EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Author:

Cantrell Kalen12,Fedarko Marcus W.12ORCID,Rahman Gibraan34ORCID,McDonald Daniel4,Yang Yimeng2,Zaw Thant2,Gonzalez Antonio4,Janssen Stefan5ORCID,Estaki Mehrbod4ORCID,Haiminen Niina6ORCID,Beck Kristen L.7ORCID,Zhu Qiyun4ORCID,Sayyari Erfan28,Morton James T.9,Armstrong George234ORCID,Tripathi Anupriya4ORCID,Gauglitz Julia M.10ORCID,Marotz Clarisse411ORCID,Matteson Nathaniel L.12,Martino Cameron234,Sanders Jon G.13ORCID,Carrieri Anna Paola14ORCID,Song Se Jin2,Swafford Austin D.2ORCID,Dorrestein Pieter C.210,Andersen Kristian G.12,Parida Laxmi6ORCID,Kim Ho-Cheol7ORCID,Vázquez-Baeza Yoshiki2ORCID,Knight Rob12415ORCID

Affiliation:

1. Department of Computer Science, Jacobs School of Engineering, University of California, San Diego, California, USA

2. Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, California, USA

3. Bioinformatics and Systems Biology Program, University of California, San Diego, California, USA

4. Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA

5. Algorithmic Bioinformatics, Justus Liebig University, Giessen, Germany

6. IBM T. J. Watson Research Center, Yorktown Heights, New York, USA

7. IBM Almaden Research Center, San Jose, California, USA

8. Department of Electrical and Computer Engineering, University of California, San Diego, California, USA

9. Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA

10. Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA

11. Scripps Institution of Oceanography, University of California, San Diego, California, USA

12. Scripps Research Institute, San Diego, California, USA

13. Cornell Institute for Host-Microbe Interaction and Disease, Cornell University, Ithaca, New York, USA

14. IBM Research, The Hartree Centre, Daresbury, United Kingdom

15. Department of Bioengineering, University of California, San Diego, California, USA

Abstract

Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research.

Publisher

American Society for Microbiology

Subject

Computer Science Applications,Genetics,Molecular Biology,Modeling and Simulation,Ecology, Evolution, Behavior and Systematics,Biochemistry,Physiology,Microbiology

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