TY - CHAP AU - Wilson, M. PY - 2009 DA - 2009// TI - Bacteriology of humans: an ecological perspective BT - John Wiley & Sons ID - Wilson2009 ER - TY - JOUR AU - Dethlefsen, L. AU - McFall-Ngai, M. AU - Relman, D. A. PY - 2007 DA - 2007// TI - An ecological and evolutionary perspective on human-microbe mutualism and disease JO - Nature VL - 449 UR - https://doi.org/10.1038/nature06245 DO - 10.1038/nature06245 ID - Dethlefsen2007 ER - TY - JOUR AU - Turnbaugh, P. J. AU - Ley, R. E. AU - Hamady, M. AU - Fraser-Liggett, C. M. AU - Knight, R. AU - Gordon, J. I. PY - 2007 DA - 2007// TI - The human microbiome project: exploring the microbial part of ourselves in a changing world JO - Nature VL - 449 UR - https://doi.org/10.1038/nature06244 DO - 10.1038/nature06244 ID - Turnbaugh2007 ER - TY - JOUR AU - Lederberg, J. PY - 2000 DA - 2000// TI - Infectious history JO - Science VL - 288 UR - https://doi.org/10.1126/science.288.5464.287 DO - 10.1126/science.288.5464.287 ID - Lederberg2000 ER - TY - JOUR AU - Eckburg, P. B. AU - Bik, E. M. AU - Bernstein, C. N. AU - Purdom, E. AU - Dethlefsen, L. AU - Sargent, M. AU - Gill, S. R. AU - Nelson, K. E. AU - Relman, D. A. PY - 2005 DA - 2005// TI - Diversity of the human intestinal microbial flora JO - Science VL - 308 UR - https://doi.org/10.1126/science.1110591 DO - 10.1126/science.1110591 ID - Eckburg2005 ER - TY - JOUR AU - Fierer, N. AU - Hamady, M. AU - Lauber, C. L. AU - Knight, R. PY - 2008 DA - 2008// TI - The influence of sex, handedness, and washing on the diversity of hand surface bacteria JO - Proceedings of the National Academy of Sciences VL - 46 UR - https://doi.org/10.1073/pnas.0807920105 DO - 10.1073/pnas.0807920105 ID - Fierer2008 ER - TY - JOUR AU - Aas, J. A. AU - Paster, B. J. AU - Stokes, L. N. AU - Olsen, I. AU - Dewhirst, F. E. PY - 2005 DA - 2005// TI - Defining the normal bacterial flora of the oral cavity JO - Journal of Clinical Microbiology VL - 43 UR - https://doi.org/10.1128/JCM.43.11.5721-5732.2005 DO - 10.1128/JCM.43.11.5721-5732.2005 ID - Aas2005 ER - TY - JOUR AU - Nasidze, I. AU - Quinque, D. AU - Li, J. AU - Li, M. AU - Tang, K. AU - Stoneking, M. PY - 2009 DA - 2009// TI - Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches JO - Analytical biochemistry VL - 391 UR - https://doi.org/10.1016/j.ab.2009.04.034 DO - 10.1016/j.ab.2009.04.034 ID - Nasidze2009 ER - TY - JOUR AU - Turnbaugh, P. J. AU - Hamady, M. AU - Yatsunenko, T. AU - Cantarel, B. L. AU - Duncan, A. AU - Ley, R. E. AU - Sogin, M. L. AU - Jones, W. J. AU - Roe, B. A. AU - Affourtit, J. P. PY - 2009 DA - 2009// TI - A core gut microbiome in obese and lean twins JO - Nature VL - 7228 UR - https://doi.org/10.1038/nature07540 DO - 10.1038/nature07540 ID - Turnbaugh2009 ER - TY - JOUR AU - Grice, E. A. AU - Kong, H. H. AU - Conlan, S. AU - Deming, C. B. AU - Davis, J. AU - Young, A. C. AU - Bouffard, G. G. AU - Blakesley, R. W. AU - Murray, P. R. PY - 2009 DA - 2009// TI - Topographical and temporal diversity of the human skin microbiome JO - Science VL - 324 UR - https://doi.org/10.1126/science.1171700 DO - 10.1126/science.1171700 ID - Grice2009 ER - TY - JOUR AU - Bik, E. M. AU - Long, C. D. AU - Armitage, G. C. AU - Loomer, P. AU - Emerson, J. AU - Mongodin, E. F. AU - Nelson, K. E. AU - Gill, S. R. AU - Fraser-Liggett, C. M. AU - Relman, D. A. PY - 2010 DA - 2010// TI - Bacterial diversity in the oral cavity of 10 healthy individuals JO - The ISME journal VL - 4 UR - https://doi.org/10.1038/ismej.2010.30 DO - 10.1038/ismej.2010.30 ID - Bik2010 ER - TY - JOUR AU - Mitreva, M. PY - 2012 DA - 2012// TI - Structure, function and diversity of the healthy human microbiome JO - Nature VL - 486 UR - https://doi.org/10.1038/nature11234 DO - 10.1038/nature11234 ID - Mitreva2012 ER - TY - JOUR AU - Costello, E. K. AU - Lauber, C. L. AU - Hamady, M. AU - Fierer, N. AU - Gordon, J. I. AU - Knight, R. PY - 2009 DA - 2009// TI - Bacterial community variation in human body habitats across space and time JO - Science VL - 5960 UR - https://doi.org/10.1126/science.1177486 DO - 10.1126/science.1177486 ID - Costello2009 ER - TY - JOUR AU - Lozupone, C. AU - Hamady, M. AU - Knight, R. PY - 2006 DA - 2006// TI - UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-371 DO - 10.1186/1471-2105-7-371 ID - Lozupone2006 ER - TY - JOUR AU - Kent, A. D. AU - Yannarell, A. C. AU - Rusak, J. A. AU - Triplett, E. W. AU - McMahon, K. D. PY - 2007 DA - 2007// TI - Synchrony in aquatic microbial community dynamics JO - The ISME journal VL - 1 UR - https://doi.org/10.1038/ismej.2007.6 DO - 10.1038/ismej.2007.6 ID - Kent2007 ER - TY - JOUR AU - Zinger, L. AU - Coissac, E. AU - Choler, P. AU - Geremia, R. A. PY - 2009 DA - 2009// TI - Assessment of microbial communities by graph partitioning in a study of soil fungi in two alpine meadows JO - Applied and environmental microbiology VL - 75 UR - https://doi.org/10.1128/AEM.00748-09 DO - 10.1128/AEM.00748-09 ID - Zinger2009 ER - TY - JOUR AU - Lloyd, S. P. PY - 1982 DA - 1982// TI - Least squares quantization in PCM JO - IEEE Transactions on Information Theory VL - 28 UR - https://doi.org/10.1109/TIT.1982.1056489 DO - 10.1109/TIT.1982.1056489 ID - Lloyd1982 ER - TY - JOUR AU - Szekely, G. J. AU - Rizzo, M. L. PY - 2005 DA - 2005// TI - Hierarchical clustering via Joint Between-Within Distances: Extending Ward's Minimum Variance Method JO - Journal of classification VL - 22 UR - https://doi.org/10.1007/s00357-005-0012-9 DO - 10.1007/s00357-005-0012-9 ID - Szekely2005 ER - TY - JOUR AU - Moon, T. K. PY - 1996 DA - 1996// TI - The expectation-maximization algorithm JO - IEEE Signal processing magazine VL - 13 UR - https://doi.org/10.1109/79.543975 DO - 10.1109/79.543975 ID - Moon1996 ER - TY - JOUR AU - Devarajan, K. PY - 2008 DA - 2008// TI - Nonnegative matrix factorization: an analytical and interpretive tool in computational biology JO - PLoS computational biology VL - 4 UR - https://doi.org/10.1371/journal.pcbi.1000029 DO - 10.1371/journal.pcbi.1000029 ID - Devarajan2008 ER - TY - JOUR AU - Qi, Q. AU - Zhao, Y. AU - Li, M. AU - Simon, R. PY - 2009 DA - 2009// TI - Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp009 DO - 10.1093/bioinformatics/btp009 ID - Qi2009 ER - TY - JOUR AU - Zhang, S. AU - Li, Q. AU - Liu, J. AU - Zhou, X. J. PY - 2011 DA - 2011// TI - A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr206 DO - 10.1093/bioinformatics/btr206 ID - Zhang2011 ER - TY - JOUR AU - Ou-Yang, L. AU - Dai, D. Q. AU - Zhang, X. F. PY - 2013 DA - 2013// TI - Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization JO - PloS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0062158 DO - 10.1371/journal.pone.0062158 ID - Ou-Yang2013 ER - TY - CHAP AU - Lancichinetti, A. AU - Fortunato, S. PY - 2012 DA - 2012// TI - Consensus clustering in complex networks BT - Scientific reports ID - Lancichinetti2012 ER - TY - JOUR AU - Kuang, D. AU - Park, H. AU - Ding, C. H. PY - 2012 DA - 2012// TI - Symmetric Nonnegative Matrix Factorization for Graph Clustering JO - SDM VL - 12 ID - Kuang2012 ER - TY - JOUR AU - Caporaso, J. G. AU - Lauber, C. L. AU - Costello, E. K. AU - Berg-Lyons, D. AU - Gonzalez, A. AU - Stombaugh, J. AU - Knights, D. AU - Gajer, P. AU - Ravel, J. AU - Fierer, N. PY - 2011 DA - 2011// TI - Moving pictures of the human microbiome JO - Genome Biol VL - 12 UR - https://doi.org/10.1186/gb-2011-12-5-r50 DO - 10.1186/gb-2011-12-5-r50 ID - Caporaso2011 ER - TY - JOUR AU - Su, X. AU - Xu, J. AU - Ning, K. PY - 2012 DA - 2012// TI - Meta-Storms: Efficient Search for Similar Microbial Communities Based on a Novel Indexing Scheme and Similarity Score for Metagenomic Data JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts470 DO - 10.1093/bioinformatics/bts470 ID - Su2012 ER - TY - JOUR AU - Kullback, S. PY - 1987 DA - 1987// TI - Letter to the Editor: The Kullback-Leibler distance JO - The American Statistician VL - 41 ID - Kullback1987 ER - TY - CHAP AU - Psorakis, I. AU - Roberts, S. AU - Sheldon, B. PY - 2010 DA - 2010// TI - Soft partitioning in networks via bayesian non-negative matrix factorization BT - Adv Neural Inf Process Syst ID - Psorakis2010 ER - TY - CHAP AU - Tan, V. Y. AU - Févotte, C. PY - 2009 DA - 2009// TI - Automatic relevance determination in nonnegative matrix factorization BT - In SPARS'09-Signal Processing with Adaptive Sparse Structured Representations ID - Tan2009 ER - TY - JOUR AU - Seung, D. AU - Lee, L. PY - 2001 DA - 2001// TI - Algorithms for non-negative matrix factorization JO - Advances in neural information processing systems VL - 13 ID - Seung2001 ER - TY - JOUR AU - Greene, D. AU - Cagney, G. AU - Krogan, N. AU - Cunningham, P. PY - 2008 DA - 2008// TI - Ensemble non-negative matrix factorization methods for clustering protein-protein interactions JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn286 DO - 10.1093/bioinformatics/btn286 ID - Greene2008 ER - TY - JOUR AU - Manning, C. D. AU - Raghavan, P. AU - Schütze, H. PY - 2008 DA - 2008// TI - Introduction to information retrieval JO - Cambridge university press VL - 1 ID - Manning2008 ER - TY - JOUR AU - McGuire, A. L. AU - Colgrove, J. AU - Whitney, S. N. AU - Diaz, C. M. AU - Bustillos, D. AU - Versalovic, J. PY - 2008 DA - 2008// TI - Ethical, legal, and social considerations in conducting the Human Microbiome Project JO - Genome Research VL - 18 UR - https://doi.org/10.1101/gr.081653.108 DO - 10.1101/gr.081653.108 ID - McGuire2008 ER - TY - JOUR AU - Dewhirst, F. E. AU - Chen, T. AU - Izard, J. AU - Paster, B. J. AU - Tanner, A. C. AU - Yu, W. H. AU - Wade, W. G. PY - 2010 DA - 2010// TI - The human oral microbiome JO - Journal of bacteriology VL - 192 UR - https://doi.org/10.1128/JB.00542-10 DO - 10.1128/JB.00542-10 ID - Dewhirst2010 ER - TY - JOUR AU - Yang, P. AU - Li, X. AU - Mei, J. P. AU - Kwoh, C. K. AU - Ng, S. K. PY - 2012 DA - 2012// TI - Positive-unlabeled learning for disease gene identification JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts504 DO - 10.1093/bioinformatics/bts504 ID - Yang2012 ER - TY - JOUR AU - Mei, J. P. AU - Kwoh, C. K. AU - Yang, P. AU - Li, X. AU - Zheng, J. PY - 2013 DA - 2013// TI - Drug-target interaction prediction by learning from local information and neighbors JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts670 DO - 10.1093/bioinformatics/bts670 ID - Mei2013 ER - TY - JOUR AU - Yang, P. AU - Li, X. AU - Wu, M. AU - Kwoh, C. K. AU - Ng, S. K. PY - 2011 DA - 2011// TI - Inferring gene-phenotype association via global protein complex network propagation JO - PloS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0021502 DO - 10.1371/journal.pone.0021502 ID - Yang2011 ER - TY - CHAP AU - Zheng, X. AU - Ding, H. AU - Mamitsuka, H. AU - Zhu, S. PY - 2013 DA - 2013// TI - Collaborative matrix factorization with multiple similarities for predicting drug-target interactions BT - In 19th ACM SIGKDD international conference on Knowledge discovery and data mining UR - https://doi.org/10.1145/2487575.2487670 DO - 10.1145/2487575.2487670 ID - Zheng2013 ER - TY - CHAP AU - Mei, J. P. AU - Kwoh, C. K. AU - Yang, P. AU - Li, X. AU - Zheng, J. PY - 2012 DA - 2012// TI - Globalized bipartite local model for drug-target interaction prediction BT - Proceedings of the 11th International Workshop on Data Mining in Bioinformatics ID - Mei2012 ER - TY - JOUR AU - Yang, P. AU - Li, X. AU - Chua, H. N. AU - Kwoh, C. K. AU - Ng, S. K. PY - 2014 DA - 2014// TI - Ensemble Positive Unlabeled Learning for Disease Gene Identification JO - PloS one VL - 9 UR - https://doi.org/10.1371/journal.pone.0097079 DO - 10.1371/journal.pone.0097079 ID - Yang2014 ER -