Results 51 to 60 of about 169,584 (184)

Plant pan-genomes are the new reference [PDF]

Nature Plants, 2020
Recent years have seen a surge in plant genome sequencing projects and the comparison of multiple related individuals. The high degree of genomic variation observed led to the realization that single reference genomes do not represent the diversity within a species, and led to the expansion of the pan-genome concept.
Philipp E. Bayer, Agnieszka A. Golicz, Armin Scheben, Jacqueline Batley, David Edwards   +4 more
openaire   +3 more sources

Getting insight into the pan-genome structure with PangTree

BMC Genomics, 2020
Background The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes ...
Paulina Dziadkiewicz, Norbert Dojer
doaj   +1 more source

The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract [PDF]

, 2015
Background Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific.
Crossman, Lisa C., Goesmann, Alexander, Juge, Nathalie, Mackenzie, Donald A., Roos, Stefan, Swarbreck, David, Walter, Jens, Wegmann, Udo, Zheng, Jinshui   +8 more
core   +1 more source

Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes [PDF]

, 2011
Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C.
Ashelford, KE, Birtles, RJ, Dorrell, N, French, NP, Gould, KA, Hall, N, Hepworth, PJ, Hinds, J, Leatherbarrow, H, Mendonca, C, Wigley, P, Williams, NJ, Winstanley, C, Witney, AA, Wren, BW   +14 more
core   +2 more sources

Genomic comparison of diverse Salmonella serovars isolated from swine. [PDF]

, 2019
Food animals act as a reservoir for many foodborne pathogens. Salmonella enterica is one of the leading pathogens that cause food borne illness in a broad host range including animals and humans.
Barrett, John B, Frye, Jonathan G, Gupta, Sushim K, Hiott, Lari M, Humayoun, Shaheen B, Jackson, Charlene R, McClelland, Michael, McMillan, Elizabeth A, Sharma, Poonam, Woodley, Tiffanie   +9 more
core   +2 more sources

Computational Pan-Genomics: Status, Promises and Challenges [PDF]

Briefings in Bioinformatics, 2016
AbstractMany disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case ofHomo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines
Marschall, Tobias, Marz, Manja, Abeel, Thomas, Dijkstra, Louis, Dutilh, Bas E., Ghaffaari, Ali, Kersey, Paul, Kloosterman, Wigard P., Makinen, Veli, Novak, Adam M., Paten, Benedict, Porubsky, David, Rivals, Eric, Alkan, Can, Baaijens, Jasmijn A., de Bakker, Paul I. W., Boeva, Valentina, Bonnal, Raoul J. P., Chiaromonte, Francesca, Chikhi, Rayan, Ciccarelli, Francesca D., Cijvat, Robin, Datema, Erwin, Duijn, Cornelia M. Van, Eichler, Evan E., Ernst, Corinna, Eskin, Eleazar, Garrison, Erik, El-Kebir, Mohammed, Klau, Gunnar, Korbel, Jan O., Lameijer, Eric-Wubbo, Langmead, Benjamin, Martin, Marcel, Medvedev, Paul, Mu, John C., Neerincx, Pieter, Ouwens, Klaasjan, Peterlongo, Pierre, Pisanti, Nadia, Rahmann, Sven, Raphael, Ben, Reinert, Knut, de Ridder, Dick, de Ridder, Jeroen, Schlesner, Matthias, Schulz-Trieglaff, Ole, Sanders, Ashley D., Sheikhizadeh, Siavash, Shneider, Carl, Smit, Sandra, Valenzuela, Daniel, Wang, Jiayin, Wessels, Lodewyk, Zhang, Ying, Guryev, Victor, Vandin, Fabio, Ye, Kai, Schönhuth, Alexander   +58 more
openaire   +18 more sources

PRAP: Pan Resistome analysis pipeline

BMC Bioinformatics, 2020
Background Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species.
Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang, Xianming Shi   +7 more
doaj   +1 more source

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. [PDF]

, 2018
Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses ...
Anand, Amitesh, Catoiu, Edward, Dillon, Nicholas, Heckmann, David, Kavvas, Erol S, Mih, Nathan, Monk, Jonathan M, Nizet, Victor, Palsson, Bernhard O, Seif, Yara, Yang, Laurence, Yurkovich, James T   +11 more
core   +2 more sources

Pan-Genome of Wild and Cultivated Soybeans [PDF]

Cell, 2020
Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced ...
Yucheng, Liu, Huilong, Du, Pengcheng, Li, Yanting, Shen, Hua, Peng, Shulin, Liu, Guo-An, Zhou, Haikuan, Zhang, Zhi, Liu, Miao, Shi, Xuehui, Huang, Yan, Li, Min, Zhang, Zheng, Wang, Baoge, Zhu, Bin, Han, Chengzhi, Liang, Zhixi, Tian   +17 more
openaire   +2 more sources

Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar

Frontiers in Microbiology, 2017
Food safety is a global concern, with upward of 2.2 million deaths due to enteric disease every year. Current whole-genome sequencing platforms allow routine sequencing of enteric pathogens for surveillance, and during outbreaks; however, a remaining ...
Chad R. Laing, Matthew D. Whiteside, Victor P. J. Gannon   +2 more
doaj   +1 more source