Results 21 to 30 of about 176,950 (261)

Reference-agnostic representation and visualization of pan-genomes

BMC Bioinformatics, 2021
Background The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.
Qihua Liang, Stefano Lonardi
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Genomic characterization of Campylobacter jejuni strain M1. [PDF]

PLoS ONE, 2010
Campylobacter jejuni strain M1 (laboratory designation 99/308) is a rarely documented case of direct transmission of C. jejuni from chicken to a person, resulting in enteritis. We have sequenced the genome of C.
Carsten Friis, Trudy M Wassenaar, Muhammad A Javed, Lars Snipen, Karin Lagesen, Peter F Hallin, Diane G Newell, Monique Toszeghy, Anne Ridley, Georgina Manning, David W Ussery   +10 more
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Prospects of pan-genomics in barley

Theoretical and Applied Genetics, 2018
The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants.
Cécile Monat, Mona Schreiber, Nils Stein, Martin Mascher   +3 more
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Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size

Frontiers in Microbiology, 2019
For more than a decade, pan-genome analysis has been applied as an effective method for explaining the genetic contents variation of prokaryotic species. However, genomic characteristics and detailed structures of gene pools have not been fully clarified,
Sang-Cheol Park, Kihyun Lee, Yeong Ouk Kim, Sungho Won, Sungho Won, Sungho Won, Jongsik Chun, Jongsik Chun   +7 more
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The pan-genome of Saccharomyces cerevisiae [PDF]

FEMS Yeast Research, 2019
ABSTRACT Understanding genotype–phenotype relationship is fundamental in biology. With the benefit from next-generation sequencing and high-throughput phenotyping methodologies, there have been generated much genome and phenome data for Saccharomyces cerevisiae. This makes it an excellent model system to understand the genotype–phenotype
Gang Li, Boyang Ji, Jens Nielsen
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PGAP: pan-genomes analysis pipeline [PDF]

Bioinformatics, 2011
Abstract Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed.
Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jing-Fa Xiao, Jun Yu 0004   +5 more
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nature Communications, 2020
With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes
Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium   +20 more
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A super pan-genomic landscape of rice

Cell Research, 2022
AbstractPan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.
Lianguang Shang, Xiaoxia Li, Huiying He, Qiaoling Yuan, Yanni Song, Zhaoran Wei, Hai Lin, Min Hu, Fengli Zhao, Chao Zhang, Yuhua Li, Hongsheng Gao, Tianyi Wang, Xiangpei Liu, Hong Zhang, Ya Zhang, Shuaimin Cao, Xiaoman Yu, Bintao Zhang, Yong Zhang, Yiqing Tan, Mao Qin, Cheng Ai, Yingxue Yang, Bin Zhang, Zhiqiang Hu, Hongru Wang, Yang Lv, Yuexing Wang, Jie Ma, Quan Wang, Hongwei Lu, Zhe Wu, Shanlin Liu, Zongyi Sun, Hongliang Zhang, Longbiao Guo, Zichao Li, Yongfeng Zhou, Jiayang Li, Zuofeng Zhu, Guosheng Xiong, Jue Ruan, Qian Qian   +43 more
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Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome

Frontiers in Genetics, 2019
It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock.
Ran Li, Weiwei Fu, Rui Su, Xiaomeng Tian, Duo Du, Yue Zhao, Zhuqing Zheng, Qiuming Chen, Shan Gao, Yudong Cai, Xihong Wang, Jinquan Li, Yu Jiang   +12 more
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Efficient oligonucleotide probe selection for pan-genomic tiling arrays

BMC Bioinformatics, 2009
Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates.
Zhang Wei, Deng Xiangyu, Phillippy Adam M, Salzberg Steven L   +3 more
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