Class Prediction and Feature Selection with Linear Optimization for Metagenomic Count Data
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pone.0053253
Download full text from publisher
References listed on IDEAS
- James Robert White & Niranjan Nagarajan & Mihai Pop, 2009. "Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples," PLOS Computational Biology, Public Library of Science, vol. 5(4), pages 1-11, April.
- Onur Dagliyan & Fadime Uney-Yuksektepe & I Halil Kavakli & Metin Turkay, 2011. "Optimization Based Tumor Classification from Microarray Gene Expression Data," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-10, February.
- Peter J. Turnbaugh & Ruth E. Ley & Micah Hamady & Claire M. Fraser-Liggett & Rob Knight & Jeffrey I. Gordon, 2007. "The Human Microbiome Project," Nature, Nature, vol. 449(7164), pages 804-810, October.
- G. Al-Jeiroudi & J. Gondzio, 2009. "Convergence Analysis of the Inexact Infeasible Interior-Point Method for Linear Optimization," Journal of Optimization Theory and Applications, Springer, vol. 141(2), pages 231-247, May.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Shilan Li & Jianxin Shi & Paul Albert & Hong-Bin Fang, 2022. "Dependence Structure Analysis and Its Application in Human Microbiome," Mathematics, MDPI, vol. 11(1), pages 1-14, December.
- Amirhossein Shamsaddini & Kimia Dadkhah & Patrick M Gillevet, 2020. "BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-13, June.
- Gregor Gorkiewicz & Gerhard G Thallinger & Slave Trajanoski & Stefan Lackner & Gernot Stocker & Thomas Hinterleitner & Christian Gülly & Christoph Högenauer, 2013. "Alterations in the Colonic Microbiota in Response to Osmotic Diarrhea," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-17, February.
- Patricio S La Rosa & Berkley Shands & Elena Deych & Yanjiao Zhou & Erica Sodergren & George Weinstock & William D Shannon, 2012. "Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-12, November.
- Pengfei Song & Wen Qin & YanGan Huang & Lei Wang & Zhenyuan Cai & Tongzuo Zhang, 2020. "Grazing Management Influences Gut Microbial Diversity of Livestock in the Same Area," Sustainability, MDPI, vol. 12(10), pages 1-12, May.
- Daphna Rothschild & Erez Dekel & Jean Hausser & Anat Bren & Guy Aidelberg & Pablo Szekely & Uri Alon, 2014. "Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-9, May.
- Stefano Cipolla & Jacek Gondzio, 2023. "Proximal Stabilized Interior Point Methods and Low-Frequency-Update Preconditioning Techniques," Journal of Optimization Theory and Applications, Springer, vol. 197(3), pages 1061-1103, June.
- Allison G. White & George S. Watts & Zhenqiang Lu & Maria M. Meza-Montenegro & Eric A. Lutz & Philip Harber & Jefferey L. Burgess, 2014. "Environmental Arsenic Exposure and Microbiota in Induced Sputum," IJERPH, MDPI, vol. 11(2), pages 1-15, February.
- Jae-Chang Cho, 2021. "Human microbiome privacy risks associated with summary statistics," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-11, April.
- Pirjo Wacklin & Harri Mäkivuokko & Noora Alakulppi & Janne Nikkilä & Heli Tenkanen & Jarkko Räbinä & Jukka Partanen & Kari Aranko & Jaana Mättö, 2011. "Secretor Genotype (FUT2 gene) Is Strongly Associated with the Composition of Bifidobacteria in the Human Intestine," PLOS ONE, Public Library of Science, vol. 6(5), pages 1-10, May.
- Yee Sang Wong & Nicholas John Osborne, 2022. "Biodiversity Effects on Human Mental Health via Microbiota Alterations," IJERPH, MDPI, vol. 19(19), pages 1-13, September.
- Weiyue Ji & Handuo Shi & Haoqian Zhang & Rui Sun & Jingyi Xi & Dingqiao Wen & Jingchen Feng & Yiwei Chen & Xiao Qin & Yanrong Ma & Wenhan Luo & Linna Deng & Hanchi Lin & Ruofan Yu & Qi Ouyang, 2013. "A Formalized Design Process for Bacterial Consortia That Perform Logic Computing," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-9, February.
- Disha Tandon & Mohammed Monzoorul Haque & Sharmila S Mande, 2016. "Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques," PLOS ONE, Public Library of Science, vol. 11(4), pages 1-16, April.
- Eric Z. Chen & Frederic D. Bushman & Hongzhe Li, 2017. "A Model-Based Approach for Species Abundance Quantification Based on Shotgun Metagenomic Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 13-27, June.
- Yong Li & Jiejie Zhang & Jianqiang Zhang & Wenlai Xu & Zishen Mou, 2019. "Microbial Community Structure in the Sediments and Its Relation to Environmental Factors in Eutrophicated Sancha Lake," IJERPH, MDPI, vol. 16(11), pages 1-15, May.
- Monica Vera-Lise Tulstrup & Ellen Gerd Christensen & Vera Carvalho & Caroline Linninge & Siv Ahrné & Ole Højberg & Tine Rask Licht & Martin Iain Bahl, 2015. "Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-17, December.
- Charles K Fisher & Thierry Mora & Aleksandra M Walczak, 2017. "Variable habitat conditions drive species covariation in the human microbiota," PLOS Computational Biology, Public Library of Science, vol. 13(4), pages 1-18, April.
- Gondzio, Jacek, 2012. "Interior point methods 25 years later," European Journal of Operational Research, Elsevier, vol. 218(3), pages 587-601.
- Bahareh Mansoorian & Emilie Combet & Areej Alkhaldy & Ada L. Garcia & Christine Ann Edwards, 2019. "Impact of Fermentable Fibres on the Colonic Microbiota Metabolism of Dietary Polyphenols Rutin and Quercetin," IJERPH, MDPI, vol. 16(2), pages 1-12, January.
- Paul J McMurdie & Susan Holmes, 2014. "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible," PLOS Computational Biology, Public Library of Science, vol. 10(4), pages 1-12, April.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0053253. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.