AIMC Topic: Epistasis, Genetic

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Deep learning of gene relationships from single cell time-course expression data.

Briefings in bioinformatics
Time-course gene-expression data have been widely used to infer regulatory and signaling relationships between genes. Most of the widely used methods for such analysis were developed for bulk expression data. Single cell RNA-Seq (scRNA-Seq) data offe...

Revisiting genome-wide association studies from statistical modelling to machine learning.

Briefings in bioinformatics
Over the last decade, genome-wide association studies (GWAS) have discovered thousands of genetic variants underlying complex human diseases and agriculturally important traits. These findings have been utilized to dissect the biological basis of dis...

Deep representation learning improves prediction of LacI-mediated transcriptional repression.

Proceedings of the National Academy of Sciences of the United States of America
Recent progress in DNA synthesis and sequencing technology has enabled systematic studies of protein function at a massive scale. We explore a deep mutational scanning study that measured the transcriptional repression function of 43,669 variants of ...

Machine Learning to Identify Gene Interactions from High-Throughput Mutant Crosses.

Methods in molecular biology (Clifton, N.J.)
Advances in molecular genetics through high-throughput gene mutagenesis and genetic crossing have enabled gene interaction mapping across whole genomes. Detecting gene interactions in even small microbial genomes relies on measuring growth phenotypes...

Epistasis Analysis: Classification Through Machine Learning Methods.

Methods in molecular biology (Clifton, N.J.)
Complex disease is different from Mendelian disorders. Its development usually involves the interaction of multiple genes or the interaction between genes and the environment (i.e. epistasis). Although the high-throughput sequencing technologies for ...

Epistasis Detection Based on Epi-GTBN.

Methods in molecular biology (Clifton, N.J.)
Epistasis detection is a hot topic in bioinformatics due to its relevance to the detection of specific phenotypic traits and gene-gene interactions. Here, we present a step-by-step protocol to apply Epi-GTBN, a machine learning-based method based on ...

A Belief Degree-Associated Fuzzy Multifactor Dimensionality Reduction Framework for Epistasis Detection.

Methods in molecular biology (Clifton, N.J.)
Epistasis is a challenge in prediction, classification, and suspicion of human genetic diseases. Many technologies, methods, and tools have been developed for epistasis detection. Multifactor dimensionality reduction (MDR) is the method commonly used...

Protocol for Epistasis Detection with Machine Learning Using GenEpi Package.

Methods in molecular biology (Clifton, N.J.)
To develop medical treatments and prevention, the association between disease and genetic variants needs to be identified. The main goal of genome-wide association study (GWAS) is to discover the underlying reason for vulnerability to disease and uti...

Deep Neural Networks for Epistatic Sequence Analysis.

Methods in molecular biology (Clifton, N.J.)
We report a step-by-step protocol to use pysster, a TensorFlow-based package for building deep neural networks on a broad range of epistatic sequences such as DNA, RNA, or annotated secondary structure sequences. Pysster provides users comprehensive ...

Brief Survey on Machine Learning in Epistasis.

Methods in molecular biology (Clifton, N.J.)
In biology, the term "epistasis" indicates the effect of the interaction of a gene with another gene. A gene can interact with an independently sorted gene, located far away on the chromosome or on an entirely different chromosome, and this interacti...