Despite the fact that the human genome was sequenced ten years ago, there exists no database of cis-regulatory architecture that is validated conclusively by rigorous …
nheritable differences in DNA sequence are a major focus of the genetic community, as such differences are known to play a role in phenotypic variation, …
The human genome exhibits a rich structure resulting from a long history of genomic changes, including single base-pair mutations and larger scale rearrangements such as …
Structural features of proteins often serve as signatures of their biological function and molecular binding activity. Elucidating these structural and dynamical features is essential for …
Ten years ago, the first RNA-seq study was published. Since then over 200 thousand RNA-seq studies have been published, spanning many different organisms, tissue types, …
Abstract of Data-Driven Mathematical Analysis with Applications in Dynamical Systems, Biology, and Social Justice, by Rebecca Santorella Ph.D., Brown University, May 2022. As data becomes …
Biological systems must regulate complex gene transcriptional programs to mediate phenotypic response to diverse stimuli. Control of gene expression requires specific DNA sequence patterns called …
Natural selection causes genetic variants that increase fitness to spread within a population. Individuals bearing such alleles will leave behind more descendants and those descendants …
Anesthesia, in particular opioids, may have significant clinical implications in cancer. This effect cannot be generalized across different cancer types, and this likely holds true …
Despite the enormous amount of biological variation and technical uncertainty in sequence data, most phylogenetic workflows propagate a single point estimate throughout the numerous analysis …
Over the past decade, genome-wide associations studies (GWAS) and other methods have used human genetic data to successfully identify thousands of genomic elements underpinning complex …
Cancer is characterized by heterogeneity at multiple scales, with implications for diagnosis, prognosis, and treatment. Major advances in genomics have led to a proliferation of …
As data structures become larger and more complex, methods of data analysis must evolve to harness the most accurate insights. Inspired by the challenges presented …
Development is a complex process governed by coordinated gene regulation at a precise time and place. Uncovering how transcription factors (TFs) and their targets communicate …
In eukaryotes, DNA is first transcribed into precursor-messenger RNA (pre-mRNA) which is then followed by extensive RNA processing events. One such event is RNA splicing, …
Cancer results from an evolutionary process where somatic mutations occur and accumulate in a population of cells. There are many types of mutations that can …
The discipline of protein evolution aims to understand the principles and driving forces whereby new protein-coding genes, protein structures, and biological functions emerge due to …
Advances in sequencing technologies in the last decade have enabled us to profile various genomic features at the single-cell resolution, such as gene expression and …
Typically, gene interaction networks are expressed as graphs, storing pairwise interactions between genes. Because of the vast amount of literature on statistical graph inference, this …
The conversion of epithelial cells to mesenchymal cells, or the epithelial-mesenchymal transition (EMT), is a phenotypic program critical to embryonic development and wound healing, however, …
Cell developmental processes – both healthy and aberrant – are controlled by complex gene expression programs. While much work has been done to unravel the …
We present an intuitive strategy for predicting the effect of sequence variation on splicing. In contrast to transcriptional elements, splicing elements appear to be strongly …