Results 21 to 30 of about 15,819 (203)

Pangenome-scale mathematical modelling of ANAMMOX bacteria metabolism

Removal of fixed nitrogen compounds such as ammonium and nitrite from wastewater is of critical importance for balancing the nitrogen cycle and protecting aquatic environments from eutrophication.
Ahsan Islam (4116055), Roman G. Bielski (22826809)   +1 more
core   +5 more sources

Personalized Pangenome References [PDF]

, 2023
Pangenomes, by including genetic diversity, should reduce reference bias by better representing new samples compared to them. Yet when comparing a new sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for
Carroll, Andrew, Eskandar, Parsa, Chang, Xian, Eizenga, Jordan M, Chang, Pi-Chuan, Paten, Benedict, Kolmogorov, Mikhail, Ungaro, Matteo Tommaso, Sirén, Jouni, Monlong, Jean, Hickey, Glenn, Novak, Adam M   +11 more
core   +1 more source

Gastric cancer genomics study using reference human pangenomes

Life Science Alliance
Using a concept called graph pangenome for many individual genomes as the baseline can improve the identification and characterization of large-sized genomic variations for disease genomics study.
Du Jiao, Xiaorui Dong, Shiyu Fan, Xinyi Liu, Yingyan Yu, Chaochun Wei   +5 more
doaj   +1 more source

Legume Pangenome: Status and Scope for Crop Improvement

, 2022
In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major ...
Mahendar Thudi, Uday Chand Jha, Yogesh Dashrath Naik, Nayyar, Harsh, Siddique, Kadambot H. M., Eric J. B. von Wettberg, Jha, Uday Chand, Thudi, Mahendar, von Wettberg, Eric J. B., Naik, Yogesh Dashrath, Harsh Nayyar, Kadambot H. M. Siddique   +11 more
core   +1 more source

Panakeia - a universal tool for bacterial pangenome analysis

BMC Genomics, 2022
Background Development of new pan-genome analysis tools is important, as the pangenome of a microbial species has become an important method to define the diversity of a selected taxon, most commonly a species, in the last years.
Sina Beier, Nicholas R Thomson
doaj   +1 more source

PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome

BMC Genomics
Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated ...
Mingwei Liu, Fan Zhang, Huimin Lu, Hongzhang Xue, Xiaorui Dong, Zhikang Li, Jianlong Xu, Wensheng Wang, Chaochun Wei   +8 more
doaj   +1 more source

Plant pangenomics, current practice and future direction

Agriculture Communications
A pangenome encompasses the complete genetic diversity of a species, by assembling a range of representative individuals from various populations. This review describes the advances in plant pangenomics, tracing its evolution since the initial plant ...
Haifei Hu, Jian Wang, Shuai Nie, Junliang Zhao, Jacqueline Batley, David Edwards   +5 more
doaj   +1 more source

Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment

mSystems, 2023
Gardnerella is the primary pathogenic bacterial genus present in the polymicrobial condition known as bacterial vaginosis (BV). Despite BV’s high prevalence and associated chronic and acute women’s health impacts, the Gardnerella pangenome is largely ...
Lillian R. Dillard, Emma M. Glass, Amanda L. Lewis, Krystal Thomas-White, Jason A. Papin   +4 more
doaj   +1 more source

Convergence of Plasmid‐Mediated tmexCD‐toprJ With Critical Resistance Genes Fuels Spread of Multidrug Resistant Bacteria

Advanced Science, EarlyView.
Global dissemination of tmexCD‐toprJ across bacterial hosts and ecological niches is accompanied by its convergence with blaKPC, blaNDM, and mcr on mobile plasmids. Recombination and acquisition of resistance modules generate distinct multidrug resistant plasmid architectures, facilitating the emergence and spread of high‐risk bacterial populations ...
Kaiwen Song, Meng Wang, Xingyu Wu, Meng Cai, Bowen Li, Qi Wang, Xiaodong Guan, Qi Ding, Ruobing Wang, Hui Wang   +9 more
wiley   +1 more source

Comparing methods for constructing and representing human pangenome graphs

, 2023
International audienceBackground As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses.
Dufresne, Yoann, Chikhi, Rayan, Andreace, Francesco, Lechat, Pierre   +3 more
core   +1 more source