First Case of 2019 Novel Coronavirus in the United States | The New England Journal of Medicine
An outbreak of novel coronavirus (2019-nCoV) that began in Wuhan, China, has spread rapidly, with cases now confirmed in multiple countries. Researchers report the first case of 2019-nCoV infection confirmed in the United States and describe the identification, diagnosis, clinical course, and management of the case, including the patient’s initial mild symptoms at presentation with progression to pneumonia on day 9 of illness. This case highlights the importance of close coordination between clinicians and public health authorities at the local, state, and federal levels, as well as the need for rapid dissemination of clinical information related to the care of patients with this emerging infection.
Sapling: Accelerating Suffix Array Queries with Learned Data Models | bioRxiv
As genomic data becomes more abundant, efficient algorithms and data structures for sequence alignment become increasingly important. The suffix array is a widely used data structure to accelerate alignment, but the binary search algorithm used to query it requires widespread memory accesses, causing a large number of cache misses on large datasets. Sapling is an algorithm for sequence alignment which uses a learned data model to augment the suffix array and enable faster queries.
decorate: Differential Epigenetic Correlation Test | Bioinformatics
Identifying correlated epigenetic features and finding differences in correlation between individuals with disease compared to controls can give novel insight into disease biology. This framework has been successful in analysis of gene expression data, but application to epigenetic data has been limited by the computational cost, lack of scalable software and lack of robust statistical tests. Decorate, differential epigenetic correlation test, identifies correlated epigenetic features and finds clusters of features that are differentially correlated between two or more subsets of the data.
