Alex J. Lee

The Dayhoff Atlas: scaling sequence diversity for improved protein generation

Kevin Yang, Sarah Alamdari, Alex J. Lee, Kaeli Kaymak-Loveless et autres

Abstract Organized information powers modern biology, a framework pioneered by Margaret Dayhoff’s Atlas of Protein Sequence and Structure and advanced by today’s databases and computational methods. Here, we extend this paradigm for the AI era, presenting the Dayhoff Atlas of protein sequence …

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Analytical quality control in targeted lipidomics: Evaluating the performance of commercial plasma as a surrogate for pooled study samples

Alanah Grant-St James, Alex J. Lee, Julien Wist, Ferdous Ahmed Sohel et autres

BACKGROUND: Pooled quality control (PQC) samples are the gold standard for data quality monitoring in metabolic phenotyping studies. Typically composed of equal parts from all study samples, PQCs can be challenging to generate in large cohorts or when sample volumes are low. …

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Antifungal Activity of Disalt of Epipyrone A from Epicoccum nigrum Likely via Disrupted Fatty Acid Elongation and Sphingolipid Biosynthesis

Alex J. Lee, Joseph Hammond, Jeffrey P. Sheridan, Simon Swift et autres

Multidrug-resistant fungal pathogens and antifungal drug toxicity have challenged our current ability to fight fungal infections. Therefore, there is a strong global demand for novel antifungal molecules with the distinct mode of action and specificity to service the medical and agricultural sectors. …

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Cross-Validation of Metabolic Phenotypes in SARS-CoV-2 Infected Subpopulations Using Targeted Liquid Chromatography–Mass Spectrometry (LC-MS)

Luke Whiley, Nathan G. Lawler, Annie Xu Zeng, Alex J. Lee et autres

High Resolution Image Download MS PowerPoint Slide To ensure biological validity in metabolic phenotyping, findings must be replicated in independent sample sets. Targeted workflows have long been heralded as ideal platforms for such validation due to their robust quantitative capability. We evaluated …

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Overview of the Nomenclature and Network of Contributors to the Development of Bioreactors for Human Gut Simulation Using Bibliometric Tools: A Fragmented Landscape

Janeth Sanabria, Siobhon L. Egan, Reika Masuda, Alex J. Lee et autres

The evolution of complex in vitro models of the human gastrointestinal system to interrogate the biochemical functionality of the gut microbiome has augmented our understanding of its role in human physiology and pathology. With 5718 authors from 52 countries, gut bioreactor research …

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First use of grape waste-derived building blocks to yield antimicrobial materials

Rebecca E. Jelley, Alex J. Lee, Zoran D. Zujovic, Silas Granato Villas-Bôas et autres

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Epipyrone A, a Broad-Spectrum Antifungal Compound Produced by Epicoccum nigrum ICMP 19927

Alex J. Lee, Melissa M. Cadelis, Simon Swift, Brent R. Copp et autres

We have isolated a filamentous fungus that actively secretes a pigmented exudate when growing on agar plates. The fungus was identified as being a strain of Epicoccum nigrum. The fungal exudate presented strong antifungal activity against both yeasts and filamentous fungi, and …

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