Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
DNA accessibility has been a powerful tool in locating active regulatory elements in a cell type, but dissecting the combinatorial logic within these regulatory elements has been a continued challenge in the field. Deep learning models have been show...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
The plant cytoskeleton is instrumental in cellular processes such as cell growth, differentiation, and immune response. Microtubules, in particular, play a crucial role in morphogenesis by governing the deposition of plant cell wall polysaccharides a...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Genome-wide DNA methylomes have contributed greatly to tumor detection and subclassification. However, interpreting the biological impact of the DNA methylome at the individual gene level remains a challenge. MethylationToActivity (M2A) is a pipeline...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Nearly all lineages of land plants have experienced at least one whole-genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD-paleologs-c...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Collective cell migration is crucial for a variety of pathophysiological processes including embryonic development, wound healing, carcinoma invasion, and sprouting angiogenesis. The behavior of leading and following cells during migration is highly ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
The visual classification of cell images according to differences in the spatial patterns of subcellular structure is an important methodology in cell and developmental biology. Experimental perturbation of cell function can induce changes in the spa...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Today, -omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ or tissue sample, allow for an unbiased, comprehensive genome-level analysis of complex diseas...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Novel design of proteins to target receptors for treatment or tissue augmentation has come to the fore owing to advancements in computing power, modeling frameworks, and translational successes. Shorter proteins, or peptides, can offer combinatorial ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Advances in high-throughput sequencing technologies have enabled comprehensive sequencing of the immune repertoire. Since repertoire analysis can help to explain the relationship between the immune system and diseases, several methods have been devel...