Biology subjects

Lefkowitz, E.

Publications and source records attributed to Lefkowitz, E..

3 recordsLinked to original sources

bioRxiv2026

First community challenge for automated virus taxonomy

The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all fifteen ranks of the virus taxonomy. We led an open community challenge for the computational taxonomic classification of viruses and assembled a dataset of virus sequences combining expert-curated and metagenomic sequences. Seventeen teams contributed a total of thirty-four automated, fully reproducible classification pipelines. Most tools correctly assigned viruses belonging to established species, genera, or families, but viruses that are unclassified at those lower ranks remain challenging. This study provides datasets, open-source software, novel approaches, and recommendations to benchmark computational taxonomic classification of viruses, and support organizing the many viruses discovered in big omics data.

microbiology↗

bioRxiv2026

Programmatic access to ICTV virus taxonomy through a public ontology API

The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. To address this, we developed a public and sustainable solution leveraging ontology-based APIs. Successive ICTV Master Species List (MSL) releases were transformed into a structured ontology and deployed as a unified representation through the Ontology Lookup Service (OLS). The framework also provides ICTV-NCBI mappings and helper libraries for integration into downstream systems. This enables, for the first time, public programmatic retrieval of current and historical virological taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness. Key pointsO_LIICTV provides the official taxonomy for classifying viruses and naming virus taxa, but lacks standardised programmatic access. C_LIO_LITransforming ICTV data into an ontology enables semantic, machine-actionable access across releases via ontology-based APIs. C_LIO_LIICTV-NCBI mappings support interoperability across bioinformatics resources. C_LIO_LIThe framework enables programmatic resolution of current and historical viral taxa. C_LIO_LIThis approach provides a reusable model for exposing biological datasets through public APIs. C_LI

bioinformatics↗

bioRxiv2025

Development of a Customizable Pacing Protocol to Induce Persistent Atrial Fibrillation in Swine

IntroductionPersistent atrial fibrillation (AFib) research is dependent on large animal models to understand pathogenesis and test new treatments and therapeutic techniques. While various methods have been established to induce persistent AFib in large animals, including electrical, surgical, pharmacological, and genetic approaches, each has distinct limitations. The most recent being the device industry no longer providing off-target rapid atrial pacing programs for use in animals. This challenge requires the development of a new accessible model of inducing atrial fibrillation in large animals. Methods UsedWe developed a wireless pacing system using a Raspberry Pi Pico W microcontroller (Pico) programmed for variable pacing frequencies. The device is powered by a subcutaneously implanted 9V battery. The Picos built-in Wi-Fi capabilities enable remote connection and real-time adjustment of pacing frequency output. This protocol describes a prospective study in which swine will undergo chronic right atrial pacing for 3-4 weeks to induce persistent AFib. We tested our device in a domestic swine. Vascular access was established through the left jugular vein and an active fixation pacing lead (Medtronic 5076) was implanted under fluoroscopic guidance in the right atrium. Proper lead positioning and pacing function were confirmed through electrocardiographic monitoring of both atrial and ventricular capture. Preliminary ResultsOscilloscope testing demonstrated frequency and voltage output concordant with the programmed frequencies while real-time adjustments were made through the Wi-Fi interface. A cardiac pacing wire was placed in the right ventricle then relocated to the right atrium and successful pacing with capture was verified using an electrocardiogram. ConclusionsThis protocol will provide a system capable of capturing atrial tissue with confirmed wireless power transfer capabilities that has minimal tissue heating and is physiologically safe. Combined with our literature review findings that electrical atrial pacing methods are most effective for inducing persistent AFib, our device provides researchers with the potential for an improved tool for creating large animal models of persistent AFib.

bioengineering↗