MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets

Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, Mira A (2012) The oral metagenome in health and disease. ISME J 6:46–56 Ben-Hur A, Noble WS (2005) Kernel methods for predicting protein-protein interactions. Bioinformatics 21(Suppl 1):i38–i46 Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120 Bottou L (2007) Large-scale kernel machines. The MIT Press, Cambridge Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R (2010a) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267 Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI et al (2010b) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336 Chang CC, Lin CJ (2011) LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol 2:27 Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287 DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072 Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461 Fan RE, Chang KW, Hsieh CJ, Wang XR, Lin CJ (2008) LIBLINEAR: a library for large linear classification. J Mach Learn Res 9:1871–1874 Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ (2014) The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15:382–392 Ghoshal UC, Shukla R, Ghoshal U, Gwee KA, Ng SC, Quigley EM (2012) The gut microbiota and irritable bowel syndrome: friend or foe? Int J Inflam 2012:151085 Goecks J, Nekrutenko A, Taylor J, Galaxy T (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11:R86 Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249 Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE, Petrosino JF, Patterson PH, Mazmanian SK (2013) Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155:1451–1463 Human Microbiome Project C (2012) A framework for human microbiome research. Nature 486:215–221 Liao L, Noble WS (2003) Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J Comput Biol 10:857–868 Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R (2011) UniFrac: an effective distance metric for microbial community comparison. ISME J 5:169–172 Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963 McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG (2012) The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience 1:7 Navas-Molina JA, Peralta-Sanchez JM, Gonzalez A, McMurdie PJ, Vazquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R (2013) Advancing our understanding of the human microbiome using QIIME. Methods Enzymol 531:371–444 Pavlidis P, Weston J, Cai J, Noble WS (2002) Learning gene functional classifications from multiple data types. J Comput Biol 9:401–411 Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650 Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D (2011) Microbial diversity in saliva of oral squamous cell carcinoma. FEMS Immunol Med Microbiol 61:269–277 Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M, LeChatelier E, Renault P, Pons N, Batto JM, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J, Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:55–60 Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, Guo J, Le Chatelier E, Yao J, Wu L, Zhou J, Ni S, Liu L, Pons N, Batto JM, Kennedy SP, Leonard P, Yuan C, Ding W, Chen Y, Hu X, Zheng B, Qian G, Xu W, Ehrlich SD, Zheng S, Li L (2014) Alterations of the human gut microbiome in liver cirrhosis. Nature 513:59–64 Rajilić-Stojanović M, Jonkers DM, Salonen A, Hanevik K, Raes J, Jalanka J, de Vos WM, Manichanh C, Golic N, Enck P, Philippou E, Iraqi FA, Clarke G, Spiller RC, Penders J (2015) Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena? Am J Gastroenterol 110:278–287 Ratsch G, Sonnenburg S, Scholkopf B (2005) RASE: recognition of alternatively spliced exons in C.elegans. Bioinformatics 21(Suppl 1):i369–i377 Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A (2012) The genboree microbiome toolset and the analysis of 16S rRNA microbial sequences. BMC Bioinform 13(Suppl 13):S11 Saeys Y, Inza I, Larranaga P (2007) A review of feature selection techniques in bioinformatics. Bioinformatics 23:2507–2517 Sankar SA, Lagier JC, Pontarotti P, Raoult D, Fournier PE (2015) The human gut microbiome, a taxonomic conundrum. Syst Appl Microbiol 38:276–286 Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J (2011) Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 141:1782–1791 Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB, Huttenhower C, Littman DR (2013) Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife 2:e01202 Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541 Sonnenburg S, Schweikert G, Philips P, Behr J, Ratsch G (2007) Accurate splice site prediction using support vector machines. BMC Bioinform 8(Suppl 10):S7 Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484 Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267