DOC: Add to citations.bib for QIIME2 (#494)

* DOC: Add to citations.bib for QIIME2 * Update README.md Co-authored-by: Marcus Fedarko <marcus.fedarko@gmail.com> * Update empress/citations.bib Co-authored-by: Marcus Fedarko <marcus.fedarko@gmail.com> * Remove citations Co-authored-by: Marcus Fedarko <marcus.fedarko@gmail.com>
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diff --git a/README.md b/README.md
@@ -552,7 +552,7 @@ Empress is available in mSystems
 Empress in your work, please cite it! The BibTeX for this paper is:
 
 ```
-@article {Cantrelle01216-20,
+@article {CantrellFedarko2021empress,
  author = {Cantrell, Kalen and Fedarko, Marcus W. and Rahman, Gibraan and McDonald, Daniel and Yang, Yimeng and Zaw, Thant and Gonzalez, Antonio and Janssen, Stefan and Estaki, Mehrbod and Haiminen, Niina and Beck, Kristen L. and Zhu, Qiyun and Sayyari, Erfan and Morton, James T. and Armstrong, George and Tripathi, Anupriya and Gauglitz, Julia M. and Marotz, Clarisse and Matteson, Nathaniel L. and Martino, Cameron and Sanders, Jon G. and Carrieri, Anna Paola and Song, Se Jin and Swafford, Austin D. and Dorrestein, Pieter C. and Andersen, Kristian G. and Parida, Laxmi and Kim, Ho-Cheol and V{\'a}zquez-Baeza, Yoshiki and Knight, Rob},
  editor = {Hug, Laura A.},
  title = {EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets},

diff --git a/empress/citations.bib b/empress/citations.bib
@@ -1,38 +1,14 @@
-@article {morton2017gneiss,
- author = {Morton, James T. and Sanders, Jon and Quinn, Robert A. and McDonald, Daniel and Gonzalez, Antonio and V{\'a}zquez-Baeza, Yoshiki and Navas-Molina, Jose A. and Song, Se Jin and Metcalf, Jessica L. and Hyde, Embriette R. and Lladser, Manuel and Dorrestein, Pieter C. and Knight, Rob},
- editor = {Jansson, Janet K.},
- title = {Balance Trees Reveal Microbial Niche Differentiation},
- volume = {2},
- number = {1},
- elocation-id = {e00162-16},
- year = {2017},
- doi = {10.1128/mSystems.00162-16},
- publisher = {American Society for Microbiology Journals},
- abstract = {Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples.IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss.Author Video: An author video summary of this article is available.},
- URL = {https://msystems.asm.org/content/2/1/e00162-16},
- eprint = {https://msystems.asm.org/content/2/1/e00162-16.full.pdf},
- journal = {mSystems}
+@article {CantrellFedarko2021empress,
+ author = {Cantrell, Kalen and Fedarko, Marcus W. and Rahman, Gibraan and McDonald, Daniel and Yang, Yimeng and Zaw, Thant and Gonzalez, Antonio and Janssen, Stefan and Estaki, Mehrbod and Haiminen, Niina and Beck, Kristen L. and Zhu, Qiyun and Sayyari, Erfan and Morton, James T. and Armstrong, George and Tripathi, Anupriya and Gauglitz, Julia M. and Marotz, Clarisse and Matteson, Nathaniel L. and Martino, Cameron and Sanders, Jon G. and Carrieri, Anna Paola and Song, Se Jin and Swafford, Austin D. and Dorrestein, Pieter C. and Andersen, Kristian G. and Parida, Laxmi and Kim, Ho-Cheol and V{\'a}zquez-Baeza, Yoshiki and Knight, Rob},
+ editor = {Hug, Laura A.},
+ title = {EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets},
+ volume = {6},
+ number = {2},
+ elocation-id = {e01216-20},
+ year = {2021},
+ doi = {10.1128/mSystems.01216-20},
+ publisher = {American Society for Microbiology Journals},
+ URL = {https://msystems.asm.org/content/6/2/e01216-20},
+ eprint = {https://msystems.asm.org/content/6/2/e01216-20.full.pdf},
+ journal = {mSystems}
 }
-
-@article{cordova2016trees,
- author = {Cordova, Joshimar; Navarro, Gonzalo},
- title = {Simple and efficient fully-functional succinct trees},
- journal = {arXiv},
- year = {2016},
- type = {Journal Article}
-}
-
-@article{mcdonald2018unifrac,
- author = {McDonald, D. and Vazquez-Baeza, Y. and Koslicki, D. and McClelland, J. and Reeve, N. and Xu, Z. and Gonzalez, A. and Knight, R.},
- title = {Striped UniFrac: enabling microbiome analysis at unprecedented scale},
- journal = {Nat Methods},
- volume = {15},
- number = {11},
- pages = {847-848},
- ISSN = {1548-7105 (Electronic)
-1548-7091 (Linking)},
- DOI = {10.1038/s41592-018-0187-8},
- url = {https://www.ncbi.nlm.nih.gov/pubmed/30377368},
- year = {2018},
- type = {Journal Article}
-}