fully tapped for understanding relationships between gene expression and human phenotypes. Here we...
Gene Expression Regulation Deep Learning Cohort Studies RNA-Seq Mice Microglia Alzheimer Disease Sex Factors Datasets as Topic Aged Aged, 80 and over Animals Male Humans Brain Female
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ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.

PLoS computational biology Sep 7, 2021
Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understan...
Computational Biology Models, Genetic Mutation Gene Expression Regulation Humans Deep Learning Genome-Wide Association Study Genes, Reporter Regulatory Sequences, Nucleic Acid Transcription Initiation, Genetic Genome, Human Promoter Regions, Genetic Molecular Sequence Annotation Enhancer Elements, Genetic
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Gene Ontology representation for transcription factor functions.

Biochimica et biophysica acta. Gene regulatory mechanisms Aug 28, 2021
Transcription plays a central role in defining the identity and functionalities of cells, as well as in their responses to changes in the cellular environment. The Gene Ontology (GO) provides a rigorously defined set of concepts that describe the fun...
Transcription Factors Databases, Genetic Gene Expression Regulation Molecular Sequence Annotation Gene Ontology Computational Biology
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Sequence Ontology terminology for gene regulation.

Biochimica et biophysica acta. Gene regulatory mechanisms Aug 11, 2021
The Sequence Ontology (SO) is a structured, controlled vocabulary that provides terms and definitions for genomic annotation. The Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) initiative has gathered input from many groups of res...
Locus Control Region Biological Ontologies Gene Expression Regulation Regulatory Elements, Transcriptional
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Identification of conserved transcriptome features between humans and Drosophila in the aging brain utilizing machine learning on combined data from the NIH Sequence Read Archive.

PloS one Aug 11, 2021
Aging is universal, yet characterizing the molecular changes that occur in aging which lead to an increased risk for neurological disease remains a challenging problem. Aging affects the prefrontal cortex (PFC), which governs executive function, lear...
Middle Aged Transcriptome Aged United States National Institutes of Health (U.S.) Humans Adult Signal Transduction Databases, Genetic Animals Machine Learning Genome, Insect Gene Expression Regulation Algorithms Aging Drosophila melanogaster Brain Conserved Sequence
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The Emerging Role of Long Non-Coding RNAs and MicroRNAs in Neurodegenerative Diseases: A Perspective of Machine Learning.

Biomolecules Jul 31, 2021
Neurodegenerative diseases (NDs) are characterized by progressive neuronal dysfunction and death of brain cells population. As the early manifestations of NDs are similar, their symptoms are difficult to distinguish, making the timely detection and d...
Information Dissemination Gene Expression Regulation Software Computational Biology Signal Transduction Amyotrophic Lateral Sclerosis Parkinson Disease Humans Databases, Genetic MicroRNAs Internet Machine Learning Neurons RNA, Long Noncoding Nerve Tissue Proteins Alzheimer Disease
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Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease.

Nature communications Jul 12, 2021
Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here w...
Cohort Studies Mice Treatment Outcome Disease Models, Animal Mice, Inbred C57BL Intestinal Mucosa Mice, Knockout AMP-Activated Protein Kinases Machine Learning Inflammatory Bowel Diseases Reproducibility of Results Animals Humans Artificial Intelligence Dextran Sulfate Multigene Family Colitis Gene Expression Regulation Organoids Molecular Targeted Therapy Likelihood Functions
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