Results 41 to 50 of about 171,414 (293)

Roary : rapid large-scale prokaryote pan genome analysis

, 2015
This work was supported by the Wellcome Trust (grant WT 098051).A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates.
Page, Andrew J, Falush, Daniel, Wong, Vanessa K, Fookes, Maria, Keane, Jacqueline A, Hunt, Martin, Holden, Matthew T G, Parkhill, Julian, Reuter, Sandra, Cummins, Carla A   +9 more
core   +1 more source

Seep-SRB1a pan-genome analysis.

, 2023
A pan-genome analysis of Seep-SRB1a clades was performed using Anvi’o [45] to demonstrate the conserved genes and differences within the syntrophic SRB clade Seep-SRB1a. (XLSX)
Danielle Goudeau (8455311), Rex R. Malmstrom (8615046), Tanja Woyke (111784), Hang Yu (278278), Fabai Wu (17041703), Kyle S. Metcalfe (17041706), Victoria J. Orphan (3944372), Antoine Crémière (17041709), Ranjani Murali (17041700), Daan R. Speth (5548529), Rafael Laso-Pèrez (17041712), Grayson L. Chadwick (11910062), Roland Hatzenpichler (487768), Stephanie A. Connon (17041715)   +13 more
core   +1 more source

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
doaj   +1 more source

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

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
openaire   +2 more sources

AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae

, 2015
The characterization and public release of genome sequences from thousands of organ- isms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due
Kisurb Choe, Benjamin J. A. Dickins (703565), Stacia Engel (703566), Barbara Dunn, Barbara Dunn (393141), Janos Demeter (5547), Song Giltae, Giltae Song, Dunn Barbara, Jennifer Gallagher, Cherry, JM, Choe, K, Dickins Benjamin J. A., J. Michael Cherry (5627), Demeter, J, Janos Demeter, Dickins, BJA, Snyder, M, Giltae Song (703564), Song, G, Dunn, B, Benjamin J A Dickins, J Michael Cherry, Gallagher, J, Stacia Engel, Engel, S, Demeter Janos, Michael Snyder, Engel Stacia, Cherry J. Michael   +29 more
core   +1 more source

Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes [PDF]

, 2019
Although the pan-genome concept originated in prokaryote genomics, an increasing number of eukaryote species pan-genomes have also been analysed. However, there is a relative lack of software intended for eukaryote pan-genome analysis compared to that ...
Fitzpatrick, David A., McCarthy, Charley G.P., David A. Fitzpatrick, Charley G. P. McCarthy   +3 more
core   +1 more source

Keratin 19 as a prognostic marker and contributing factor of metastasis and chemoresistance in high‐grade serous ovarian cancer

Molecular Oncology, EarlyView.
Keratin 19 (KRT19) is overexpressed in high‐grade serous ovarian cancer with high levels of Kallikrein‐related peptidases (KLK) 4–7 and is associated with poor survival. In vivo analyses demonstrate that elevated KRT19 increases peritoneal tumour burden.
Sophia Bielesch, Isabel Vogel, Sina Nokodian, Johanna Moeller, Antonia Blechschmidt, Vicky Hecht, Vanessa Kuentzel, Katharina Thiedig, Melissa Schwab, Oliver Schilling, Holger Bronger, Marion Kiechle, Viktor Magdolen, Tobias Dreyer   +13 more
wiley   +1 more source

Longitudinal circulating tumor DNA profiling in patients with advanced endometrial cancer using an off‐the‐shelf targeted NGS panel

Molecular Oncology, EarlyView.
Intratumour heterogeneity complicates precision management of advanced endometrial cancer. Circulating tumor DNA (ctDNA) offers a minimally invasive strategy to capture tumor evolution and therapeutic resistance. Here, we compare tumor‐agnostic NGS with tumor‐informed ddPCR, outlining their relative sensitivity, concordance, and clinical implications ...
Carlos Casas‐Arozamena, Karin Teien Lande, Eva Diaz, Ana Vilar, Juan Cueva, Efigenia Arias, Victoria Sampayo, Alicia Abalo, Nerea González, Eva Colás, Antonio Gil‐Moreno, Miguel Abal, Gema Moreno‐Bueno, Therese Sørlie, Kristina Lindemann, Laura Muinelo‐Romay   +15 more
wiley   +1 more source

Towards comparative pan-genomics

, 2020
Comparative genomics investigates the genomic makeup of species to unravel their unique variations and evolutionary relationships. High-throughput sequencing technologies have enabled reading the DNA content of a wide variety of species at an unprecedented rate.
openaire   +2 more sources