Literature DB >> 24021386

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.

Charles E Robertson1, J Kirk Harris, Brandie D Wagner, David Granger, Kathy Browne, Beth Tatem, Leah M Feazel, Kristin Park, Norman R Pace, Daniel N Frank.   

Abstract

Studies of the human microbiome, and microbial community ecology in general, have blossomed of late and are now a burgeoning source of exciting research findings. Along with the advent of next-generation sequencing platforms, which have dramatically increased the scope of microbiome-related projects, several high-performance sequence analysis pipelines (e.g. QIIME, MOTHUR, VAMPS) are now available to investigators for microbiome analysis. The subject of our manuscript, the graphical user interface-based Explicet software package, fills a previously unmet need for a robust, yet intuitive means of integrating the outputs of the software pipelines with user-specified metadata and then visualizing the combined data.

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Mesh:

Year:  2013        PMID: 24021386      PMCID: PMC3834795          DOI: 10.1093/bioinformatics/btt526

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  12 in total

Review 1.  The last word: books as a statistical metaphor for microbial communities.

Authors:  Patrick D Schloss; Jo Handelsman
Journal:  Annu Rev Microbiol       Date:  2007       Impact factor: 15.500

2.  Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

Authors:  Patrick D Schloss; Sarah L Westcott; Thomas Ryabin; Justine R Hall; Martin Hartmann; Emily B Hollister; Ryan A Lesniewski; Brian B Oakley; Donovan H Parks; Courtney J Robinson; Jason W Sahl; Blaz Stres; Gerhard G Thallinger; David J Van Horn; Carolyn F Weber
Journal:  Appl Environ Microbiol       Date:  2009-10-02       Impact factor: 4.792

Review 3.  The role of the intestinal microbiota in type 1 diabetes.

Authors:  Naoko Hara; Aimon K Alkanani; Diana Ir; Charles E Robertson; Brandie D Wagner; Daniel N Frank; Danny Zipris
Journal:  Clin Immunol       Date:  2012-12-11       Impact factor: 3.969

4.  Culture-independent analysis of aerosol microbiology in a metropolitan subway system.

Authors:  Charles E Robertson; Laura K Baumgartner; J Kirk Harris; Kristen L Peterson; Mark J Stevens; Daniel N Frank; Norman R Pace
Journal:  Appl Environ Microbiol       Date:  2013-03-29       Impact factor: 4.792

5.  Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

Authors:  Amber L Hartman; Sean Riddle; Timothy McPhillips; Bertram Ludäscher; Jonathan A Eisen
Journal:  BMC Bioinformatics       Date:  2010-06-12       Impact factor: 3.169

6.  Topographical and temporal diversity of the human skin microbiome.

Authors:  Elizabeth A Grice; Heidi H Kong; Sean Conlan; Clayton B Deming; Joie Davis; Alice C Young; Gerard G Bouffard; Robert W Blakesley; Patrick R Murray; Eric D Green; Maria L Turner; Julia A Segre
Journal:  Science       Date:  2009-05-29       Impact factor: 47.728

7.  Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Authors:  Justin Kuczynski; Jesse Stombaugh; William Anton Walters; Antonio González; J Gregory Caporaso; Rob Knight
Journal:  Curr Protoc Microbiol       Date:  2012-11

8.  Application of two-part statistics for comparison of sequence variant counts.

Authors:  Brandie D Wagner; Charles E Robertson; J Kirk Harris
Journal:  PLoS One       Date:  2011-05-23       Impact factor: 3.240

9.  BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing.

Authors:  Daniel N Frank
Journal:  BMC Bioinformatics       Date:  2009-10-29       Impact factor: 3.169

10.  XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.

Authors:  Daniel N Frank
Journal:  BMC Bioinformatics       Date:  2008-10-07       Impact factor: 3.169

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  112 in total

1.  Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration.

Authors:  Christopher A Lopez; Brittany M Miller; Fabian Rivera-Chávez; Eric M Velazquez; Mariana X Byndloss; Alfredo Chávez-Arroyo; Kristen L Lokken; Renée M Tsolis; Sebastian E Winter; Andreas J Bäumler
Journal:  Science       Date:  2016-09-15       Impact factor: 47.728

2.  FUT2 Variants Confer Susceptibility to Familial Otitis Media.

Authors:  Regie Lyn P Santos-Cortez; Charlotte M Chiong; Daniel N Frank; Allen F Ryan; Arnaud P J Giese; Tori Bootpetch Roberts; Kathleen A Daly; Matthew J Steritz; Wasyl Szeremeta; Melquiadesa Pedro; Harold Pine; Talitha Karisse L Yarza; Melissa A Scholes; Erasmo Gonzalo D V Llanes; Saira Yousaf; Norman Friedman; Ma Leah C Tantoco; Todd M Wine; Patrick John Labra; Jeanne Benoit; Amanda G Ruiz; Rhodieleen Anne R de la Cruz; Christopher Greenlee; Ayesha Yousaf; Jonathan Cardwell; Rachelle Marie A Nonato; Dylan Ray; Kimberly Mae C Ong; Edward So; Charles E Robertson; Jordyn Dinwiddie; Sheryl Mae Lagrana-Villagracia; Samuel P Gubbels; Rehan S Shaikh; Stephen P Cass; Elisabet Einarsdottir; Nanette R Lee; David A Schwartz; Teresa Luisa I Gloria-Cruz; Michael J Bamshad; Ivana V Yang; Juha Kere; Generoso T Abes; Jeremy D Prager; Saima Riazuddin; Abner L Chan; Patricia J Yoon; Deborah A Nickerson; Eva Maria Cutiongco-de la Paz; Sven-Olrik Streubel; Maria Rina T Reyes-Quintos; Herman A Jenkins; Petri Mattila; Kenny H Chan; Karen L Mohlke; Suzanne M Leal; Lena Hafrén; Tasnee Chonmaitree; Michele M Sale; Zubair M Ahmed
Journal:  Am J Hum Genet       Date:  2018-10-25       Impact factor: 11.025

3.  Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer.

Authors:  Roberto Mendez; Kousik Kesh; Nivedita Arora; Leá Di Martino; Florencia McAllister; Nipun Merchant; Sulagna Banerjee; Santanu Banerjee
Journal:  Carcinogenesis       Date:  2020-07-10       Impact factor: 4.944

4.  Bile acid sequestration reverses liver injury and prevents progression of nonalcoholic steatohepatitis in Western diet-fed mice.

Authors:  Shogo Takahashi; Yuhuan Luo; Suman Ranjit; Cen Xie; Andrew E Libby; David J Orlicky; Alexander Dvornikov; Xiaoxin X Wang; Komuraiah Myakala; Bryce A Jones; Kanchan Bhasin; Dong Wang; James L McManaman; Kristopher W Krausz; Enrico Gratton; Diana Ir; Charles E Robertson; Daniel N Frank; Frank J Gonzalez; Moshe Levi
Journal:  J Biol Chem       Date:  2020-02-19       Impact factor: 5.157

5.  Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes.

Authors:  Aimon K Alkanani; Naoko Hara; Peter A Gottlieb; Diana Ir; Charles E Robertson; Brandie D Wagner; Daniel N Frank; Danny Zipris
Journal:  Diabetes       Date:  2015-06-11       Impact factor: 9.461

6.  The effect of PPI use on human gut microbiota and weight loss in patients undergoing laparoscopic Roux-en-Y gastric bypass.

Authors:  Emily K Ward; Dara P Schuster; Katie H Stowers; Amanda K Royse; Diana Ir; Charles E Robertson; Daniel N Frank; Gregory L Austin
Journal:  Obes Surg       Date:  2014-09       Impact factor: 4.129

7.  Airway microbiota across age and disease spectrum in cystic fibrosis.

Authors:  Edith T Zemanick; Brandie D Wagner; Charles E Robertson; Richard C Ahrens; James F Chmiel; John P Clancy; Ronald L Gibson; William T Harris; Geoffrey Kurland; Theresa A Laguna; Susanna A McColley; Karen McCoy; George Retsch-Bogart; Kurtis T Sobush; Pamela L Zeitlin; Mark J Stevens; Frank J Accurso; Scott D Sagel; J Kirk Harris
Journal:  Eur Respir J       Date:  2017-11-16       Impact factor: 16.671

8.  Changes in Airway Microbiome and Inflammation with Ivacaftor Treatment in Patients with Cystic Fibrosis and the G551D Mutation.

Authors:  J Kirk Harris; Brandie D Wagner; Edith T Zemanick; Charles E Robertson; Mark J Stevens; Sonya L Heltshe; Steven M Rowe; Scott D Sagel
Journal:  Ann Am Thorac Soc       Date:  2020-02

9.  Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy.

Authors:  Tyler Lewy; Bo-Young Hong; Barbara Weiser; Harold Burger; Andrew Tremain; George Weinstock; Kathryn Anastos; Michael D George
Journal:  AIDS Res Hum Retroviruses       Date:  2018-07-23       Impact factor: 2.205

10.  Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis.

Authors:  Vijay R Ramakrishnan; Sarah Gitomer; Jennifer M Kofonow; Charles E Robertson; Daniel N Frank
Journal:  Int Forum Allergy Rhinol       Date:  2016-09-14       Impact factor: 3.858

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