{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T18:07:17Z","timestamp":1775844437953,"version":"3.50.1"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,6,15]],"date-time":"2018-06-15T00:00:00Z","timestamp":1529020800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2205-3","type":"journal-article","created":{"date-parts":[[2018,6,15]],"date-time":"2018-06-15T04:17:15Z","timestamp":1529036235000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":84,"title":["Taxonomy-aware feature engineering for microbiome classification"],"prefix":"10.1186","volume":"19","author":[{"given":"Mai","family":"Oudah","sequence":"first","affiliation":[]},{"given":"Andreas","family":"Henschel","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,6,15]]},"reference":[{"issue":"Supplement 1","key":"2205_CR1","doi-asserted-by":"publisher","first-page":"4516","DOI":"10.1073\/pnas.1000080107","volume":"108","author":"JG Caporaso","year":"2011","unstructured":"Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, et al. Global patterns of 16s rrna diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci. 2011;108(Supplement 1):4516\u201322.","journal-title":"Proc Natl Acad Sci"},{"key":"2205_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.15252\/msb.20145645","volume":"10","author":"G Zeller","year":"2014","unstructured":"Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Bohm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol. 2014;10:1\u201318.","journal-title":"Mol Syst Biol"},{"key":"2205_CR3","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1158\/1940-6207.CAPR-14-0129","volume":"7","author":"JP Zackular","year":"2014","unstructured":"Zackular JP, Rogers MAM, Ruffin MT, Schloss PD. The human gut microbiome as a screening tool for colorectal cancer. Cancer Prev Res. 2014;7:1112\u201321.","journal-title":"Cancer Prev Res"},{"key":"2205_CR4","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/nature09944","volume":"473","author":"M Arumugam","year":"2011","unstructured":"Arumugam M, Raes J, Pelletier E, Paslier DL, Yamada T, et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174\u201380. https:\/\/doi.org\/10.1038\/nature09944 .","journal-title":"Nature"},{"issue":"5960","key":"2205_CR5","doi-asserted-by":"publisher","first-page":"1694","DOI":"10.1126\/science.1177486","volume":"326","author":"EK Costello","year":"2009","unstructured":"Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009;326(5960):1694\u20137.","journal-title":"Science"},{"key":"2205_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1004468","volume":"11","author":"A Henschel","year":"2015","unstructured":"Henschel A, Anwar MZ, Manohar V. Comprehensive meta-analysis of ontology annotated 16s rrna profiles identifies beta diversity clusters of environmental bacterial communities. PLoS Comput Biol. 2015;11:1\u201324.","journal-title":"PLoS Comput Biol"},{"key":"2205_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0039242","volume":"7","author":"E Papa","year":"2012","unstructured":"Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, Giannoukos G, Ciulla D, Tabbaa D, Ingram J, Schauer DB, Ward DV, Korzenik JR, Xavier RJ, Bousvaros A, Alm EJ. Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS One. 2012;7:1\u201312.","journal-title":"PLoS One"},{"key":"2205_CR8","doi-asserted-by":"publisher","first-page":"4158","DOI":"10.1073\/pnas.1015676108","volume":"108","author":"JJ Werner","year":"2011","unstructured":"Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT. Bacterial community structures are unique and resilient in full-scale bioenergy systems. PNAS. 2011;108:4158\u201363.","journal-title":"PNAS"},{"issue":"2","key":"2205_CR9","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1111\/j.1574-6976.2010.00251.x","volume":"35","author":"D Knights","year":"2011","unstructured":"Knights D, Costello EK, Knight R. Supervised classification of human microbiota. FEMS Microbiol Rev. 2011;35(2):343\u201359.","journal-title":"FEMS Microbiol Rev"},{"issue":"2","key":"2205_CR10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0087830","volume":"9","author":"D Beck","year":"2014","unstructured":"Beck D, Foster JA. Machine learning techniques accurately classify microbial communities by bacterial vaginosis characteristics. PLoS One. 2014;9(2):87830.","journal-title":"PLoS One"},{"key":"2205_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-015-0793-8","volume":"16","author":"G Ditzler","year":"2015","unstructured":"Ditzler G, Morrison JC, Lan Y, Rosen GL. Fizzy: feature subset selection for metagenomics. BMC Bioinformatics. 2015;16:1\u20138. https:\/\/doi.org\/10.1186\/s12859-015-0793-8 .","journal-title":"BMC Bioinformatics"},{"key":"2205_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1004977","volume":"12","author":"E Pasolli","year":"2016","unstructured":"Pasolli E, Truong DT, Malik F, Waldron L, Segata N. Machine learning meta-analysis of large metagenomic datasets: tools and biological insights. PLoS Comput Biol. 2016;12:1\u201326. https:\/\/doi.org\/10.1371\/journal.pcbi.1004977 .","journal-title":"PLoS Comput Biol"},{"key":"2205_CR13","first-page":"359","volume-title":"Proceedings of the seventeenth international conference on machine learning. ICML \u201800","author":"MA Hall","year":"2000","unstructured":"Hall MA. Correlation-based feature selection for discrete and numeric class machine learning. In: Proceedings of the seventeenth international conference on machine learning. ICML \u201800; 2000. p. 359\u201366."},{"issue":"2","key":"2205_CR14","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1101\/gr.126573.111","volume":"22","author":"AD Kostic","year":"2012","unstructured":"Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, et al. Genomic analysis identifies association of fusobacterium with colorectal carcinoma. Genome Res. 2012;22(2):292\u20138.","journal-title":"Genome Res"},{"key":"2205_CR15","first-page":"288","volume":"8777","author":"P Ristoski","year":"2014","unstructured":"Ristoski P, Paulheim H. Feature selection in hierarchical feature spaces. Discovery. Science. 2014;8777:288\u2013300.","journal-title":"Science"},{"key":"2205_CR16","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335\u20136.","journal-title":"Nat Methods"},{"key":"2205_CR17","doi-asserted-by":"crossref","unstructured":"Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLOS Computational Biology. 2012;8(9)","DOI":"10.1371\/journal.pcbi.1002687"},{"key":"2205_CR18","volume-title":"Machine learning, 1st edn","author":"TM Mitchell","year":"1997","unstructured":"Mitchell TM. Machine learning, 1st edn. New York, NY, USA: McGraw-Hill, Inc.; 1997."},{"key":"2205_CR19","first-page":"1022","volume-title":"IJCAI\u201393","author":"U Fayyad","year":"1993","unstructured":"Fayyad U, Irani K. Multi-interval discretization of continuousvalued attributes for classification learning. In: IJCAI\u201393; 1993. p. 1022\u20137."},{"key":"2205_CR20","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1145\/1656274.1656278","volume":"11","author":"M Hall","year":"2009","unstructured":"Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten IH. The weka data mining software: an update. ACM SIGKDD Explorations Newsletter. 2009;11:10\u20138.","journal-title":"ACM SIGKDD Explorations Newsletter"},{"key":"2205_CR21","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198538493.001.0001","volume-title":"Neural networks for pattern recognition","author":"C Bishop","year":"1995","unstructured":"Bishop C. Neural networks for pattern recognition. NY: Oxford University Press; 1995."},{"key":"2205_CR22","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","volume":"486","author":"The Human Microbiome Project Consortium","year":"2012","unstructured":"The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207\u201314.","journal-title":"Nature"},{"key":"2205_CR23","doi-asserted-by":"crossref","unstructured":"Feng, Q., Liang, S., Jia, H., Stadlmayr, A., Tang, L., Lan, Z., Zhang, D., Xia, H., Xu, X., Jie, Z., et al.: Gut microbiome development along the colorectal adenoma\u2013carcinoma sequence. Nat Commun 6, 1\u201313 (2015).","DOI":"10.1038\/ncomms7528"},{"key":"2205_CR24","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1136\/gutjnl-2014-308778","volume":"65","author":"MC Dao","year":"2016","unstructured":"Dao MC, Everard A, Aron-Wisnewsky J, Sokolovska N, Prifti E. Other: Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut. 2016;65:426\u201336. https:\/\/doi.org\/10.1136\/gutjnl-2014-308778 .","journal-title":"Gut"},{"key":"2205_CR25","doi-asserted-by":"publisher","unstructured":"Derrien M, Belzer C, de Vos WM. Akkermansia muciniphila and its role in regulating host functions. Microb Pathog. 2016; https:\/\/doi.org\/10.1016\/j.micpath.2016.02.005 .","DOI":"10.1016\/j.micpath.2016.02.005"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2205-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2205-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2205-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,7]],"date-time":"2024-07-07T13:54:10Z","timestamp":1720360450000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2205-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,6,15]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2205"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2205-3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,15]]},"assertion":[{"value":"12 March 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 May 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 June 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors declare that they have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"227"}}