Literature DB >> 30049790

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens.

Zhemin Zhou1, Nabil-Fareed Alikhan1, Martin J Sergeant1, Nina Luhmann1, Cátia Vaz2,3, Alexandre P Francisco2,4, João André Carriço5, Mark Achtman1.   

Abstract

Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.
© 2018 Zhou et al.; Published by Cold Spring Harbor Laboratory Press.

Mesh：

Year:  2018        PMID： 30049790      PMCID： PMC6120633          DOI： 10.1101/gr.232397.117

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  28 in total

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Authors:  Martin C J Maiden; Melissa J Jansen van Rensburg; James E Bray; Sarah G Earle; Suzanne A Ford; Keith A Jolley; Noel D McCarthy
Journal:  Nat Rev Microbiol       Date:  2013-09-02       Impact factor: 60.633

2.  Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Authors:  Gytis Dudas; Luiz Max Carvalho; Trevor Bedford; Andrew J Tatem; Guy Baele; Nuno R Faria; Daniel J Park; Jason T Ladner; Armando Arias; Danny Asogun; Filip Bielejec; Sarah L Caddy; Matthew Cotten; Jonathan D'Ambrozio; Simon Dellicour; Antonino Di Caro; Joseph W Diclaro; Sophie Duraffour; Michael J Elmore; Lawrence S Fakoli; Ousmane Faye; Merle L Gilbert; Sahr M Gevao; Stephen Gire; Adrianne Gladden-Young; Andreas Gnirke; Augustine Goba; Donald S Grant; Bart L Haagmans; Julian A Hiscox; Umaru Jah; Jeffrey R Kugelman; Di Liu; Jia Lu; Christine M Malboeuf; Suzanne Mate; David A Matthews; Christian B Matranga; Luke W Meredith; James Qu; Joshua Quick; Suzan D Pas; My V T Phan; Georgios Pollakis; Chantal B Reusken; Mariano Sanchez-Lockhart; Stephen F Schaffner; John S Schieffelin; Rachel S Sealfon; Etienne Simon-Loriere; Saskia L Smits; Kilian Stoecker; Lucy Thorne; Ekaete Alice Tobin; Mohamed A Vandi; Simon J Watson; Kendra West; Shannon Whitmer; Michael R Wiley; Sarah M Winnicki; Shirlee Wohl; Roman Wölfel; Nathan L Yozwiak; Kristian G Andersen; Sylvia O Blyden; Fatorma Bolay; Miles W Carroll; Bernice Dahn; Boubacar Diallo; Pierre Formenty; Christophe Fraser; George F Gao; Robert F Garry; Ian Goodfellow; Stephan Günther; Christian T Happi; Edward C Holmes; Brima Kargbo; Sakoba Keïta; Paul Kellam; Marion P G Koopmans; Jens H Kuhn; Nicholas J Loman; N'Faly Magassouba; Dhamari Naidoo; Stuart T Nichol; Tolbert Nyenswah; Gustavo Palacios; Oliver G Pybus; Pardis C Sabeti; Amadou Sall; Ute Ströher; Isatta Wurie; Marc A Suchard; Philippe Lemey; Andrew Rambaut
Journal:  Nature       Date:  2017-04-12       Impact factor: 49.962

3.  Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain.

Authors:  Keith A Jolley; Carly M Bliss; Julia S Bennett; Holly B Bratcher; Carina Brehony; Frances M Colles; Helen Wimalarathna; Odile B Harrison; Samuel K Sheppard; Alison J Cody; Martin C J Maiden
Journal:  Microbiology (Reading)       Date:  2012-01-27       Impact factor: 2.777

4.  BIGSdb: Scalable analysis of bacterial genome variation at the population level.

Authors:  Keith A Jolley; Martin C J Maiden
Journal:  BMC Bioinformatics       Date:  2010-12-10       Impact factor: 3.169

5.  Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.

Authors:  Alexander Mellmann; Dag Harmsen; Craig A Cummings; Emily B Zentz; Shana R Leopold; Alain Rico; Karola Prior; Rafael Szczepanowski; Yongmei Ji; Wenlan Zhang; Stephen F McLaughlin; John K Henkhaus; Benjamin Leopold; Martina Bielaszewska; Rita Prager; Pius M Brzoska; Richard L Moore; Simone Guenther; Jonathan M Rothberg; Helge Karch
Journal:  PLoS One       Date:  2011-07-20       Impact factor: 3.240

6.  TreeDyn: towards dynamic graphics and annotations for analyses of trees.

Authors:  François Chevenet; Christine Brun; Anne-Laure Bañuls; Bernard Jacq; Richard Christen
Journal:  BMC Bioinformatics       Date:  2006-10-10       Impact factor: 3.169

7.  BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness.

Authors:  Oriol Mazariegos-Canellas; Trien Do; Tim Peto; David W Eyre; Anthony Underwood; Derrick Crook; David H Wyllie
Journal:  BMC Bioinformatics       Date:  2017-11-13       Impact factor: 3.169

8.  PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.

Authors:  Alexandre P Francisco; Cátia Vaz; Pedro T Monteiro; José Melo-Cristino; Mário Ramirez; Joäo A Carriço
Journal:  BMC Bioinformatics       Date:  2012-05-08       Impact factor: 3.169

9.  Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees.

Authors:  Zilong He; Huangkai Zhang; Shenghan Gao; Martin J Lercher; Wei-Hua Chen; Songnian Hu
Journal:  Nucleic Acids Res       Date:  2016-04-30       Impact factor: 16.971

10.  Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.

Authors:  Zhemin Zhou; Inge Lundstrøm; Alicia Tran-Dien; Sebastián Duchêne; Nabil-Fareed Alikhan; Martin J Sergeant; Gemma Langridge; Anna K Fotakis; Satheesh Nair; Hans K Stenøien; Stian S Hamre; Sherwood Casjens; Axel Christophersen; Christopher Quince; Nicholas R Thomson; François-Xavier Weill; Simon Y W Ho; M Thomas P Gilbert; Mark Achtman
Journal:  Curr Biol       Date:  2018-07-19       Impact factor: 10.834
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  173 in total

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2.  Phylogenetic Methods for Genome-Wide Association Studies in Bacteria.

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3.  Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group.

Authors:  Timothy J Johnson; Ehud Elnekave; Elizabeth A Miller; Jeannette Munoz-Aguayo; Cristian Flores Figueroa; Brian Johnston; Daniel W Nielson; Catherine M Logue; James R Johnson
Journal:  Antimicrob Agents Chemother       Date:  2018-12-21       Impact factor: 5.191

4.  Atti Le giornate della ricerca scientificae delle esperienze professionali dei giovani: Società Italiana di Igiene, Medicina Preventiva e Sanità Pubblica (SItI) Roma 20-21 dicembre 2019.

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Journal:  J Prev Med Hyg       Date:  2020-02-13

5.  Genome-Wide Identification of Host-Segregating Single-Nucleotide Polymorphisms for Source Attribution of Clinical Campylobacter coli Isolates.

Authors:  Quentin Jehanne; Ben Pascoe; Lucie Bénéjat; Astrid Ducournau; Alice Buissonnière; Evangelos Mourkas; Francis Mégraud; Emilie Bessède; Samuel K Sheppard; Philippe Lehours
Journal:  Appl Environ Microbiol       Date:  2020-11-24       Impact factor: 4.792

6.  ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.

Authors:  Natasha Pavlovikj; Joao Carlos Gomes-Neto; Jitender S Deogun; Andrew K Benson
Journal:  PeerJ       Date:  2021-05-21       Impact factor: 2.984

7.  Carbapenemase-Producing Gram-Negative Bacteria from American Crows in the United States.

Authors:  Iva Kutilova; Adam Valcek; Costas C Papagiannitsis; Darina Cejkova; Martina Masarikova; Veronika Paskova; Lenka Davidova-Gerzova; Petra Videnska; Jaroslav Hrabak; Ivan Literak; Monika Dolejska
Journal:  Antimicrob Agents Chemother       Date:  2020-12-16       Impact factor: 5.191

8.  Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates.

Authors:  Sabrina Diemert; Tao Yan
Journal:  Appl Environ Microbiol       Date:  2019-05-02       Impact factor: 4.792

9.  Horsing around: Escherichia coli ST1250 of equine origin harbouring epidemic IncHI1/ST9 plasmid with bla CTX-M-1 and an operon for short-chain fructooligosaccharides metabolism.

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Journal:  Antimicrob Agents Chemother       Date:  2021-02-22       Impact factor: 5.191

10.  Escherichia coli Sequence Type 457 Is an Emerging Extended-Spectrum-β-Lactam-Resistant Lineage with Reservoirs in Wildlife and Food-Producing Animals.

Authors:  Steven P Djordjevic; Monika Dolejska; Kristina Nesporova; Ethan R Wyrsch; Adam Valcek; Ibrahim Bitar; Khin Chaw; Patrick Harris; Jaroslav Hrabak; Ivan Literak
Journal:  Antimicrob Agents Chemother       Date:  2020-12-16       Impact factor: 5.191
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