@BOOK{kaptchukbook,
AUTHOR = " Kaptchuk, T J",
YEAR = {(1983)}, 
TITLE = "The web that has no weaver: understanding Chinese medicine",
PUBLISHER = "Congdon and Weed",
ADDRESS = "New York"
}

@BOOK{schafer,
AUTHOR = "Schafer, J L",
YEAR = {(1997)}, 
TITLE = "Analysis of Incomplete Multivariate Data",
PUBLISHER = "Chapman \& Hall",
ADDRESS = "London"
}

@BOOK{rubin,
AUTHOR = "Rubin, D B",
YEAR = {(1987)}, 
TITLE = "Multiple Imputation for Nonresponse in Surveys",
PUBLISHER = "J. Wiley \& Sons",
ADDRESS = "New York"
}

@BOOK{dasarathy,
AUTHOR = "Dasarathy, B V",
YEAR = {(1990)}, 
TITLE = "Nearest neighbor (NN) norms: NN pattern classification techniques",
PUBLISHER = "IEEE Computer Society Press",
ADDRESS = "Los Alamitos"
}

@Article{Williams:1985:Arthritis-Rheum:3893441,
author = "Williams, H J and Willkens, R F and Samuelson, C O and Alarc{\'o}n, G S and Guttadauria, M and Yarboro, C and Polisson, R P and Weiner, S R and Luggen, M E and Billingsley, L M",
title = {Comparison of low-dose oral pulse methotrexate and placebo in the treatment of rheumatoid arthritis. A controlled clinical trial},
journal = "Arthritis Rheum",
year = "1985",
volume = "28",
number = "7",
pages = "721-730",
month = "Jul",
pmid = "3893441",
url = "http://www.hubmed.org/display.cgi?uids=3893441",
doi = ""
}

@Article{Ferraz:1994:Scand-J-Rheumatol:7973475,
author = "Ferraz, M B and Pinheiro, G R and Helfenstein, M and Albuquerque, E and Rezende, C and Roimicher, L and Brandao, L and Silva, S C and Pinheiro, G C and Atra, E",
title = {Combination therapy with methotrexate and chloroquine in rheumatoid arthritis. A multicenter randomized placebo-controlled trial},
journal = "Scand J Rheumatol",
year = "1994",
volume = "23",
number = "5",
pages = "231-236",
month = "",
pmid = "7973475",
url = "http://www.hubmed.org/display.cgi?uids=7973475",
doi = ""
}

@Article{Kremer:1995:Arthritis-Rheum:7748214,
author = "Kremer, J M and Davies, J M and Rynes, R I and Fink, S and Lawrence, D A and Petrillo, G F and Mullaly, P M",
title = {Every-other-week methotrexate in patients with rheumatoid arthritis. A double-blind, placebo-controlled prospective study},
journal = "Arthritis Rheum",
year = "1995",
volume = "38",
number = "5",
pages = "601-607",
month = "May",
pmid = "7748214",
url = "http://www.hubmed.org/display.cgi?uids=7748214",
doi = ""
}



@inproceedings{cite:hutter-01xentropy,
  author =       "M. Hutter",
  title =        "Distribution of Mutual Information",
  booktitle =    "Advances in Neural Information Processing Systems 14",
  editor =       "T. G. Dietterich and S. Becker and Z. Ghahramani",
  publisher =    "MIT Press",
  address =      "Cambridge, MA",
  pages =        "399--406",
  year =         "2002",
  journal =      "Proceedings of the 14th International Conference on
                  Neural Information Processing Systems (NIPS-2001)",
   keywords =     "Mutual Information, Cross Entropy, Dirichlet
                  distribution, Second order distribution, expectation
                  and variance of mutual information."
}

@article{ICHnoninf,
AUTHOR = "ICH Working Group",
TITLE = "E10: Choice of Control Group and Related Issues in Clinical Trials ",
JOURNAL = "FDA Federal Register",
VOLUME =  {66},  
number = {93},
PAGES = {24390-24391}, 
YEAR = {2001}, }

@Article{Arnett:1988:Arthritis-Rheum:3358796,
author = "Arnett, F C and Edworthy, S M and Bloch, D A and McShane, D J and Fries, J F and Cooper, N S and Healey, L A and Kaplan, S R and Liang, M H and Luthra, H S",
title = {The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis},
journal = "Arthritis Rheum",
year = "1988",
volume = "31",
number = "3",
pages = "315-324",
month = "Mar",
pmid = "3358796",
url = "http://www.hubmed.org/display.cgi?uids=3358796",
doi = ""
}


@article{altheide,
AUTHOR = "D.L. Altheide",
TITLE = "Terrorism and the politics of Fear",
JOURNAL = "Cultural Studies - Critical Methodologies",
VOLUME =  {6},  
PAGES = {415}, 
YEAR = {2006}, }

@Article{Alamanos:2006:Semin-Arthritis-Rheum:17045630,
author = "Alamanos, Y and Voulgari, P V and Drosos, A A",
title = {Incidence and prevalence of rheumatoid arthritis, based on the 1987 American College of Rheumatology criteria: a systematic review},
journal = "Semin Arthritis Rheum",
year = "2006",
volume = "36",
number = "3",
pages = "182-188",
}

@book{mueller,
AUTHOR = "J. Mueller",
TITLE = "The Remnants of War",
PUBLISHER = "Cornell University Press",  
YEAR = {2004}, }

@book{nordhaus,
AUTHOR = "T. Nordhaus and M. Shellenberger",
TITLE = "Break Through From the Death of Environmentalism to the Politics of Possibility",
PUBLISHER = "Houghton Mifflin Company",  
YEAR = {2007}, }

@ARTICLE{arrexp,
AUTHOR = "H. Parkinson and M. Kapushesky and M. Shojatalab and N. Abeygunawardena and R. Coulson and A. Farne and E. Holloway and N. Kolesnikov and P. Lilja and M. Lukk and R. Mani and T. Rayner and A. Sharma and E. William and U. Sarkans and A. Brazma.",
TITLE = "{A}rray{E}xpressÑa public database of microarray experiments and gene expression profiles.",
JOURNAL = "Nucleic Acids Res",
VOLUME =  {35(Database Issue)},  
PAGES = {D747-50}, 
YEAR = {2007}, }

@ARTICLE{barabasi,
AUTHOR = "A.-L. Barab{'}asi and Z.N. Oltvai",
TITLE = "Network Biology: Understanding the cellÕs functional organization",
JOURNAL = "Nat. Rev. Genet.",
VOLUME =  {5},  
NUMBER =  {},
PAGES = {101-113}, 
YEAR = {2004}, }

@Article{Brater:2000,
author = "Brater, D C and Daly, W J",
title = {Clinical pharmacology in the Middle Ages: principles that presage the 21st century},
abstract = {},
journal = "Clin Pharmacol Ther",
year = "2000",
volume = "67",
number = "5",
pages = "447-450",
month = "May",
pmid = "10824622",
url = "http://www.hubmed.org/display.cgi?uids=10824622",
doi = "10.1067/mcp.2000.106465"
}

@ARTICLE{buess,
AUTHOR = "M. Buess  and D.S. Nuyten  and T. Hastie and T. Nielsen and R. Pesich and P.O. Brown",
TITLE = "Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer",
JOURNAL = "Genome Biol",
VOLUME =  {8},  
NUMBER =  {9},
PAGES = {R191}, 
YEAR = {2007}, }

@Article{Daly:2000,
author = "Daly, W J and Brater, D C",
title = {Medieval contributions to the search for truth in clinical medicine},
abstract = {},
journal = "Perspect Biol Med",
year = "2000",
volume = "43",
number = "4",
pages = "530-540",
month = "",
pmid = "11058989",
url = "http://www.hubmed.org/display.cgi?uids=11058989",
doi = ""
}

@ARTICLE{diehn08,
AUTHOR = "M. Diehn and C. Nardini and D. S. Wang and S. McGovern and M. Jayaraman and Y. Liang and K. Aldape and S. Cha and M. D. Kuo",
TITLE = "Identification of non-invasive imaging surrogates for brain tumor gene expression modules",
JOURNAL = "Proc. Natl. Acad. Sci.",
VOLUME =  {105},  
NUMBER =  {13},
PAGES = {5213-5218}, 
YEAR = {2008}, }

@ARTICLE{garzon,
AUTHOR = "R. Garzon and M. Garofalo and M.P. Martelli and R. Briesewitz and L Wang and C. Fernandez-Cymering and S. Volinia and C.G. Liu and S. Schnittger and T. Haferlach and A. Liso  and D. Diverio and M. Mancini and G. Meloni and R. Foa and M.F. Martelli and C. Mecucci and C. M. Croce and B. Falini",
TITLE = "Distinctive microRNA signature of acute myeloid leukemia bearing cytoplasmic mutated nucleophosmin.",
JOURNAL = "Proc. Natl. Acad. Sci.",
VOLUME =  {in press},  
PAGES = {}, 
YEAR = {2008}, }

@ARTICLE{geo,
AUTHOR = "T. Barrett and D. B. Troup and S. E. Wilhite and P. Ledoux and D Rudnev and C. Evangelista and I. F. Kim and A. Soboleva and M. Tomashevsky and R. Edgar",
TITLE = "{NCBI GEO}: mining tens of millions of expression profiles--database and tools update.",
JOURNAL = "Nucleic Acids Res",
VOLUME =  {35(Database Issue)},  
PAGES = {D760-D765}, 
YEAR = {2007}, }

@ARTICLE{guiducci,
AUTHOR = "C. Guiducci and C. Nardini",
TITLE = "High Parallelism, Portability and Broad Accessibility: Technologies for Genomics.",
JOURNAL = "ACM J. Emerg. Technol. Comput. Syst.",
VOLUME =  {4}, 
NUMBER =  {1}, 
PAGES = {Article 3}, 
YEAR = {2008}, }

@ARTICLE{lamb,
AUTHOR = "J. Lamb and E. D. Crawford and D. Peck and J. W. Modell and I. C. and M. J. Wrobel and J. Lerner and J.-P. Brunet and A. Subramanian and K. N. Ross and M. Reich and H. Hieronymus and G. Wei and S. A. Armstrong and S. J. Haggarty and P. A. Clemons and R. Wei and S. A. Carr and E. S. Lander and T. R. Golub",
TITLE = "The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease",
JOURNAL = "Science",
VOLUME =  {313},  
NUMBER =  {5795},
PAGES = {1929-1935}, 
YEAR = {2006}, }

@ARTICLE{Ji2006,
AUTHOR = "H. Ji and R. W. Davis",
TITLE = "Data quality in genomics and microarrays",
JOURNAL = "Nat. Biotechnol.",
VOLUME =  {24},  
PAGES = {1112 - 1113}, 
YEAR = {2006}, }

@Article{McQueen:2001,
author = "McQueen, M J",
title = {Overview of evidence-based medicine: challenges for evidence-based laboratory medicine},
journal = "Clin Chem",
year = "2001",
volume = "47",
number = "8",
pages = "1536-1546",
doi = ""
}

@ARTICLE{nardinifisher,
AUTHOR = "C. Nardini and M. D. Kuo and L. Benini",
TITLE = "Statistical Significance in omic data analyses",
JOURNAL = "Proceedings of International Conference on bio-inspired systems and signal processing",
VOLUME =  {},
NUMBER =  {},
PAGES = {},
YEAR = 2008 }

@Article{neumayer:2007,
author = "Neumayer, L and Meterissian, S and McMasters, K and , ",
title = {Canadian Association of General Surgeons and American College of Surgeons Evidence Based Reviews in Surgery. 23. ASCO recommended guidelines for sentinel lymph node biopsy for early-stage breast cancer. Evidence-based medicine. A new approach to teaching the practice of medicine},
abstract = {},
journal = "Can J Surg",
year = "2007",
volume = "50",
number = "6",
pages = "482-484",
month = "Dec",
pmid = "18053378",
url = "http://www.hubmed.org/display.cgi?uids=18053378",
doi = ""
}

@ARTICLE{smd,
AUTHOR = "J. Demeter and C. Beauheim and J. Gollub and T. Hernandez-Boussard and H. Jin and D. Maier and J.C. Matese and M. Nitzberg and F. Wymore and Z.K. Zachariah and P.O. Brown and G. Sherlock and C.A. Ball",
TITLE = "The {S}tanford {M}icroarray {D}atabase: implementation of new analysis tools and open source release of software.",
JOURNAL = "Nucleic Acids Res",
VOLUME =  {35(Database Issue)},  
PAGES = {D766-770}, 
YEAR = {2007}, }

@ARTICLE{Silverman,
AUTHOR = "B. W. Silverman and G. A. Young",
TITLE = "The bootstrap: To smooth or not to smooth?",
JOURNAL = "Biometrika",
VOLUME =  {74},  
NUMBER =  {3},
PAGES = {469-479}, 
YEAR = {1987}, }

@ARTICLE{voit,
AUTHOR = "E. Voit and A.R. Neves and H. Santos",
TITLE = "The intricate side of Systems biology",
JOURNAL = "Proc. Natl. Acad. Sci.",
VOLUME =  {103},  
NUMBER =  {25},
PAGES = {9452-9457}, 
YEAR = {2006}, }

@BOOK{cover,
AUTHOR = " T. M. Cover and J. A. Thomas",
YEAR = {2001}, 
TITLE = "Elements of Information Theory",
PUBLISHER = "John Wiley and Sons",
}

@ARTICLE{bouwens,
AUTHOR = "M. Bouwens and L. A. Afman and M. M{\"u}ller",
TITLE = "Fasting induces changes in peripheral blood mononuclear cell gene expression profiles related to increases in fatty acid §-oxidation: functional role of peroxisome proliferatorÐactivated receptor {$\alpha$} in human peripheral blood mononuclear cells",
JOURNAL = "American Journal of Clinical Nutrition",
VOLUME =  {86},  
NUMBER =  {5},
PAGES = {1515-1523}, 
YEAR = {2007}, }

@ARTICLE{bull,
AUTHOR = "T. M. Bull and C. D. Coldren and M. Moore and S. M. Sotto-Santiago and D. V. Pham and S. P. Nana-Sinkam and N. F. Voelkel and M. W. Geraci",
TITLE = "Gene Microarray Analysis of Peripheral Blood Cells in Pulmonary Arterial Hypertension",
JOURNAL = "American Journal of Respiratory and Critical Care Medicine",
VOLUME =  {170},  
NUMBER =  {},
PAGES = {911-919}, 
YEAR = {2004}, }

@Article{Yu:2004:Bioinformatics:15284094,
author = "Yu, J and Smith, V A and Wang, P P and Hartemink, A J and Jarvis, E D",
title = {Advances to Bayesian network inference for generating causal networks from observational biological data},
journal = "Bioinformatics",
year = "2004",
volume = "20",
number = "18",
pages = "3594-3603",
}



@ARTICLE{zieker,
AUTHOR = "D. Zieker and E. Fehrenbach and J. Dietzsch and J. Fliegner and M. Waidmann and K. Nieselt and P. Gebicke-Haerter and R. Spanagel and P. Simon and A. M. Niess and H. Northoff",
TITLE = "c{DNA} microarray analysis reveals novel candidate genes expressed in human peripheral blood following exhaustive exercise",
JOURNAL = "Physiol. Genomics",
VOLUME =  {23},  
NUMBER =  {},
PAGES = {287-294}, 
DOI = {doi:10.1152/physiolgenomics.00096.2005
1094-8341/05},
YEAR = {2005}, }

 @ARTICLE{gu,
AUTHOR = "J. Gu and E. M{\"a}rker-Hermann and D. Baeten and W. C. Tsai and D. Gladman and M. Xiong and H. Deister and J. G. Kuipers and F. Huang and Y. W. Song and W. Maksymowych and J. Kalsi and M. Bannai and N. Seta and M. Rihl and L. J. Crofford and E. Veys and F. De Keyser and D. T. Y. Yu",
TITLE = "A 588-gene microarray analysis of the peripheral blood mononuclear cells of spondyloarthropathy patients",
JOURNAL = "Rheumatology",
VOLUME =  {41},  
NUMBER =  {},
PAGES = {759-766}, 
DOI = {},
YEAR = {2002}, }

 @ARTICLE{tougan,
AUTHOR = "T. Tougan and H. Onda and D. Okuzaki and S. Kobayashi and H. Hashimoto and H. Nojima",
TITLE = "Focused Microarray Analysis of Peripheral Mononuclear Blood Cells from ChurgÐStrauss Syndrome Patients",
JOURNAL = "DNA Research",
VOLUME =  {15},  
NUMBER =  {2},
PAGES = {103-114}, 
DOI = {doi:10.1093/dnares/dsm035},
YEAR = {2008}, }
 
@ARTICLE{takaoka,
AUTHOR = "Y. Takaoka and M. Ohta and A. Ito and K. Takamatsu and A. Sugano and K. Funakoshi and N. Takaoka and N. Sato and H. Yokozaki and N. Arizono and S. Goto and E. Maeda",
TITLE = "Electroacupuncture suppresses myostatin gene expression: cell proliferative reaction in mouse skeletal muscle",
JOURNAL = "Physiol. Genomics",
VOLUME =  {30},  
NUMBER =  {},
PAGES = {102-110}, 
DOI = {doi:10.1152/physiolgenomics.00057.2006},
YEAR = {2007}, }

%RA and Moxa
@ARTICLE{YANGXin07,
AUTHOR = "Yang X. and Li J. and Yang S.Q. and Zhang X. and Zhang T. and Zhou H. and Liu X.",
TITLE = "Influence of Moxibustion on {JAK-STAT} Signal Transduction Pathways of Synovial Cells in Rheumatoid Arthritis Rabbits",
JOURNAL = "ACUPUNCTURE RESEARCH",
VOLUME =  {32},  
NUMBER =  {2},
PAGES = {75-82}, 
DOI = {},
YEAR = {2007}, }

@ARTICLE{YANGXin07CATCM,
AUTHOR = "Yang X. and Yabg S. and Zhou H. and Yu S. and Leng W. and  Liu X.",
TITLE = "The Influence on {MAPK} Signal Pathway in {RA} Synovial Cell of Experimental Rabbits by Moxibustion",
JOURNAL = "Chinese Archives of Traditional Chinese Medicine",
VOLUME =  {25},  
NUMBER =  {3},
PAGES = {470-474}, 
DOI = {},
YEAR = {2007}, }

@ARTICLE{LuCheng06,
AUTHOR = "Lu C and Xiao C. and Zhao L. and Zha Q. and Yan X. and Wang J. and Zhang Y. and Zhou Y. and Xu S. and Li S. and Lu A",
TITLE = "Comparison of Gene Profile of peripheral {CD4}$^+$ Lymphocytes in Rheumatoid Arthritis with Cold and Heat Syndrome",
JOURNAL = "Chinese Journal of Basic Medicine in Traditional Chinese Medicine",
VOLUME =  {12},  
NUMBER =  {2},
PAGES = {130-133}, 
DOI = {},
YEAR = {2006}, }

@ARTICLE{XiaoC06,
AUTHOR = "Xiao C and Lu C. and Zhao L.",
TITLE = "Comparison on Gene Expression Proflle of Periphery {CD4}$^?$ Positive Cells in Active and Stable Stages of Rheumatold Arthritis",
JOURNAL = "Chinese Journal of Information on Traditional Chinese Medicine",
VOLUME =  {13},  
NUMBER =  {3},
PAGES = {14-16}, 
DOI = {},
YEAR = {2006}, }

@ARTICLE{HUANGR07,
AUTHOR = "Huang R. and Huang Q. and Shen Y. and Wei S. and Han X.",
TITLE = "Use Gene Chip Technology to Investigate the Establishment of Traditional Chinese Medicine Syndrome Genomics of Rheumatoid Arthritis",
JOURNAL = "Chinese Archives of Traditional Chinese Medicine",
VOLUME =  {25},  
NUMBER =  {10},
PAGES = {2107-2108}, 
DOI = {},
YEAR = {2007}, }

@Article{vanderPouwKraan:2007:Ann-Rheum-Dis:17223656,
author = "van der Pouw Kraan, T C and Wijbrandts, C A and van Baarsen, L G and Voskuyl, A E and Rustenburg, F and Baggen, J M and Ibrahim, S M and Fero, M and Dijkmans, B A and Tak, P P and Verweij, C L",
title = {Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients},
journal = "Ann Rheum Dis",
year = "2007",
volume = "66",
number = "8",
pages = "1008-1014",
doi = "10.1136/ard.2006.063412"
}

@Article{Olsen:2004:Ann-Rheum-Dis:15479887,
author = "Olsen, N and Sokka, T and Seehorn, C L and Kraft, B and Maas, K and Moore, J and Aune, T M",
title = {A gene expression signature for recent onset rheumatoid arthritis in peripheral blood mononuclear cells},
journal = "Ann Rheum Dis",
year = "2004",
volume = "63",
number = "11",
pages = "1387-1392",
doi = "10.1136/ard.2003.017194"
}

@Article{Lu:2008:Xi-Bao-Yu-Fen-Zi-Mian-Yi-Xue-Za-Zhi:18237535,
author = "Lu, C and Xu, S J and Xiao, C and Yan, X P and Zhao, L H and Wang, J M and Li, S and Lu, A P",
title = {[Gene expression profile of the peripheral CD4(+)T cells in patients with RF(+) and RF(-) rheumatoid arthritis.]},
journal = "Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi",
year = "2008",
volume = "24",
number = "2",
pages = "159-161",
doi = ""
}

@Article{wubing1999,
author = "B. Wu and R. Zhou and J. He",
title = {Current Situation and Prospects of Research in Acupuncture Regulation of Immunologic Function},
journal = "Shanghai Journal of Acupuncture and Moxibustion",
year = "1999",
volume = "18",
number = "1",
pages = "46-48",
doi = ""
}

@Article{yu07,
author = "Z. Yu and Z. Jian and S.-H. Shen and E. Purisima and E. Wang",
title = {Global analysis of micro{RNA} target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos},
journal = "Nucleic Acids Research",
year = "2007",
volume = "35",
number = "1",
pages = "152-164",
}

@Article{feber,
author = "A. Feber and J. Chen and L. Xi and T. Godfrey",
title = {mi{RNA} expression profiling using a custom {A}ffymetrix mi{RNA} array},
journal = "AACR Meeting Abstracts",
year = "2007",
volume = "",
number = "",
pages = "LB-242",
}

@Article{zwang1989,
author = "Z Wang",
title = {Treatment of Rheumatoid Arthritis using Moxa-grain Moxibustion for 20 cases},
journal = "Chinese Acupuncture {\&} Moxibustion",
year = "1989",
volume = "9",
number = "2",
pages = "18",
doi = ""
}

@Article{sluo1998,
author = "S. Luo",
title = {Treatment of Rheumatoid Arthritis using snake moxibustion for 65 cases},
journal = "Chinese Acupuncture {\&} Moxibustion",
year = "1998",
volume = "8",
number = "2",
pages = "8",
doi = ""
}

@Article{arnett,
author = "FC Arnett and SM Edworthy and DA Bloch and DJ McShane and JF Fries and NS Cooper",
title = {The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis},
journal = "Arthritis Rheum",
year = "1988",
volume = "31",
number = "",
pages = "315-324",
doi = ""
}

@Article{wang09,
author = "Wang, Z and Gerstein, M and Snyder, M",
title = {RNA-Seq: a revolutionary tool for transcriptomics},
journal = "Nat Rev Genet",
year = "2009",
volume = "10",
number = "1",
pages = "57-63",
month = "Jan",
pmid = "19015660",
doi = "10.1038/nrg2484"
}

@Article{neretti07,
author = "Neretti, N and Remondini, D and Tatar, M and Sedivy, J M and Pierini, M and Mazzatti, D and Powell, J and Franceschi, C and Castellani, G C",
title = {Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation},
journal = "BMC Bioinformatics",
year = "2007",
volume = "8 Suppl 1",
number = "",
pages = "",
month = "",
pmid = "17430560",
doi = "10.1186/1471-2105-8-S1-S16"
}

@Article{margolin,
author = "Margolin, A A and Nemenman, I and Basso, K and Wiggins, C and Stolovitzky, G and Dalla Favera, R and Califano, A",
title = {ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context},
journal = "BMC Bioinformatics",
year = "2006",
volume = "7 Suppl 1",
number = "",
pages = "",
month = "",
pmid = "16723010",
doi = "10.1186/1471-2105-7-S1-S7"
}

@Article{nardinispringer08,
author = "Nardini, C. and Wang, L. and Peng, H. and Benini, L. and Kuo, M D",
title = {MM-Correction: Meta-analysis-Based Multiple Hypotheses Correction in Omic Studies},
journal = "Springer CCIS",
year = "2008",
volume = "25",
number = "",
pages = "242-255",
month = "",
}

@Article{steuer,
author = "Steuer, R and Kurths, J and Daub, C O and Weise, J and Selbig, J",
title = {The mutual information: detecting and evaluating dependencies between variables},
journal = "Bioinformatics",
year = "2002",
volume = "18 Suppl 2",
number = "",
pages = "231-240",
month = "",
pmid = "12386007",
doi = ""
}

@Article{basso,
author = "Basso, K and Margolin, A A and Stolovitzky, G and Klein, U and Dalla-Favera, R and Califano, A",
title = {Reverse engineering of regulatory networks in human B cells},
journal = "Nat Genet",
year = "2005",
volume = "37",
number = "4",
pages = "382-390",
month = "Apr",
pmid = "15778709",
doi = "10.1038/ng1532"
}

@Article{jeong,
author = "Jeong, H and Tombor, B and Albert, R and Oltvai, Z N and Barab{\'a}si, A L",
title = {The large-scale organization of metabolic networks},
journal = "Nature",
year = "2000",
volume = "407",
number = "6804",
pages = "651-654",
month = "Oct",
pmid = "11034217",
doi = "10.1038/35036627"
}

@Article{meyer,
author = "Meyer, P E and Lafitte, F and Bontempi, G",
title = {minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information},
journal = "BMC Bioinformatics",
year = "2008",
volume = "9",
number = "",
pages = "461-461",
month = "",
pmid = "18959772",
doi = "10.1186/1471-2105-9-461"
}

@Article{hoops,
author = "Hoops, S and Sahle, S and Gauges, R and Lee, C and Pahle, J and Simus, N and Singhal, M and Xu, L and Mendes, P and Kummer, U",
title = {COPASI--a COmplex PAthway SImulator},
journal = "Bioinformatics",
year = "2006",
volume = "22",
number = "24",
pages = "3067-3074",
month = "Dec",
pmid = "17032683",
doi = "10.1093/bioinformatics/btl485"
}

@Article{yangy03,
author = "Yang, Y and Webb, GI",
title = {On why discretization works for naive-bayes 
classifiers},
journal = "Proceedings of the 16th Australian Joint Conference on Artificial Intelligence",
year = "2003",
volume = "",
number = "",
pages = "",
month = "",
pmid = "",
doi = ""
}

@Article{funahashi,
author = "Funahashi, A. and Tanimura, N. and Morohashi, M. and Kitano, H.",
title = {CellDesigner: a process diagram editor for gene-regulatory and biochemical networks},
journal = "BIOSILICO",
year = "2003",
volume = "1",
number = "",
pages = "159-162",
}

@Article{scott,
author = "Scott, S.W. and Deare, J. C.",
title = {Acupuncture for Migraine:  
A Systematic Review },
journal = "Aust J Acupunct Chin Med",
year = "2006",
volume = "1",
number = "",
pages = "3Ð14",
}

@Article{parkinson,
author = "Parkinson, H and Kapushesky, M and Shojatalab, M and Abeygunawardena, N and Coulson, R and Farne, A and Holloway, E and Kolesnykov, N and Lilja, P and Lukk, M and Mani, R and Rayner, T and Sharma, A and William, E and Sarkans, U and Brazma, A",
title = {ArrayExpress--a public database of microarray experiments and gene expression profiles},
journal = "Nucleic Acids Res",
year = "2007",
volume = "35",
number = "Database issue",
pages = "747-750",
}

@unpublished{dream,
        author = "",
        title = "The DREAM Initiative",
        note = "
        \texttt{wiki.c2b2.columbia.edu/dream}",
}

@Article{nicholson03,
author = "Nicholson, J K and Wilson I D",
title = {Understanding 'Global' Systems Biology: Metabonomics and the Continuum of Metabolism},
journal = "Nature",
year = "2003",
volume = "2",
number = "",
pages = "668-675",
}

@Article{nicholson04,
author = "Nicholson, J K and Holmes, E and Lindon, C J and Wilson, I D",
title = {The challenges of modeling mammalian biocomplexity},
journal = "Nature Biotech.",
year = "2004",
volume = "22",
number = "10",
pages = "1268-1274",
}

@Article{nicholson05,
author = "Nicholson, J K and Holmes, E and Wilson, I D",
title = {Gut microorganisms, mammalian metabolism and personalized health care},
journal = "Nature Reviews Microbiology",
year = "2005",
volume = "3",
number = "",
pages = "431-438",
}

@Article{nicholson08,
author = "Martin, F-P J and Wang, Y and Sprenger, N and Yap, I K S and Rezzi, S and Ramadan, Z and Per{\'{e}}-Trepat, E and Rochat, F and Cherbut, C and van Bladeren, P and Fay, L B and Kochhar, S and Lindon, J C and Holmes, E and Nicholson, J K",
title = {Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model},
journal = "Mol Syst Biol",
year = "2008",
volume = "4",
number = "",
pages = "205",
}

@Article{ahn1,
author = "Ahn, A C and Tewari, M and Poon, C-S and Phillips, R S",
title = {The Limits of Reductionism in Medicine: Could Systems Biology Offer an Alternative?},
journal = "PLoS Medicine",
year = "2006",
volume = "3",
number = "6",
pages = "e208",
}

@Article{ahn2,
author = "Ahn, A C and Tewari, M and Poon, C-S and Phillips, R S",
title = {The Clinical Applications of a Systems Approach},
journal = "PLoS Medicine",
year = "2006",
volume = "3",
number = "7",
pages = "e209",
}

@Article{turnbaugh06,
author = "Turnbaugh, P J and Ley, R E and Mahowald, M A and Magrini, V and Mardis, E R and Gordon, J I",
title = {An obesity-associated gut microbiome with increased capacity for energy harvest},
journal = "Nature",
year = "2006",
volume = "444",
number = "7122",
pages = "1027-1031",
month = "Dec",
pmid = "17183312",
doi = "10.1038/nature05414"
}

@Article{cani07,
author = "Cani, P D and Amar, J and Iglesias, M A and Poggi, M and Knauf, C and Bastelica, D and Neyrinck, A M and Fava, F and Tuohy, K M and Chabo, C and Waget, A and Delm{\'e}e, E and Cousin, B and Sulpice, T and Chamontin, B and Ferri{\`e}res, J and Tanti, J F and Gibson, G R and Casteilla, L and Delzenne, N M and Alessi, M C and Burcelin, R",
title = {Metabolic endotoxemia initiates obesity and insulin resistance},
journal = "Diabetes",
year = "2007",
volume = "56",
number = "7",
pages = "1761-1772",
month = "Jul",
pmid = "17456850",
doi = "10.2337/db06-1491"
}

@Article{holmes08,
author = "Holmes, E and Loo, R L and Stamler, J and Bictash, M and Yap, I K and Chan, Q and Ebbels, T and De Iorio, M and Brown, I J and Veselkov, K A and Daviglus, M L and Kesteloot, H and Ueshima, H and Zhao, L and Nicholson, J K and Elliott, P",
title = {Human metabolic phenotype diversity and its association with diet and blood pressure},
journal = "Nature",
year = "2008",
volume = "453",
number = "7193",
pages = "396-400",
month = "May",
pmid = "18425110",
doi = "10.1038/nature06882"
}

@Article{wen08,
author = "Wen, L. and Ley, R. E. and Volchkov, P. Y.. and Stranges, P. B. and Avanesyan, L. and Stonebraker, A. C. and Hu, C. and Wong, F. S. and Szot, G. L. and Bluestone, J. A. and Gordon, J. I. and Chervonsky, A. V.",
title = {Innate immunity and intestinal microbiota in the development of Type 1 diabetes},
journal = "Nature",
year = "2008",
volume = "455",
number = "7216",
pages = "1109-1113",
month = "Oct",
pmid = "18806780",
doi = "10.1038/nature07336"
}

@Article{lehar08,
author = "Leh{\'{a}}r, J. and Stockwell, B. R. and Giaever, G. and Nislow, C.",
title = {Combination chemical genetics},
journal = "Nature Chemical Biology",
year = "2008",
volume = "4",
pages = "674 - 681",
}

@Article{tsuji,
author = "Tsuji, M and Komatsu, N and Kawamoto, S and Suzuki, K and Kanagawa, O and Honjo, T and Hori, S and Fagarasan S",
title = {Preferential Generation of Follicular B Helper T Cells from Foxp3+ T Cells in Gut Peyer's Patches},
journal = "Science",
year = "2009",
volume = "323",
number = "5920",
pages = "1488 - 1492",
}

@Article{butte02,
author = "Butte, A.",
title = {The use and analysis of microarray data},
journal = "Nature Reviews Drug Discovery",
year = "2002",
volume = "1",
number = "",
pages = "951-960",
}

@Article{bonneau,
author = "Bonneau, R.",
title = {Learning biological networks: from modules to dynamics},
journal = "Nature Chemical Biology",
year = "2008",
volume = "4",
number = "11",
pages = "658-664",
}

@Article{masotti,
author = "Masotti, D and Nardini, C and Rossi, S. and Bonora, E and Romeo, G and Volinia, S and Benini, L",
title = {Learning biological networks: from modules to dynamics},
journal = "Bioinformatics",
year = "2008",
volume = "24",
number = "3",
pages = "428-429",
}

@Article{Katagiri01,
author = "Katagiri, F and Glazebrook, J",
title = {Overview of mRNA expression profiling using DNA microarrays},
abstract = {DNA microarray technology allows simultaneous measurement of the mRNA levels of thousands of genes. This powerful technology has applications in addressing many biological questions that were not approachable previously; however, the enormous size of microarray data sets leads to issues of experimental design and statistical analysis that are unfamiliar to many molecular biologists. The type of array used, the design of the biological experiment, the number of experimental replicates, and the statistical method for data analysis should all be chosen based on the scientific goals of the investigator. This overview presents a discussion of the relative merits and limitations of various methods with respect to some common applications of microarray experiments.},
journal = "Curr Protoc Mol Biol",
year = "2009",
volume = "Chapter 22",
number = "",
pages = "",
}

@Article{Jia01,
author = "Jia W and Li, H and Zhao, L and Nicholson, J K",
title = {Gut microbiota: a potential new territory for drug targeting},
journal = "Nat Rev Drug Discov",
year = "2008",
volume = "7",
number = "",
pages = "123-129",
}

@Article{Nicholson01,
author = "Tsuji, M and Komatsu, N and Kawamoto, S and Suzuki, K and Kanagawa, O and Honjo, T and Hori, S and Fagarasan, S",
title = {Preferential generation of follicular B helper T cells from Foxp3+ T cells in gut Peyer's patches},
abstract = {Most of the immunoglobulin A (IgA) in the gut is generated by B cells in the germinal centers of Peyer's patches through a process that requires the presence of CD4+ follicular B helper T(TFH) cells. The nature of these T(FH) cells in Peyer's patches has been elusive. Here, we demonstrate that suppressive Foxp3+CD4+ T cells can differentiate into TFH cells in mouse Peyer's patches. The conversion of Foxp3+ T cells into TFH cells requires the loss of Foxp3 expression and subsequent interaction with B cells. Thus, environmental cues present in gut Peyer's patches promote the selective differentiation of distinct helper T cell subsets, such as TFH cells.},
journal = "Science",
year = "2009",
volume = "323",
number = "5920",
pages = "1488-1492",
}

@Article{Martin01,
author = "Martin, F P and Wang, Y and Sprenger, N and Yap, I K and Rezzi, S and Ramadan, Z and Per{\'e}-Trepat, E and Rochat, F and Cherbut, C and van Bladeren, P and Fay, L B and Kochhar, S and Lindon, J C and Holmes, E and Nicholson, J K",
title = {Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model},
abstract = {Gut microbiome-host metabolic interactions affect human health and can be modified by probiotic and prebiotic supplementation. Here, we have assessed the effects of consumption of a combination of probiotics (Lactobacillus paracasei or L. rhamnosus) and two galactosyl-oligosaccharide prebiotics on the symbiotic microbiome-mammalian supersystem using integrative metabolic profiling and modeling of multiple compartments in germ-free mice inoculated with a model of human baby microbiota. We have shown specific impacts of two prebiotics on the microbial populations of HBM mice when co-administered with two probiotics. We observed an increase in the populations of Bifidobacterium longum and B. breve, and a reduction in Clostridium perfringens, which were more marked when combining prebiotics with L. rhamnosus. In turn, these microbial effects were associated with modulation of a range of host metabolic pathways observed via changes in lipid profiles, gluconeogenesis, a
 nd amino-acid and methylamine metabolism associated to fermentation of carbohydrates by different bacterial strains. These results provide evidence for the potential use of prebiotics for beneficially modifying the gut microbial balance as well as host energy and lipid homeostasis.},
journal = "Mol Syst Biol",
year = "2008",
volume = "4",
number = "",
pages = "205-205",
}

@Article{Turnbaugh01,
author = "Turnbaugh, P J and Ley, R E and Mahowald, M A and Magrini, V and Mardis, E R and Gordon, J I",
title = {An obesity-associated gut microbiome with increased capacity for energy harvest},
abstract = {The worldwide obesity epidemic is stimulating efforts to identify host and environmental factors that affect energy balance. Comparisons of the distal gut microbiota of genetically obese mice and their lean littermates, as well as those of obese and lean human volunteers have revealed that obesity is associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes. Here we demonstrate through metagenomic and biochemical analyses that these changes affect the metabolic potential of the mouse gut microbiota. Our results indicate that the obese microbiome has an increased capacity to harvest energy from the diet. Furthermore, this trait is transmissible: colonization of germ-free mice with an 'obese microbiota' results in a significantly greater increase in total body fat than colonization with a 'lean microbiota'. These results identify the gut microbiota as an additional contributing factor to the patho
 physiology of obesity.},
journal = "Nature",
year = "2006",
volume = "444",
number = "7122",
pages = "1027-1031",
}

@Article{Holmes01,
author = "Holmes, E and Loo, R L and Stamler, J and Bictash, M and Yap, I K and Chan, Q and Ebbels, T and De Iorio, M and Brown, I J and Veselkov, K A and Daviglus, M L and Kesteloot, H and Ueshima, H and Zhao, L and Nicholson, J K and Elliott, P",
title = {Human metabolic phenotype diversity and its association with diet and blood pressure},
abstract = {Metabolic phenotypes are the products of interactions among a variety of factors-dietary, other lifestyle/environmental, gut microbial and genetic. We use a large-scale exploratory analytical approach to investigate metabolic phenotype variation across and within four human populations, based on 1H NMR spectroscopy. Metabolites discriminating across populations are then linked to data for individuals on blood pressure, a major risk factor for coronary heart disease and stroke (leading causes of mortality worldwide). We analyse spectra from two 24-hour urine specimens for each of 4,630 participants from the INTERMAP epidemiological study, involving 17 population samples aged 40-59 in China, Japan, UK and USA. We show that urinary metabolite excretion patterns for East Asian and western population samples, with contrasting diets, diet-related major risk factors, and coronary heart disease/stroke rates, are significantly differentiated (P < 10(-16)), as are Chinese/J
 apanese metabolic phenotypes, and subgroups with differences in dietary vegetable/animal protein and blood pressure. Among discriminatory metabolites, we quantify four and show association (P < 0.05 to P < 0.0001) of mean 24-hour urinary formate excretion with blood pressure in multiple regression analyses for individuals. Mean 24-hour urinary excretion of alanine (direct) and hippurate (inverse), reflecting diet and gut microbial activities, are also associated with blood pressure of individuals. Metabolic phenotyping applied to high-quality epidemiological data offers the potential to develop an area of aetiopathogenetic knowledge involving discovery of novel biomarkers related to cardiovascular disease risk.},
journal = "Nature",
year = "2008",
volume = "453",
number = "7193",
pages = "396-400",
}

@Article{Wen01,
author = "Wen, L and Ley, R E and Volchkov, P Y and Stranges, P B and Avanesyan, L and Stonebraker, A C and Hu, C and Wong, F S and Szot, G L and Bluestone, J A and Gordon, J I and Chervonsky, A V",
title = {Innate immunity and intestinal microbiota in the development of Type 1 diabetes},
abstract = {Type 1 diabetes (T1D) is a debilitating autoimmune disease that results from T-cell-mediated destruction of insulin-producing beta-cells. Its incidence has increased during the past several decades in developed countries, suggesting that changes in the environment (including the human microbial environment) may influence disease pathogenesis. The incidence of spontaneous T1D in non-obese diabetic (NOD) mice can be affected by the microbial environment in the animal housing facility or by exposure to microbial stimuli, such as injection with mycobacteria or various microbial products. Here we show that specific pathogen-free NOD mice lacking MyD88 protein (an adaptor for multiple innate immune receptors that recognize microbial stimuli) do not develop T1D. The effect is dependent on commensal microbes because germ-free MyD88-negative NOD mice develop robust diabetes, whereas colonization of these germ-free MyD88-negative NOD mice with a defined microbial consortium
  (representing bacterial phyla normally present in human gut) attenuates T1D. We also find that MyD88 deficiency changes the composition of the distal gut microbiota, and that exposure to the microbiota of specific pathogen-free MyD88-negative NOD donors attenuates T1D in germ-free NOD recipients. Together, these findings indicate that interaction of the intestinal microbes with the innate immune system is a critical epigenetic factor modifying T1D predisposition.},
journal = "Nature",
year = "2008",
volume = "455",
number = "7216",
pages = "1109-1113",
}

@Article{Leek01,
author = "Leek, J T and Storey, J D",
title = {A general framework for multiple testing dependence},
abstract = {We develop a general framework for performing large-scale significance testing in the presence of arbitrarily strong dependence. We derive a low-dimensional set of random vectors, called a dependence kernel, that fully captures the dependence structure in an observed high-dimensional dataset. This result shows a surprising reversal of the "curse of dimensionality" in the high-dimensional hypothesis testing setting. We show theoretically that conditioning on a dependence kernel is sufficient to render statistical tests independent regardless of the level of dependence in the observed data. This framework for multiple testing dependence has implications in a variety of common multiple testing problems, such as in gene expression studies, brain imaging, and spatial epidemiology.},
journal = "Proc Natl Acad Sci U S A",
year = "2008",
volume = "105",
number = "48",
pages = "18718-18723",
}

@article{Benjamini01,
author = "Benjamini, Y and Hochberg, Y",
title = {Controlling the false discovery rate: A practical and powerful approach to multiple testing},
abstract = {The common approach to the multiplicity problem calls for controlling the familywise error rate (FWER). This approach, though, has faults, and we point out a few. A different approach to problems of multiple significance testing is presented. It calls for controlling the expected proportion of falsely rejected hypotheses-the false discovery rate. This error rate is equivalent to the FWER when all hypotheses are true but is smaller otherwise. Therefore, in problems where the control of the false discovery rate rather than that of the FWER is desired, there is potential for a gain in power. A simple sequential Bonferroni-type procedure is proved to control the false discovery rate for independent test statistics, and a simulation study shows that the gain in power is substantial. The use of the new procedure and the appropriateness of the criterion are illustrated with examples.},
journal = "J R Stat Soc",
year = "1995",
volume = "B 57",
number = "",
pages = "289-300",
}

@Article{Zhang01,
author = "Zhang, C and Zhang, M and Wang, S and Han, R and Cao, Y and Hua, W and Mao, Y and Zhang, X and Pang, X and Wei, C and Zhao, and Chen, Y and Zhao, L",
title = {Gut microbiota: a potential new territory for drug targeting},
journal = "Nat Rev Drug Discov",
year = "2008",
volume = "7",
number = "",
pages = "123-129",
}

@Article{Tsuji01,
author = "Tsuji, M and Komatsu, N and Kawamoto, S and Suzuki, K and Kanagawa, O and Honjo, T and Hori, S and Fagarasan, S",
title = {Preferential generation of follicular B helper T cells from Foxp3+ T cells in gut Peyer's patches},
abstract = {Most of the immunoglobulin A (IgA) in the gut is generated by B cells in the germinal centers of Peyer's patches through a process that requires the presence of CD4+ follicular B helper T(TFH) cells. The nature of these T(FH) cells in Peyer's patches has been elusive. Here, we demonstrate that suppressive Foxp3+CD4+ T cells can differentiate into TFH cells in mouse Peyer's patches. The conversion of Foxp3+ T cells into TFH cells requires the loss of Foxp3 expression and subsequent interaction with B cells. Thus, environmental cues present in gut Peyer's patches promote the selective differentiation of distinct helper T cell subsets, such as TFH cells.},
journal = "Science",
year = "2009",
volume = "323",
number = "5920",
pages = "1488-1492",
}

@Article{storey,
author = "Storey, J D and Tibshirani R",
title = {Statistical significance for genomewide studies},
journal = "Proc Natl Acad Sci U S A",
year = "2003",
volume = "100",
number = "16",
pages = "9440-9445",
}

@Article{smyth,
author = "Smyth, G., K.",
title = {Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments},
journal = "Statistical Applications in Genetics and Molecular Biology",
year = "2004",
volume = "3",
number = "1",
pages = "Article 3",
}

@Article{efron,
author = "Efron, B. and Tibshirani, R.",
title = {Microarrays, Empirical Bayes Methods, and False Discovery Rates},
journal = "Genet Epidemiol.",
year = "2002",
volume = "23",
number = "1",
pages = "70-86 ",
}

@Article{reiner,
author = "Reiner-Benaim, A and Yekutieli, D and Letwin, N E and Elmer, G I and Lee, N H and Kafkafi, N and Benjamini, Y",
title = {Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay},
journal = "Bioinformatics",
year = "2007",
volume = "23",
number = "17",
pages = "2239-2246",
month = "Sep",
pmid = "17827208",
}

@Article{dudoit02,
author = "Dudoit, S and Fridlyand, J and Speed, T P",
title = {Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data},
journal = "Journal of the American Statistical Association",
year = "2002",
volume = "97",
number = "457",
pages = "77",
}

@Article{cantone,
author = "Cantone, I and Marucci, L and Iorio, F and Ricci, M A and Belcastro, V and Bansal, M and Santini, S and di Bernardo, M and di Bernardo, D and Cosma, M P",
title = {A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches},
journal = "Cell",
year = "2009",
volume = "137",
number = "1",
pages = "172-181",
month = "Apr",
pmid = "19327819",
}

@Article{faith07,
author = "Faith, J J and Hayete, B and Thaden, J T and Mogno, I and Wierzbowski, J and Cottarel, G and Kasif, S and Collins, J J and Gardner, T S",
title = {Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles},
journal = "PLoS Biol",
year = "2007",
volume = "5",
number = "1",
pages = "",
month = "Jan",
pmid = "17214507",
}

@Article{davis,
author = "Davis, J and Goadrich, M",
title = {The Relationship Between Precision-Recall and {ROC} Curves},
journal = "Proceedings of the 23rd international conference on Machine learning",
year = "2006",
volume = "",
number = "",
pages = "",
month = "",
pmid = "",
}
 
@Article{altman,
author = "Altman, D G and Bland J M",
title = {Statistics Notes: Diagnostic tests 1: sensitivity and specificity},
journal = "BMJ",
year = "1994",
volume = "308",
number = "", 
pages = "1552",
month = "",
pmid = "",
}

@Article{nelander08,
author = "Nelander, S and Wang, W and Nilsson, B and She, Q B and Pratilas, C and Rosen, N and Gennemark, P and Sander C",
title = {Models from experiments: combinatorial drug perturbations of cancer cells},
journal = "Mol Syst Biol",
year = "2008",
volume = "4",
number = "216",
pages = "",
month = "",
pmid = "",
doi="10.1038/msb.2008.53",
}

@Article{hopkins,
author = "Hopkins, A L",
title = {Network pharmacology: the next paradigm in  drug discovery},
journal = "Nat Chem Biol",
year = "2008",
volume = "4",
number = "11",
pages = "682-690",
month = "Nov",
pmid = "18936753",
doi = "10.1038/nchembio.118"
}

@Article{kaptchuk98,
author = "Kaptchuk, T J",
title = {Powerful Placebo: The Dark Side of the Randomized Controlled Trial},
journal = "Lancet",
year = "1998",
volume = "351",
number = "",
pages = "1722-1725",
}

@Article{ling09,
author = "Ling, X B and Cohen, H and Jin, J and Lau, I and Schilling, J",
title = {{FDR} made easy in differential feature discovery and correlation analyses},
journal = "Bioinformatics",
year = "2009",
volume = "",
number = "",
pages = "",
doi="10.1093/bioinformatics/btp176",
}


@Article{gardner03,
author = "Gardner, T S and di Bernardo, D and Lorenz, D and Collins, J J",
title = {Inferring genetic networks and identifying compound mode of action via expression profiling},
journal = "Science",
year = "2003",
volume = "301",
number = "5629",
pages = "102-105",
month = "Jul",
pmid = "12843395",
url = "http://www.hubmed.org/display.cgi?uids=12843395",
doi = "10.1126/science.1081900"
}


@BOOK{duda,
AUTHOR = " R.O Duda and P.E. Hart and D. G. Stork",
YEAR = {(2001)}, 
TITLE = "Pattern Classification 2nd Edition",
PUBLISHER = "Whiley",
ADDRESS = "New York"
}

@Article{Bernardo05,
author = "di Bernardo, D and Thompson, M J and Gardner, T S and Chobot, S E and Eastwood, E L and Wojtovich, A P and Elliott, S J and Schaus, S E and Collins, J J",
title = {Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks},
journal = "Nat Biotechnol",
year = "2005",
volume = "23",
number = "3",
pages = "377-383",
month = "Mar",
pmid = "15765094",
url = "http://www.hubmed.org/display.cgi?uids=15765094",
doi = "10.1038/nbt1075"
}

@Article{Bansal07,
author = "Bansal, M and di Bernardo, D",
title = {Inference of gene networks from temporal gene expression profiles},
journal = "IET Syst Biol",
year = "2007",
volume = "1",
number = "5",
pages = "306-312",
month = "Sep",
pmid = "17907680",
url = "http://www.hubmed.org/display.cgi?uids=17907680",
}



