Results 1 to 10 of about 198,179 (117)

EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research

iMeta, 2023
It is difficult for beginners to learn and use amplicon analysis software because there are so many software tools to choose from, and all of them need multiple steps of operation. Herein, we provide a cross‐platform, open‐source, and community‐supported
Yong‐Xin Liu, Lei Chen, Tengfei Ma, Xiaofang Li, Maosheng Zheng, Xin Zhou, Liang Chen, Xubo Qian, Jiao Xi, Hongye Lu, Huiluo Cao, Xiaoya Ma, Bian Bian, Pengfan Zhang, Jiqiu Wu, Ren‐You Gan, Baolei Jia, Linyang Sun, Zhicheng Ju, Yunyun Gao, Tao Wen, Tong Chen   +21 more
doaj   +2 more sources

Herpes Virus Amplicon Vectors

Viruses, 2009
Since its emergence onto the gene therapy scene nearly 25 years ago, the replication-defective Herpes Simplex Virus Type-1 (HSV-1) amplicon has gained significance as a versatile gene transfer platform due to its extensive transgene capacity, widespread ...
Suresh de Silva, William J. Bowers
doaj   +3 more sources

Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment

Frontiers in Microbiology, 2021
Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics.
Megan S. Beaudry, Jincheng Wang, Jincheng Wang, Troy J. Kieran, Jesse Thomas, Jesse Thomas, Natalia J. Bayona-Vásquez, Natalia J. Bayona-Vásquez, Bei Gao, Alison Devault, Brian Brunelle, Kun Lu, Jia-Sheng Wang, Jia-Sheng Wang, Olin E. Rhodes, Travis C. Glenn, Travis C. Glenn, Travis C. Glenn   +17 more
doaj   +1 more source

SNP4OrphanSpecies: A bioinformatics pipeline to isolate molecular markers for studying genetic diversity of orphan species [PDF]

Biodiversity Data Journal, 2022
For several decades, an increase in disease or pest emergences due to anthropogenic introduction or environmental changes has been recorded. This increase leads to serious threats to the genetic and species diversity of numerous ecosystems. Many of these
Benjamin Penaud, Benoit Laurent, Marine Milhes, Camille Noüs, François Ehrenmann, Cyril Dutech   +5 more
doaj   +3 more sources

Biannual Administrations of Azithromycin and the Gastrointestinal Microbiome of Malawian Children: A Nested Cohort Study Within a Randomized Controlled Trial

Frontiers in Public Health, 2022
Community-level mass treatment with azithromycin has been associated with a mortality benefit in children. However, antibiotic exposures result in disruption of the gut microbiota and repeated exposures may reduce recovery of the gut flora.
David Chaima, David Chaima, Harry Pickering, John D. Hart, Sarah E. Burr, Sarah E. Burr, Joanna Houghton, Kenneth Maleta, Khumbo Kalua, Khumbo Kalua, Robin L. Bailey, Martin J. Holland   +11 more
doaj   +1 more source

General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways

Metabolites, 2021
General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data ...
Boštjan Murovec, Leon Deutsch, Blaž Stres   +2 more
doaj   +1 more source

Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance

Viruses, 2023
Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns.
John Juma, Samson L. Konongoi, Isidore Nsengimana, Reuben Mwangi, James Akoko, Richard Nyamota, Collins Muli, Paul O. Dobi, Edward Kiritu, Shebbar Osiany, Amos A. Onwong’a, Rachael W. Gachogo, Rosemary Sang, Alan Christoffels, Kristina Roesel, Bernard Bett, Samuel O. Oyola   +16 more
doaj   +1 more source

Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome

mSphere, 2020
The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition.
Luisa W. Hugerth, Marcela Pereira, Yinghua Zha, Maike Seifert, Vilde Kaldhusdal, Fredrik Boulund, Maria C. Krog, Zahra Bashir, Marica Hamsten, Emma Fransson, Henriette Svarre Nielsen, Ina Schuppe-Koistinen, Lars Engstrand   +12 more
doaj   +1 more source

Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology

Diagnostics, 2022
Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively becoming platforms of choice to facilitate this, owing ...
Rajesh R. Singh
doaj   +1 more source

Biological soil crusts on agricultural soils of mesic regions promote microbial cross-kingdom co-occurrences and nutrient retention

Frontiers in Microbiology, 2023
IntroductionBiological soil crusts (biocrusts) are known as biological hotspots on undisturbed, nutrient-poor bare soil surfaces and until now, are mostly observed in (semi-) arid regions but are currently poorly understood in agricultural systems.
Julia Katharina Kurth, Julia Katharina Kurth, Martin Albrecht, Karin Glaser, Ulf Karsten, Gisle Vestergaard, Martin Armbruster, Susanne Kublik, Christoph A. O. Schmid, Michael Schloter, Michael Schloter, Stefanie Schulz   +11 more
doaj   +1 more source