Metagenomic Data Analysis ------------------------- (x in front of a number means the paper has been chosen) 1: Carr R, Shen-Orr SS, Borenstein E. Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PLoS Comput Biol. 2013;9(10):e1003292. doi: 10.1371/journal.pcbi.1003292. Epub 2013 Oct 17. PubMed PMID: 24146609; PubMed Central PMCID: PMC3798274. 2: Koslicki D, Foucart S, Rosen G. Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. Bioinformatics. 2013 Sep 1;29(17):2096-102. doi: 10.1093/bioinformatics/btt336. Epub 2013 Jun 20. PubMed PMID: 23786768. 3: Porter MS, Beiko RG. SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles. Bioinformatics. 2013 Aug 1;29(15):1858-64. doi: 10.1093/bioinformatics/btt313. Epub 2013 Jun 3. PubMed PMID: 23732273; PubMed Central PMCID: PMC3712219. 4: Mirauta B, Nicolas P, Richard H. Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models. Bioinformatics. 2014 Feb 20. [Epub ahead of print] PubMed PMID: 24470570. x5: Gusnanto A, Taylor CC, Nafisah I, Wood HM, Rabbitts P, Berri S. Estimating optimal window size for analysis of low-coverage next-generation sequence data. Bioinformatics. 2014 Mar 23. [Epub ahead of print] PubMed PMID: 24603986. 6: Wang TY, Su CH, Tsai HK. MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions. Bioinformatics. 2011 Dec 15;27(24):3341-7. doi: 10.1093/bioinformatics/btr583. Epub 2011 Oct 20. PubMed PMID: 22016405. 7: Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C. Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. Bioinformatics. 2011 Dec 1;27(23):3242-9. doi: 10.1093/bioinformatics/btr547. Epub 2011 Oct 7. PubMed PMID: 21984758; PubMed Central PMCID: PMC3223360. 8: Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics. 2011 Nov 1;27(21):2964-71. doi: 10.1093/bioinformatics/btr520. Epub 2011 Sep 16. PubMed PMID: 21926123; PubMed Central PMCID: PMC3198580. 9: Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol. 2011 Jan 20;7(1):e1001061. doi: 10.1371/journal.pcbi.1001061. PubMed PMID: 21283775; PubMed Central PMCID: PMC3024254. 10: Gerlach W, Stoye J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res. 2011 Aug;39(14):e91. doi: 10.1093/nar/gkr225. Epub 2011 May 17. PubMed PMID: 21586583; PubMed Central PMCID: PMC3152360. 11: Wang M, Ye Y, Tang H. A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community. J Comput Biol. 2012 Jun;19(6):814-25. doi: 10.1089/cmb.2012.0058. PubMed PMID: 22697249; PubMed Central PMCID: PMC3375647. 12: Jiao D, Ye Y, Tang H. Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. PLoS Comput Biol. 2013;9(3):e1002981. doi: 10.1371/journal.pcbi.1002981. Epub 2013 Mar 21. PubMed PMID: 23555216; PubMed Central PMCID: PMC3605055. 13: Tanaseichuk O1, Borneman J, Jiang T. Phylogeny-based classification of microbial communities. Bioinformatics. 2014 Feb 15;30(4):449-56. doi: 10.1093/bioinformatics/btt700. Epub 2013 Dec 24. 14: Albanese D, De Filippo C, Cavalieri D, Donati C. Explaining diversity in metagenomic datasets by phylogenetic-based feature weighting. PLoS Comput Biol. 2015 Mar 27;11(3):e1004186. doi: 10.1371/journal.pcbi.1004186. eCollection 2015. 15: Liu Z, Sun F, Braun J, McGovern DP, Piantadosi S. Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data. Bioinformatics. 2015 Apr 1;31(7):1067-74. doi: 10.1093/bioinformatics/btu778. Epub 2014 Nov 20. 16: Liu Z, Lin S, Piantadosi S. Network construction and structure detection with metagenomic count data. BioData Min. 2015 Dec 12;8:40. doi: 10.1186/s13040-015-0072-2. eCollection 2015. 17: Hugerth LW, Larsson J, Alneberg J, Lindh MV, Legrand C, Pinhassi J, Andersson AF. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol. 2015 Dec 14;16:279. doi: 10.1186/s13059-015-0834-7. 18: Mehrshad M, Amoozegar MA, Ghai R, Shahzadeh Fazeli SA, Rodriguez-Valera F. Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea. Appl Environ Microbiol. 2016 Jan 4;82(5):1599-612. doi: 10.1128/AEM.03381-15.