AIMC Topic: Gene Expression Regulation

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SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions.

BMC bioinformatics Jul 8, 2021
BACKGROUND: The topology of metabolic networks is both well-studied and remarkably well-conserved across many species. The regulation of these networks, however, is much more poorly characterized, though it is known to be divergent across organisms-t...
Machine Learning Algorithms Gene Regulatory Networks Gene Expression Regulation Metabolomics Metabolic Networks and Pathways
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Dual-Organ Transcriptomic Analysis of Rainbow Trout Infected With Through Co-Expression and Machine Learning.

Frontiers in immunology Jul 8, 2021
is a major pathogen that causes a high mortality rate in trout farms. However, systemic responses to the pathogen and its interactions with multiple organs during the course of infection have not been well described. In this study, dual-organ transc...
Ciliophora Infections Immunity, Innate Hymenostomatida Fish Diseases Gills Liver RNA-Seq Machine Learning Head Kidney Gene Expression Regulation Virulence Factors Gene Regulatory Networks Animals Oncorhynchus mykiss Host-Pathogen Interactions Virulence Signal Transduction Transcriptome
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A deep learning algorithm to translate and classify cardiac electrophysiology.

eLife Jul 2, 2021
The development of induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) has been a critical in vitro advance in the study of patient-specific physiology, pathophysiology, and pharmacology. We designed a new deep learning multitask network ...
Action Potentials Cell Differentiation Models, Biological Sulfonamides Algorithms Electrophysiological Phenomena Humans Computer Simulation Induced Pluripotent Stem Cells Deep Learning Electrophysiologic Techniques, Cardiac Phenethylamines ERG1 Potassium Channel Myocytes, Cardiac Gene Expression Regulation
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Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact.

Nature communications Jun 8, 2021
Chromatin architecture plays an important role in gene regulation. Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. However, leveraging these comple...
Neural Networks, Computer Deep Learning DNA Multigene Family Gene Expression Regulation Algorithms Computer Simulation Animals Enhancer Elements, Genetic Genome, Insect Chromatin Gene Silencing Promoter Regions, Genetic Drosophila melanogaster Transcription, Genetic
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Finding gene network topologies for given biological function with recurrent neural network.

Nature communications May 25, 2021
Searching for possible biochemical networks that perform a certain function is a challenge in systems biology. For simple functions and small networks, this can be achieved through an exhaustive search of the network topology space. However, it is di...
Gene Regulatory Networks Computational Biology Models, Genetic Gene Expression Regulation Algorithms Computer Simulation Humans Reproducibility of Results Neural Networks, Computer Animals Software
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MichiGAN: sampling from disentangled representations of single-cell data using generative adversarial networks.

Genome biology May 20, 2021
Deep generative models such as variational autoencoders (VAEs) and generative adversarial networks (GANs) generate and manipulate high-dimensional images. We systematically assess the complementary strengths and weaknesses of these models on single-c...
Neural Networks, Computer Algorithms Humans RNA-Seq Gene Expression Regulation Statistics, Nonparametric Computer Simulation Gene Expression Profiling Single-Cell Analysis
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Feasibility of predicting allele specific expression from DNA sequencing using machine learning.

Scientific reports May 19, 2021
Allele specific expression (ASE) concerns divergent expression quantity of alternative alleles and is measured by RNA sequencing. Multiple studies show that ASE plays a role in hereditary diseases by modulating penetrance or phenotype severity. Howev...
Alleles Gene Expression Regulation Genome, Human Machine Learning ROC Curve Humans Polymorphism, Single Nucleotide Bias Models, Genetic Feasibility Studies Sequence Analysis, DNA
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Comparison of machine-learning methodologies for accurate diagnosis of sepsis using microarray gene expression data.

PloS one May 17, 2021
We investigate the feasibility of molecular-level sample classification of sepsis using microarray gene expression data merged by in silico meta-analysis. Publicly available data series were extracted from NCBI Gene Expression Omnibus and EMBL-EBI Ar...
Humans Machine Learning Sepsis Gene Expression Regulation Female Oligonucleotide Array Sequence Analysis Male Databases, Nucleic Acid Gene Expression Profiling
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Neural network aided approximation and parameter inference of non-Markovian models of gene expression.

Nature communications May 11, 2021
Non-Markovian models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parame...
Gene Expression Regulation Transcription, Genetic Stochastic Processes Feedback, Physiological Neural Networks, Computer Computer Simulation Models, Genetic Kinetics
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Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities.

Genome biology May 3, 2021
A complete understanding of biological processes requires synthesizing information across heterogeneous modalities, such as age, disease status, or gene expression. Technological advances in single-cell profiling have enabled researchers to assay mul...
Organ Specificity Chromatin Chromatin Assembly and Disassembly Single-Cell Analysis Computational Biology Gene Expression Regulation Gene Expression Profiling Transcriptome Machine Learning
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