Results 21 to 30 of about 174,716 (299)

Standard operating procedure for computing pangenome trees [PDF]

, 2010
We present the pan-genome tree as a tool for visualizing similarities and differences between closely related microbial genomes within a species or genus. Distance between genomes is computed as a weighted relative Manhattan distance based on gene family
Lars Snipen, David W. Ussery
core   +1 more source

PGAweb: A Web Server for Bacterial Pan-Genome Analysis

Frontiers in Microbiology, 2018
An astronomical increase in microbial genome data in recent years has led to strong demand for bioinformatic tools for pan-genome analysis within and across species.
Xinyu Chen, Yadong Zhang, Yadong Zhang, Yadong Zhang, Zhewen Zhang, Zhewen Zhang, Yongbing Zhao, Chen Sun, Ming Yang, Jinyue Wang, Jinyue Wang, Jinyue Wang, Qian Liu, Qian Liu, Baohua Zhang, Baohua Zhang, Meili Chen, Meili Chen, Jun Yu, Jun Yu, Jiayan Wu, Zhong Jin, Zhong Jin, Jingfa Xiao, Jingfa Xiao, Jingfa Xiao   +25 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

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
doaj   +1 more source

Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae [PDF]

, 2019
The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacteria populations occupying different niches is not well understood.
Abbott, Abby, Almeida, Baily, Bankevich, Beerli, Beerli, Benjamini, Bertels, Bikard, Bisharat, Bishop, Bohnsack, Borchardt, Brett M Probert, Brochet, Bruen, Brynildsrud, Capella-Gutierrez, Chen, Chen, Cheng, Chiara Crestani, Chopra, Christopher D Town, Conrad, Croucher, Da Cunha, Delannoy, Delannoy, Dogan, Edgar, Enright, Erwin, Fernandez, Ferreira, Flores, Fluegge, Garrett H Springer, Gauthier, Glazko, Glazko, Greig, Guglielmini, Gupta, Hayley B Hassler, Heaps, Holt, Imperi, Inouye, Irina M Velsko, Jafar, Jaskowiak, Jeukens, Johri, Jones, Jones, Jorgensen, Joubrel, Kalimuddin, Kim, Konig, Langdon, Librado, Lin, Lindahl, Liu, Liu, Lopez-Sanchez, Loytynoja, Lyhs, Manning, Manning, Martins, Marttinen, Mather, McArthur, Md Tauqeer Alam, Michael J Stanhope, Morse, Murrell, Page, Pal, Paulina D Pavinski Bitar, Pedersen, Petrovska, Pond, Poyart, Price, Qin, Richards, Richards, Richards, Rosinski-Chupin, Ruth N Zadoks, Sahl, Sahl, Sahl, Scheffer, Schrieber, Seemann, Shannon D Manning, Shapiro, Shepheard, Sheppard, Spoor, Springman, Srivastava, Stamatakis, Stoddard, Sukhnanand, Supek, Tettelin, Tettelin, Tian, van der Mee-Marquet, Verani, Viana, Vincent P Richards, Yu, Zadoks, Zankari, Zerbino, Zhang, Zhu   +124 more
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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
doaj   +1 more source

Explaining microbial population genomics through phage predation [PDF]

, 2009
The remarkable diversity of genes within the pool of prokaryotic genomes belonging to the same species or pan-genome is difficult to reconcile with the widely accepted paradigm which asserts that periodic selection within bacterial populations would ...
Alex Mira, Ana-Belé, Beltrá, Forest Rohwer, Francisco Rodriguez-Valera, Lejla Pasic, T. Frede Thingstad   +6 more
core   +2 more sources

A representation of a compressed de Bruijn graph for pan-genome analysis that enables search [PDF]

, 2016
Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species.
Beller, Timo, Ohlebusch, Enno
core   +2 more sources

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. [PDF]

, 2018
Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism.
Kavvas, Erol, Monk, Jonathan M, Norsigian, Charles J, Palsson, Bernhard O, Seif, Yara   +4 more
core   +2 more sources

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
doaj   +1 more source