Results 31 to 40 of about 15,819 (203)

Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia

Scientific Data
The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple individuals. Here
Maxat Kulmanov, Saeideh Ashouri, Yang Liu, Marwa Abdelhakim, Ebtehal Alsolme, Masao Nagasaki, Yasuyuki Ohkawa, Yutaka Suzuki, Rund Tawfiq, Katsushi Tokunaga, Toshiaki Katayama, Malak S. Abedalthagafi, Robert Hoehndorf, Yosuke Kawai   +13 more
doaj   +1 more source

Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp

Advanced Science, EarlyView.
By integrating 516 whole‐genome resequencing datasets and 236 transcriptomes of allotetraploid common carp, this study establishes the first population‐scale atlas of transposable element (TE) variation in teleost species. TE bursts, relaxed purifying selection, and lineage‐specific loss of ancient insertions shape genome evolution and phenotypic ...
Shuimu Hu, Zhou Jiang, Lin Chen, Gowena Ling Yi Goh, Weijing Li, Qian He, Xintong Chen, Rui Li, Yuxuan Liu, Ning Li, Tao Zhou, Peng Xu   +11 more
wiley   +1 more source

PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers

BMC Bioinformatics
Background Pangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graphs rely primarily on technical parameters (e.g., total length, number of nodes/edges, growth curves ...
Tristan Cumer, Sotiria Milia, Alexander S. Leonard, Hubert Pausch   +3 more
doaj   +1 more source

Rice Pangenome Research Progress: From Diversity Dissection to Breeding Applications

Guangdong nongye kexue
Rice is one of the world's most important staple crops. Traditional rice genomic research has long relied on a single reference genome (e.g., Nipponbare), which suffers from "reference bias" and fails to capture the full breadth of genetic diversity in ...
Haifei HU, Wenli TENG, Hai ZHOU, Junliang ZHAO, Jingbo ZHOU   +4 more
doaj   +1 more source

Host‐Specific Interactions Between Staphylococcus aureus and Pseudomonas aeruginosa Impair Epithelial Repair in Chronic Rhinosinusitis

International Forum of Allergy &Rhinology, EarlyView.
ABSTRACT Background Chronic rhinosinusitis (CRS) is frequently associated with polymicrobial biofilms involving Staphylococcus aureus and Pseudomonas aeruginosa. Interactions between these organisms are thought to influence disease severity, but the epithelial effects of exoproteins derived from patient‐matched cocultures remain poorly defined ...
Xiaohan Sun, Mahnaz Ramezanpour, George Bouras, Emma Barry, Alkis J. Psaltis, Peter‐John Wormald, Sarah Vreugde   +6 more
wiley   +1 more source

Element-based graph pangenome [PDF]

, 2023
Genomic analyses are based on using a single reference genome that does not represent the whole intraspecies diversity. Instead, a pangenome contains the whole genome content of a species.
LOPATRIELLO GIULIA
core   +1 more source

Standardized Research Methodology for Akkermansia muciniphila: Multi‐Omics Integration, Functional Evaluation, and Clinical Translation Pathways

Gut Medicine, EarlyView.
ABSTRACT Background Akkermansia muciniphila has emerged as a leading next‐generation beneficial microbe candidate in gut microbiome research, linked to host metabolic homeostasis, mucosal immune regulation, and intestinal barrier integrity. However, marked methodological heterogeneity in isolation and culture conditions, detection and quantification ...
Jiaxin Chen, Mantang Qiu
wiley   +1 more source

Bovine Pangenome Consortium

, 2023
The Bovine Pangenome Consortium is an international research consortium dedicated to the sequencing and assembly of bovid species for research applications. We are comprised of experts in the field of Genetics, Genomics, Bioinformatics and Animal Science
USDA ARS (17854841), Bovine Pangenome Consortium (17857625)   +1 more
core  

From wild to tamed: Reimagining novel crops through omics and local plant diversity

PLANTS, PEOPLE, PLANET, EarlyView.
The global food system faces growing pressure from climate change, biodiversity loss, and rising nutritional demands. Agriculture has increased yields but reduced crop diversity, flavor, and nutritional quality, leaving societies vulnerable and dependent on a narrow set of staple species.
Alexandra Sanfeliu Meliá, Pablo D. Cárdenas   +1 more
wiley   +1 more source

The need for manual curation of the cotton proteome leads to a solution primed for undergraduate involvement

PLANTS, PEOPLE, PLANET, EarlyView.
Cotton is a global crop cultivated worldwide, yet a significant portion of the cotton genome remains functionally unannotated. Attempts have been made to automate this annotation but have been unable to completely bridge the gap. Human curation is still needed for accurate interpretations and predictions to be made.
Jonathan Zirkel, Amanda R. Storm, Grant T. Billings, Amanda M. Hulse‐Kemp   +3 more
wiley   +1 more source