A method for estimating coherence of molecular mechanisms in major human disease and traits.

Background: Phenotypes such as height and intelligence, are thought to be a product of the collective effects of multiple phenotype-associated genes and interactions among their protein products. High/low degree of interactions is suggestive of coherent/random molecular mechanisms, respectively. Comparing the degree of interactions may help to better understand the coherence of phenotype-specific molecular mechanisms and the potential for therapeutic intervention.

Correction to: SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering.

An amendment to this paper has been published and can be accessed via the original article.

SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering.

Background: The three-dimensional (3D) structure of the genome plays a crucial role in gene expression regulation. Chromatin conformation capture technologies (Hi-C) have revealed that the genome is organized in a hierarchy of topologically associated domains (TADs), sub-TADs, and chromatin loops. Identifying such hierarchical structures is a critical step in understanding genome regulation.

TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains.

Recent research using chromatin conformation capture technologies, such as Hi-C, has demonstrated the importance of topologically associated domains (TADs) and smaller chromatin loops, collectively referred hereafter as "interacting domains." Many such domains change during development or disease, and exhibit cell- and condition-specific differences. Quantification of the dynamic behavior of interacting domains will help to better understand genome regulation.

Prevalence of hematologic toxicity from copperhead envenomation: an observational study.

Copperhead snakes () are considered as the least toxic of the North American pit vipers. The reported incidence of coagulopathy from copperhead envenomation is variable, possibly secondary to regional variation in subspecies and venom potency. Coagulation studies are often obtained when evaluating for the coagulopathic effects of copperhead venom, but the clinical utility of these indices is unclear.

multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments.

Motivation: With the development of chromatin conformation capture technology and its high-throughput derivative Hi-C sequencing, studies of the three-dimensional interactome of the genome that involve multiple Hi-C datasets are becoming available. To account for the technology-driven biases unique to each dataset, there is a distinct need for methods to jointly normalize multiple Hi-C datasets. Previous attempts at removing biases from Hi-C data have made use of techniques which normalize individual Hi-C datasets, or, at best, jointly normalize two datasets.

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets.

Background: Changes in spatial chromatin interactions are now emerging as a unifying mechanism orchestrating the regulation of gene expression. Hi-C sequencing technology allows insight into chromatin interactions on a genome-wide scale. However, Hi-C data contains many DNA sequence- and technology-driven biases.

Making Football Safer: Assessing the Current National Football League Policy on the Type of Helmets Allowed on the Playing Field.

In an effort to reduce concussions in football, a helmet safety-rating system was developed in 2011 that rated helmets based on their ability to reduce g-forces experienced by the head across a range of impact forces measured on the playing field. Although this was considered a major step in making the game safer, the National Football League (NFL) continues to allow players the right to choose what helmet to wear during play. This prompted us to ask: What helmets do NFL players wear and does this helmet policy make the game safer? Accordingly, we identified the helmets worn by nearly 1000 players on Week 13 of the 2015-2016 season and Week 1 of the 2016-2017 season.

Quantifying Variation in Gait Features from Wearable Inertial Sensors Using Mixed Effects Models.

The emerging technology of wearable inertial sensors has shown its advantages in collecting continuous longitudinal gait data outside laboratories. This freedom also presents challenges in collecting high-fidelity gait data. In the free-living environment, without constant supervision from researchers, sensor-based gait features are susceptible to variation from confounding factors such as gait speed and mounting uncertainty, which are challenging to control or estimate.