Results 71 to 80 of about 28,177 (251)

Avian MHC Evolution in the Era of Genomics: Phase 1.0

Cells, 2019
Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest.
Emily A. O’Connor, Helena Westerdahl, Reto Burri, Scott V. Edwards   +3 more
doaj   +1 more source

SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models

Genome Biology
Accurate inference of orthologous genes constitutes a prerequisite for comparative and evolutionary genomics. SonicParanoid is one of the fastest tools for orthology inference; however, its scalability and accuracy have been hampered by time-consuming ...
Salvatore Cosentino, S. Sriswasdi, Wataru Iwasaki   +2 more
semanticscholar   +1 more source

Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes

Briefings Bioinform., 2020
Insights into the evolution of ancestral complexes and pathways are generally achieved through careful and time-intensive manual analysis often using phylogenetic profiles of the constituent proteins.
E. S. Deutekom, B. Snel, Teunis J. P. van Dam   +2 more
semanticscholar   +1 more source

Integrated Single‐Cell and TCR Profiling Reveals Protection‐Associated CD8+ T Cell Subsets Linked to Viral Control in PRRSV

Advanced Science, EarlyView.
PRRSV vaccine‐mediated protection is associated with clonally expanded cytotoxic CD8+ T cell subsets driven by viral structural proteins and supported by innate TLR4/TLR8 signaling and CD4+ T cell help, whereas non‐protective responses are characterized by dysfunctional exhausted‐like CD8+ T cells linked to poor viral control.
Can Kong, Siang Chen, Maolin Li, Meng Wang, Hailin Zhang, Bolun Zhou, Zhenhua Xie, Chen Wang, Peng Gao, Jianjun Luo, Hanchun Yang, Runsheng Chen, Dongdong Zhang, Jie Li, Jun Han   +14 more
wiley   +1 more source

The Orthologic of Epistemic Modals

Journal of Philosophical Logic
Minor edits for final version forthcoming in Journal of Philosophical ...
Wesley H. Holliday, Matthew Mandelkern
openaire   +4 more sources

Standardized benchmarking in the quest for orthologs [PDF]

Nature Methods, 2016
Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision–recall trade-offs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C   +27 more
openaire   +13 more sources

OXidative Stress PREDictor: A Supervised Learning Approach for Annotating Cellular Oxidative Stress States in Inflammatory Cells

Advanced Intelligent Systems, Volume 7, Issue 3, March 2025.
OxSpred, an eXtreme‐Gradient‐Boosting‐‐based supervised learning model, accurately annotates oxidative stress in innate immune cells at the single‐cell level, providing interpretable embeddings with significant biological relevance. This innovative tool revolutionizes the understanding of innate immune cell functions during inflammation and enhances ...
Po‐Yuan Chen, Tai‐Ming Ko
wiley   +1 more source

The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study. [PDF]

PLoS ONE, 2013
The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference
Daniel A Dalquen, Adrian M Altenhoff, Gaston H Gonnet, Christophe Dessimoz   +3 more
doaj   +1 more source

Advances and Applications in the Quest for Orthologs [PDF]

Molecular Biology and Evolution, 2019
AbstractGene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses.
Glover, Natasha, Dessimoz, Christophe, Ebersberger, Ingo, Forslund, Sofia, Gabaldon, Toni, Huerta-Cepas, Jaime, Martin, Maria J, Muffato, Matthieu, Patricio, Mateus, Pereira, C., Sousa da Silva, A., Wang, Yan, The Quest For Orthologs Consortium, Qfo, Lecompte, Odile, Hurstel, Alexandre, Sonnhammer, Erik, Thomas, Paul D   +16 more
openaire   +8 more sources

Longitudinal Modulation of the Gut Microbiome and Growth Performance by Phytochemicals as Antibiotic Alternatives in Swine Production

Animal Research and One Health, EarlyView.
We conducted a longitudinal trial across nursery, growing, and finishing phases, showing that phytochemical supplementation as a potential antibiotic alternative reduced potential pathogens and promoted beneficial Lactobacillus amylovorus in the nursery phase, and enriched amino acid and carbohydrate metabolism pathways (prediction) during finishing ...
Ziyu Liu, Samantha Howe, Yang Tian, Alisun N. Watson, Jason E. Farrar, Christopher E. Randolph, Jaime Andrés Ángel Isaza, Álvaro José Uribe, Yan Huang, Michael Looper, Jiangchao Zhao, Tsungcheng Tsai   +11 more
wiley   +1 more source