Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.

Oligopool synthesis and next-generation sequencing enable the construction and characterization of large libraries of designed genetic parts and systems. As library sizes grow, it becomes computationally challenging to optimally design large numbers of primer binding sites, barcode sequences, and overlap regions to obtain efficient assemblies and precise measurements. We present the Oligopool Calculator, an end-to-end suite of algorithms and data structures that rapidly designs many thousands of oligonucleotides within an oligopool and rapidly analyzes many billions of barcoded sequencing reads.

Whole-genome sequencing of carbapenem-resistant Enterobacterales isolates in southeast Louisiana reveals persistent genetic clusters spanning multiple locations.

Background: We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions in the Ochsner Health network in southeast Louisiana.

Methods: Short genomic reads were generated using Illumina sequencing and assembled for each isolate. Isolates were classified as Enterobacter spp.

Distinct HIV-1 Population Structure across Meningeal and Peripheral T Cells and Macrophage Lineage Cells.

HIV-1 sequence population structure among brain and nonbrain cellular compartments is incompletely understood. Here, we compared proviral and high-quality consensus single-molecule real-time (SMRT) sequences derived from CD3 T cells and CD14 macrophage lineage cells from meningeal or peripheral (spleen, blood) tissues obtained at autopsy from two individuals with viral suppression on antiretroviral therapy (ART). Phylogenetic analyses showed strong evidence of population structure between CD3 and CD14 virus populations.

Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria.

Transcription rates are regulated by the interactions between RNA polymerase, sigma factor, and promoter DNA sequences in bacteria. However, it remains unclear how non-canonical sequence motifs collectively control transcription rates. Here, we combine massively parallel assays, biophysics, and machine learning to develop a 346-parameter model that predicts site-specific transcription initiation rates for any σ promoter sequence, validated across 22132 bacterial promoters with diverse sequences.

SARS-CoV-2 genomic surveillance as an evidence-based infection control approach in an offshore petroleum employee population.

Background: Industrial hygienists (IH) in the oil and gas business instituted an extraordinary number of safety protocols to limit spread of SARS-CoV-2 onto offshore platforms in the Gulf of Mexico. We used genomic surveillance to provide actionable information concerning the efficacy of their efforts.

Methods: Over 6 months, employees at a single company were serology and PCR tested during a 1-5 day predeployment quarantine and when postdeployment symptoms were reported.