TY - JOUR AU - Sun, Y. AU - Cai, Y. AU - Huse, S. M. AU - Knight, R. AU - Farmerie, W. G. AU - Wang, X. PY - 2011 DA - 2011// TI - A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis JO - Brief Bioinform VL - 13 UR - https://doi.org/10.1093/bib/bbr009 DO - 10.1093/bib/bbr009 ID - Sun2011 ER - TY - JOUR AU - Schloss, P. D. AU - Westcott, S. L. PY - 2011 DA - 2011// TI - Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis JO - Appl Environ Microbiol VL - 77 UR - https://doi.org/10.1128/AEM.02810-10 DO - 10.1128/AEM.02810-10 ID - Schloss2011 ER - TY - JOUR AU - Cole, J. R. AU - Chai, B. AU - Farris, B. J. AU - Wang, Q. AU - Kulam, S. A. AU - McGarrell, D. M. PY - 2005 DA - 2005// TI - The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki038 DO - 10.1093/nar/gki038 ID - Cole2005 ER - TY - JOUR AU - Desantis, T. Z. AU - Hugenholtz, P. AU - Larsen, N. AU - Rojas, M. AU - Brodie, E. L. AU - Keller, K. AU - Huber, T. AU - Dalevi, D. AU - Hu, P. AU - Andersen, G. L. PY - 2006 DA - 2006// TI - Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB JO - Appl Environ Microbiol VL - 72 UR - https://doi.org/10.1128/AEM.03006-05 DO - 10.1128/AEM.03006-05 ID - Desantis2006 ER - TY - JOUR AU - Huse, S. M. AU - Dethlefsen, L. AU - Huber, J. A. AU - Welch, D. M. AU - Relman, D. A. AU - Sogin, M. L. PY - 2008 DA - 2008// TI - Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing JO - PLoS Genet VL - 4 UR - https://doi.org/10.1371/journal.pgen.1000255 DO - 10.1371/journal.pgen.1000255 ID - Huse2008 ER - TY - JOUR AU - Li, W. AU - Godzik, A. PY - 2006 DA - 2006// TI - Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl158 DO - 10.1093/bioinformatics/btl158 ID - Li2006 ER - TY - JOUR AU - Sun, Y. AU - Cai, Y. AU - Liu, L. AU - Yu, F. AU - Farrell, M. L. AU - McKendree, W. AU - Farmerie, W. PY - 2009 DA - 2009// TI - ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp285 DO - 10.1093/nar/gkp285 ID - Sun2009 ER - TY - JOUR AU - Schloss, P. D. AU - Handelsman, J. PY - 2005 DA - 2005// TI - Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness JO - Appl Environ Microbiol VL - 71 UR - https://doi.org/10.1128/AEM.71.3.1501-1506.2005 DO - 10.1128/AEM.71.3.1501-1506.2005 ID - Schloss2005 ER - TY - JOUR AU - Schloss, P. D. AU - Westcott, S. L. AU - Ryabin, T. AU - Hall, J. R. AU - Hartmann, M. PY - 2009 DA - 2009// TI - Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities JO - Appl Environ Microbiol VL - 75 UR - https://doi.org/10.1128/AEM.01541-09 DO - 10.1128/AEM.01541-09 ID - Schloss2009 ER - TY - JOUR AU - Cai, Y. AU - Sun, Y. PY - 2011 DA - 2011// TI - ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr349 DO - 10.1093/nar/gkr349 ID - Cai2011 ER - TY - JOUR AU - Edgar, R. C. PY - 2010 DA - 2010// TI - Search and clustering orders of magnitude faster than BLAST JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq461 DO - 10.1093/bioinformatics/btq461 ID - Edgar2010 ER - TY - JOUR AU - White, J. R. AU - Navlakha, S. AU - Nagarajan, N. AU - Ghodsi, M. AU - Kingsfor, C. AU - Pop, M. PY - 2010 DA - 2010// TI - Alignment and clustering of phylogenetic markers - implications for microbial diversity studies JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-152 DO - 10.1186/1471-2105-11-152 ID - White2010 ER - TY - JOUR AU - Hao, X. AU - Jiang, R. AU - Chen, T. PY - 2011 DA - 2011// TI - Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btq725 DO - 10.1093/bioinformatics/btq725 ID - Hao2011 ER - TY - CHAP AU - Cheng, L. AU - Walke, A. W. AU - Corander, J. PY - 2012 DA - 2012// TI - Bayesian estimation of bacterial community composition from 454 sequencing data BT - Nucleic Acids Res ID - Cheng2012 ER - TY - JOUR AU - Newman, M. E. J. PY - 2004 DA - 2004// TI - Analysis of weighted networks JO - Phys Rev VL - 70 ID - Newman2004 ER - TY - JOUR AU - Newman, M. E. J. PY - 2006 DA - 2006// TI - Modularity and community structure in networks JO - PNAS VL - 103 UR - https://doi.org/10.1073/pnas.0601602103 DO - 10.1073/pnas.0601602103 ID - Newman2006 ER - TY - JOUR AU - Fortunato, S. PY - 2010 DA - 2010// TI - Community detection in graphs JO - Phys Rep VL - 486 UR - https://doi.org/10.1016/j.physrep.2009.11.002 DO - 10.1016/j.physrep.2009.11.002 ID - Fortunato2010 ER - TY - CHAP AU - Blondel, V. D. AU - Cuillaume, J. L. AU - Lambiotte, R. AU - Lefebvre, E. PY - 2008 DA - 2008// TI - Fast unfolding of communities in large networks BT - J Stat Mech ID - Blondel2008 ER - TY - JOUR AU - Lancichinetti, A. AU - Fortunato, S. AU - Lancichinetti, A. AU - Fortunato, S. PY - 2009 DA - 2009// TI - Community detection algorithms: a comparative analysis JO - Phys Rev VL - 80 ID - Lancichinetti2009 ER - TY - JOUR AU - Fortunato, S. AU - Barthelemy, M. PY - 2007 DA - 2007// TI - Resolution limit in community detection JO - PNAS VL - 104 UR - https://doi.org/10.1073/pnas.0605965104 DO - 10.1073/pnas.0605965104 ID - Fortunato2007 ER - TY - JOUR AU - Handl, J. AU - Knowles, J. AU - Kell, D. B. PY - 2005 DA - 2005// TI - Computational cluster validation in post-genomic data analysis JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti517 DO - 10.1093/bioinformatics/bti517 ID - Handl2005 ER - TY - BOOK AU - Manning, C. D. AU - Raghavan, P. AU - Schütze, H. PY - 2008 DA - 2008// TI - Introduction to Information Retrieval UR - https://doi.org/10.1017/CBO9780511809071 DO - 10.1017/CBO9780511809071 ID - Manning2008 ER - TY - JOUR AU - Amigo, E. AU - Gonzalo, J. AU - Artiles, J. AU - Verdejo, F. PY - 2009 DA - 2009// TI - A comparison of extrinsic clustering evaluation metrics based on formal constrains JO - Inf Retrieval VL - 12 UR - https://doi.org/10.1007/s10791-008-9066-8 DO - 10.1007/s10791-008-9066-8 ID - Amigo2009 ER - TY - JOUR AU - Rosseeuw, P. J. PY - 1987 DA - 1987// TI - Sihouettes: a graphical aid to the interpretation and validation of cluster analysis JO - J Comput Appl Math VL - 20 UR - https://doi.org/10.1016/0377-0427(87)90125-7 DO - 10.1016/0377-0427(87)90125-7 ID - Rosseeuw1987 ER - TY - JOUR AU - Dunn, J. C. PY - 1973 DA - 1973// TI - A Fuzzy Relative of the ISODATA Process and Its Use in Detecting Compact Well-Separated Clusters JO - J Cybernetics VL - 3 UR - https://doi.org/10.1080/01969727308546046 DO - 10.1080/01969727308546046 ID - Dunn1973 ER - TY - JOUR AU - Giongo, A. AU - Richardson, A. G. D. AU - Crabb, D. B. AU - Triplett, E. W. PY - 2010 DA - 2010// TI - Tax Collector: modifying current 16S rRNA databases for the rapid classification at six taxonomic levels JO - Diversity VL - 2 UR - https://doi.org/10.3390/d2071015 DO - 10.3390/d2071015 ID - Giongo2010 ER - TY - JOUR AU - Turnbaugh, P. J. AU - Hamady, M. AU - Yatsunenko, T. AU - Cantarel, B. L. AU - Duncan, A. AU - Ley, R. E. PY - 2009 DA - 2009// TI - A core gut microbiome in obese and lean twins JO - Nature VL - 457 UR - https://doi.org/10.1038/nature07540 DO - 10.1038/nature07540 ID - Turnbaugh2009 ER - TY - JOUR AU - Luiz, F. W. PY - 2007 DA - 2007// TI - Pyrosequencing enumerates and contrasts soil microbial diversity JO - ISME J VL - 1 ID - Luiz2007 ER - TY - JOUR AU - Ruan, J. AU - Zhang, W. PY - 2008 DA - 2008// TI - Identifying network communities with a high resolution JO - Phys Rev VL - 77 ID - Ruan2008 ER -