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...
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...
Proceedings of the National Academy of Sciences of the United States of America
Jul 6, 2021
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 ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
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...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
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 ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
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 ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
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...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
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...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
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 ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
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...
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