Results 41 to 50 of about 4,042,841 (387)

Utilizing systems biology to reveal cellular responses to peroxisome proliferator-activated receptor γ ligand exposure

Current Research in Toxicology, 2021
Peroxisome proliferator-activated receptor γ (PPARγ) is a nuclear receptor that, upon activation by ligands, heterodimerizes with retinoid X receptor (RXR), binds to PPAR response elements (PPREs), and activates transcription of downstream genes.
Vanessa Cheng, Aalekhya Reddam, Anil Bhatia, Manhoi Hur, Jay S. Kirkwood, David C. Volz   +5 more
doaj   +1 more source

HierCC: a multi-level clustering scheme for population assignments based on core genome MLST

bioRxiv, 2020
Motivation Routine infectious disease surveillance is increasingly based on large-scale whole genome sequencing databases. Real-time surveillance would benefit from immediate assignments of each genome assembly to hierarchical population structures. Here
Zhemin Zhou, J. Charlesworth, M. Achtman
semanticscholar   +1 more source

A robust pipeline for efficient knock-in of point mutations and epitope tags in zebrafish using fluorescent PCR based screening

BMC Genomics, 2022
Background Genome editing using CRISPR/Cas9 has become a powerful tool in zebrafish to generate targeted gene knockouts models. However, its use for targeted knock-in remains challenging due to inefficient homology directed repair (HDR) pathway in ...
Blake Carrington, Ramanagouda Ramanagoudr-Bhojappa, Erica Bresciani, Tae-Un Han, Raman Sood   +4 more
doaj   +1 more source

Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. [PDF]

, 2015
BACKGROUND: Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis.
Bode, Helge B, Cano, Liliana M, Dep Biologie, Evangelisti, Edouard, Govers, Francine, Judelson, Howard, Kamoun, Sophien, Kemen, Eric, Kitner, Miloslav, Klein, Joël, Meijer, Harold J G, Oome, Stan, Plant Microbe Interactions, Sambles, Christine, Schornack, Sebastian, Sharma, Rahul, Spring, Otmar, Studholme, David J, Sub Plant-Microbe Interactions, Thines, Marco, Van den Ackerveken, Guido, van den Hoogen, D Johan, Win, Joe, Xia, Xiaojuan, Zipper, Reinhard   +24 more
core   +5 more sources

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools [PDF]

, 2016
This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data.
Cheng, Yinhe, Ogasawara, Takeshi, Tzeng, Tzy-Hwa Kathy   +2 more
core   +6 more sources

Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files

BMC Genomics, 2020
Background DNA sequencing is at the core of many molecular biology laboratories. Despite its long history, there is a lack of user-friendly Sanger sequencing data analysis tools that can be run interactively as a web application or at large-scale in ...
Tobias Rausch, Markus Hsi-Yang Fritz, Andreas Untergasser, Vladimir Benes   +3 more
doaj   +1 more source

Thermal proteome profiling in bacteria: probing protein state in vivo

Molecular Systems Biology, 2018
Increasing antibiotic resistance urges for new technologies for studying microbes and antimicrobial mechanism of action. We adapted thermal proteome profiling (TPP) to probe the thermostability of Escherichia coli proteins in vivo. E.
André Mateus, Jacob Bobonis, Nils Kurzawa, Frank Stein, Dominic Helm, Johannes Hevler, Athanasios Typas, Mikhail M Savitski   +7 more
doaj   +1 more source

Molecular Epidemiology of Staphylococcus aureus in China Reveals the Key Gene Features Involved in Epidemic Transmission and Adaptive Evolution

Microbiology Spectrum, 2022
Staphylococcus aureus is a Gram-positive pathogen that causes various infections in humans and domestic animals. In China, S. aureus is the most common Gram-positive pathogen that causes clinical infections.
Zhen Xu, Chao Yuan
doaj   +1 more source

Epistasis, core-genome disharmony, and adaptation in recombining bacteria. [PDF]

mBio
ABSTRACT Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis.
Taylor AJ, Yahara K, Pascoe B, Ko S, Mageiros L, Mourkas E, Calland JK, Puranen S, Hitchings MD, Jolley KA, Kobras CM, Bayliss S, Williams NJ, van Vliet AHM, Parkhill J, Maiden MCJ, Corander J, Hurst LD, Falush D, Keim P, Didelot X, Kelly DJ, Sheppard SK.   +22 more
europepmc   +9 more sources

Comparative genomics of 40 Weissella paramesenteroides strains

Frontiers in Microbiology, 2023
Weissella strains are often detected in spontaneously fermented foods. Because of their abilities to produce lactic acid and functional exopolysaccharides as well as their probiotic traits, Weissella spp.
Xing Wan, Xing Wan, Timo M. Takala, Vy A. Huynh, Susanna L. Ahonen, Lars Paulin, Johanna Björkroth, Tarja Sironen, Tarja Sironen, Ravi Kant, Ravi Kant, Ravi Kant, Per Saris   +12 more
doaj   +1 more source