Methods in molecular biology (Clifton, N.J.)
34590279
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...
Rational protein design aims at the targeted modification of existing proteins. To reach this goal, software suites like Rosetta propose sequences to introduce the desired properties. Challenging design problems necessitate the representation of a pr...
Methods in molecular biology (Clifton, N.J.)
33733366
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.)
33733365
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.)
33733364
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.)
33733363
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...
Proceedings of the National Academy of Sciences of the United States of America
34187888
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 ...
Drug resistance mutations (DRMs) appear in HIV under treatment pressure. DRMs are commonly transmitted to naive patients. The standard approach to reveal new DRMs is to test for significant frequency differences of mutations between treated and naive...
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...
BACKGROUND: Identifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionality reduction (MDR) is a popul...