[HTML][HTML] The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

…, AJ Lee, BZ Kacsoh, AW Crocker, KA Lewis… - Genome biology, 2019 - Springer
Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global,
community-driven effort to evaluate and improve the computational annotation of protein …

[HTML][HTML] Unsupervised extraction of stable expression signatures from public compendia with an ensemble of neural networks

J Tan, G Doing, KA Lewis, CE Price, KM Chen… - Cell systems, 2017 - cell.com
Cross-experiment comparisons in public data compendia are challenged by unmatched
conditions and technical noise. The ADAGE method, which performs unsupervised integration …

Social cooperativity of bacteria during reversible surface attachment in young biofilms: a quantitative comparison of Pseudomonas aeruginosa PA14 and PAO1

…, AE Baker, RR Bennett, CR Armbruster, KA Lewis… - MBio, 2020 - Am Soc Microbiol
What are bacteria doing during “reversible attachment,” the period of transient surface
attachment when they initially engage a surface, besides attaching themselves to the surface? …

[HTML][HTML] Regulation of Pseudomonas aeruginosa-Mediated Neutrophil Extracellular Traps

…, J Theprungsirikul, KA Lewis… - Frontiers in …, 2019 - frontiersin.org
Pseudomonas aeruginosa is the most prevalent opportunistic pathogen in the airways of
cystic fibrosis (CF) patients. The pulmonary disorder is characterized by recurrent microbial …

Nonmotile Subpopulations of Pseudomonas aeruginosa Repress Flagellar Motility in Motile Cells through a Type IV Pilus- and Pel-Dependent Mechanism

KA Lewis, DM Vermilyea, SS Webster… - Journal of …, 2022 - Am Soc Microbiol
The downregulation of Pseudomonas aeruginosa flagellar motility is a key event in biofilm
formation, host colonization, and the formation of microbial communities, but the external …

In vivo functional analysis and genetic modification of in vitro‐derived mouse neutrophils

…, L Fossati‐Jimack, GS Ling, KJ Lewis… - The FASEB …, 2011 - Wiley Online Library
Mature neutrophils are notoriously short‐lived immune cells that cannot be genetically
manipulated. Analysis of gene function therefore requires genetically modified animals, which is …

Ethanol decreases Pseudomonas aeruginosa flagellar motility through the regulation of flagellar stators

KA Lewis, AE Baker, AI Chen, CE Harty… - Journal of …, 2019 - Am Soc Microbiol
Pseudomonas aeruginosa frequently encounters microbes that produce ethanol. Low
concentrations of ethanol reduced P. aeruginosa swim zone area by up to 45% in soft agar. The …

[HTML][HTML] Health-related quality-of-life and health-utility reporting in critical care

…, OG Rewa, J Basmaji, KA Lewis… - World Journal of …, 2022 - ncbi.nlm.nih.gov
Mortality is a well-established patient-important outcome in critical care studies. In contrast,
morbidity is less uniformly reported (given the myriad of critical care illnesses and …

How P. aeruginosa cells with diverse stator composition collectively swarm

…, SL Kuchma, SS Webster, A Boromand, KA Lewis… - Mbio, 2024 - Am Soc Microbiol
It is now known that there exist multifactorial influences on swarming motility for P. aeruginosa
, but it is not clear precisely why stator selection in the flagellum motor is so important. We …

Glycogen Synthase Kinase-3 Is Required for Efficient Dictyostelium Chemotaxis

R Teo, KJ Lewis, JE Forde, WJ Ryves… - Molecular biology of …, 2010 - Am Soc Cell Biol
Glycogen synthase kinase-3 (GSK3) is a highly conserved protein kinase that is involved in
several important cell signaling pathways and is associated with a range of medical …