Results 161 to 170 of about 169,584 (184)

Bacterial pan-genomes

Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, 2013
Bacterial genomes at NCBI represent a large collection of strains with different levels of sequence and assembly quality as well as sampling density. Among these, there are densely-sampled sets of related genomes, usually human pathogens, whose organization and protein content could be directly analyzed within the concept of pan-genome.
Leonid Zaslavsky, Boris Fedorov, Tatiana Tatusova   +2 more
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Orthopoxvirus pan-genomic DNA assay

Journal of Virological Methods, 2007
A genome-spanning assay is described that enables laboratory confirmation of infections with orthopoxviruses (OPVs), particularly Vaccinia, Monkeypox, and Variola viruses, which can cause vesiculo-pustular rash illnesses in humans. The assay uses a series of polymerase chain reaction (PCR) amplicons that overlap to span the approximately 200kilobase ...
Yu, Li, Susan L, Ropp, Hui, Zhao, Inger K, Damon, Joseph J, Esposito   +4 more
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Bacterial Pan-Genomics

2019
Due to their tendency to have a high recombination rate, bacterial genomes are highly diverse across different strains. This diversity may even be in the form of the presence or absence of entire genes; therefore, each strain might have its own combination of genes. The pan-genome represents the complete gene pool of a species.
Arash Iranzadeh, Nicola Jane Mulder
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Pan-Genome Storage and Analysis Techniques

2017
Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the concept has spread to a variety of species, such as plants or viruses. Characterizing a pan-genome provides insights into intra-species evolution, functions, and diversity.
Zekic, Tina, Holley, Guillaume, Stoye, Jens, Setubal, João C., Stadler, Peter, Stoye, Jens   +5 more
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Ten years of pan-genome analyses

Current Opinion in Microbiology, 2015
Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have transitioned from single or few genomes to hundreds to thousands of genomes. Pan-genome analyses provide a framework for estimating the genomic diversity of the dataset at hand and predicting the number of additional whole ...
George, Vernikos, Duccio, Medini, David R, Riley, Hervé, Tettelin   +3 more
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Comparative genomics: the bacterial pan-genome

Current Opinion in Microbiology, 2008
Bacterial genome sequencing has become so easy and accessible that the genomes of multiple strains of more and more individual species have been and will be generated. These data sets provide for in depth analysis of intra-species diversity from various aspects.
Tettelin H, Riley D, Cattuto C, Medini D
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FGFR2: A pan-genomic target.

Journal of Clinical Oncology, 2019
3099 Background: FGFR2 genomic alterations (GA) have been described in a variety of solid tumors and emerged as biomarkers for investigational agents undergoing clinical trials. Methods: 201,766 primarily relapsed/refractory malignancies were evaluated with a hybrid-capture based sequencing assay Tumor mutational burden (TMB) was determined on 0.8-1 ...
Russell Madison, Ethan Sokol, Alexa Betzig Schrock, Adrienne Johnson, Dean Pavlick, Julia Andrea Elvin, Jo-Anne Vergilio, Nhu Ngo, Jonathan Keith Killian, Douglas I. Lin, Shakti Ramkissoon, Eric Allan Severson, Amanda Hemmerich, Daniel Duncan, Siraj Mahamed Ali, Prasanth Reddy, Kimberly McGregor, Brian Alexander, Vincent A. Miller, Jeffrey S. Ross   +19 more
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The Maize Pan-Genome

2018
The pan-genome of a species is comprised of genes/sequences that are present in all individuals in the species (core genome) and genes/sequences that are present in only a subset of individuals within the species (dispensable genome). In maize, the study of the pan-genome began in the 1940s through cytogenetic experiments and has seen an increased ...
Alex B. Brohammer, Thomas J. Y. Kono, Candice N. Hirsch   +2 more
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Pan-Genome of Brucella Species

Indian Journal of Microbiology, 2014
Whole-genome sequencing of bacterial pathogens has high impact on diagnosis and development of prophylaxis to human and veterinary disease. To study the genetic variations and relatedness among Brucella spp., we have examined the pan-genomic content of 18 Brucella complete genomes from NCBI using GView and Panseq server.
Jagadesan Sankarasubramanian, Udayakumar S. Vishnu, Jayavel Sridhar, Paramasamy Gunasekaran, Jeyaprakash Rajendhran   +4 more
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Exploring Frequented Regions in Pan-Genomic Graphs

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017
We consider the problem of identifying regions within a pan-genome De Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In this work, we formalize the FR problem and describe an efficient algorithm for finding FRs. Subsequently, we propose some applications of
Alan Cleary, Thiruvarangan Ramaraj, Indika Kahanda, Joann Mudge, Brendan Mumey   +4 more
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