microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data.

Microbial research generates vast and complex data from diverse omics technologies, necessitating innovative analytical solutions. microGalaxy (Galaxy for Microbiology) addresses these needs with a user-friendly platform that integrates >220 tool suites and >65 curated workflows for microbial analyses, including taxonomic profiling, assembly, annotation, and functional analysis. Hosted on the main EU Galaxy server (microgalaxy.

Comparative genomics of the sexually transmitted parasite reveals relaxed and convergent evolution and genes involved in spillover from birds to humans.

is the causative agent of the venereal disease trichomoniasis which infects men and women globally and is associated with serious outcomes during pregnancy and cancers of the human reproductive tract. Trichomonads parasitize a range of hosts in addition to humans including birds, livestock, and domesticated animals. Recent genetic analysis of trichomonads recovered from columbid birds has provided evidence that these parasite species undergo frequent host-switching, and that a current epoch spillover event from columbids likely gave rise to in humans.

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.

Modern maize (Zea mays ssp. mays) was domesticated from Teosinte parviglumis (Zea mays ssp. parviglumis), with subsequent introgressions from Teosinte mexicana (Zea mays ssp.

Employing Simulated Participants to Develop Communication Skills in Medical Education: A Systematic Review.

Simulated participants (SPs) are often employed to teach communication skills in medical education. Although there is a large number of qualitative and/or noncomparative studies in this field, there is no current evidence for the effectiveness of this teaching method based on quantitative comparative meta-data. The aim of this review was to evaluate the effectiveness of SP-based teaching on patient-centered communication skills in medical education compared with traditional teaching formats such as lecture or peer role play focusing on quantitative and comparative data.

AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.

Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows.

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.

The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy.

BEATRICE: Bayesian fine-mapping from summary data using deep variational inference.

Motivation: We introduce a novel framework BEATRICE to identify putative causal variants from GWAS statistics. Identifying causal variants is challenging due to their sparsity and high correlation in the nearby regions. To account for these challenges, we rely on a hierarchical Bayesian model that imposes a binary concrete prior on the set of causal variants.

Differences in activity and stability drive transposable element variation in tropical and temperate maize.

Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.

Patient-Reported Outcome Measure Development and Validation: A Primer for Clinicians.

A comprehensive definition of health includes the assessment of patient experiences of a disease and its treatment. These patient experiences are best captured by standardized patient-reported outcome (PRO) instruments. A PRO is reported directly by the patient (or caregiver) and provides the patient's perspective into how a disease and its treatment impact their lives.

Neighborhood Deprivation and Crime on Asthma Exacerbations and Utilization in Mild Adult Asthma.

Background: Social determinants of health have a significant impact on asthma outcomes, and factors such as income level and neighborhood environment have crucial roles.

Objective: This study aimed to assess the impact of the Neighborhood Deprivation Index (NDI) and Total Crime Index (TCI) on acute asthma exacerbation (AAE) and asthma-related emergency department and urgent care (ED/UC) visits in adults with mild asthma.

Methods: This retrospective cohort study used administrative data from Kaiser Permanente Southern California among 198,873 adult patients with mild asthma between January 1, 2013 and December 31, 2018.

ModDotPlot-rapid and interactive visualization of tandem repeats.

Motivation: A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy.

Convergent evolution of plant prickles by repeated gene co-option over deep time.

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles-sharp epidermal projections-that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus .

Correction to "Interplay of Local pH and Cation Hydrolysis during Electrochemical CO Reduction Visualized by In Operando Chemical Shift-Resolved Magnetic Resonance Imaging".

[This corrects the article DOI: 10.1021/acs.jpcc.

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.

Knowledge of locations and activities of -regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project.

MEM-based pangenome indexing for -mer queries.

Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations. Methods based on graph pangenomes require a computationally expensive multiple-alignment step, which can leave out some variation.

Risk Factors for Acute Asthma Exacerbations in Adults With Mild Asthma.

Background: Although individuals with mild asthma account for 30% to 40% of acute asthma exacerbations (AAEs), relatively little attention has been paid to risk factors for AAEs in this population.

Objective: To identify risk factors associated with AAEs in patients with mild asthma.

Methods: This was a retrospective cohort study.

ModDotPlot-Rapid and interactive visualization of complex repeats.

Motivation: A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy.

Real-world assessment of anaphylaxis and eosinophilic esophagitis with 12 SQ house dust mite SLIT-tablet sublingual immunotherapy.

Background: Sublingual immunotherapy (SLIT) with 12 SQ house dust mile SLIT-tablet (HDM SLIT-tablet) for dust mite-induced perennial allergic rhinitis is reported as effective and safe. Although serious allergic reactions (SARs) and eosinophilic esophagitis (EoE) have infrequently occurred under trial conditions, the safety of HDM SLIT-tablet challenge under real-world conditions is unknown.

Objective: Our aim was to estimate the incidence of SARs and EoE due to HDM SLIT-tablet challenge.

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.

Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.