Sparse Negative Binomial Signal Recovery for Genomic Variant Prediction in Diploid Species.

Structural variants (SVs) - such as insertions, deletions, and duplications of an individual's genome - are associated with genetic diseases and promotion of genetic diversity. Detecting SVs of an unknown genome is a mathematically challenging problem since SVs are rare and prone to low-coverage noise. Common approaches to detect SVs in an unknown genome require sequencing fragments of the genome, comparing them to a high-quality reference genome, and predicting SVs based on identified discordant fragments.

Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals.

Bacterial viruses (known as "phages") shape the ecology and evolution of microbial communities, making them promising targets for microbiome engineering. However, knowledge of phage biology is constrained because it remains difficult to study phage transmission dynamics within multi-member communities and living animal hosts. We therefore created "Phollow": a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution.

NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency.

The National Institute of Health (NIH) Library of integrated network-based cellular signatures (LINCS) program is premised on the generation of a publicly available data resource of cell-based biochemical responses or "signatures" to genetic or environmental perturbations. NeuroLINCS uses human inducible pluripotent stem cells (hiPSCs), derived from patients and healthy controls, and differentiated into motor neuron cell cultures. This multi-laboratory effort strives to establish i) robust multi-omic workflows for hiPSC and differentiated neuronal cultures, ii) public annotated data sets and iii) relevant and targetable biological pathways of spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS).

Associations between forensic loci and expression levels of neighboring genes may compromise medical privacy.

A set of 20 short tandem repeats (STRs) is used by the US criminal justice system to identify suspects and to maintain a database of genetic profiles for individuals who have been previously convicted or arrested. Some of these STRs were identified in the 1990s, with a preference for markers in putative gene deserts to avoid forensic profiles revealing protected medical information. We revisit that assumption, investigating whether forensic genetic profiles reveal information about gene-expression variation or potential medical information.