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MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

View ORCID ProfileFrancislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr., Gabriel R. Fernandes, View ORCID ProfileDavid S. Roos, Daniel P. Beiting
doi: https://doi.org/10.1101/176784
Francislon S. Oliveira
8Instituto René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
9Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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  • ORCID record for Francislon S. Oliveira
John Brestelli
2Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104
3Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Shon Cade
7Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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Jie Zheng
2Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104
3Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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John Iodice
2Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104
3Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Steve Fischer
2Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104
3Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Cristina Aurrecoechea
4Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
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Jessica C. Kissinger
4Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
5Department of Genetics, University of Georgia, Athens, GA 30602, USA
6Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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Brian P. Brunk
2Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104
7Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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Christian J. Stoeckert Jr.
2Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104
3Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Gabriel R. Fernandes
8Instituto René Rachou, FIOCRUZ/Minas, Belo Horizonte, Minas Gerais, Brazil
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David S. Roos
7Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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  • For correspondence: beiting@upenn.edu dsroos@sas.upenn.edu
Daniel P. Beiting
1Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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  • For correspondence: beiting@upenn.edu dsroos@sas.upenn.edu
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ABSTRACT

MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical ‘strategy’ approach. The current release of the database integrates microbial census data with sample details for nearly 14,000 samples originating from human, animal and environmental sources, including over 9,000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate.

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Posted August 16, 2017.
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MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments
Francislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr., Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting
bioRxiv 176784; doi: https://doi.org/10.1101/176784
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MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments
Francislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr., Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting
bioRxiv 176784; doi: https://doi.org/10.1101/176784

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