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@article{krejci2008p53,
	Author = {Krejci, Ondrej and Wunderlich, Mark and Geiger, Hartmut and Chou, Fu-Sheng and Schleimer, David and Jansen, Michael and Andreassen, Paul R and Mulloy, James C},
	Date-Added = {2017-01-17 21:42:21 +0000},
	Date-Modified = {2017-01-17 21:42:29 +0000},
	Journal = {Blood},
	Number = {4},
	Pages = {2190--2199},
	Publisher = {Am Soc Hematology},
	Title = {{p53 signaling in response to increased DNA damage sensitizes AML1-ETO cells to stress-induced death}},
	Volume = {111},
	Year = {2008}}

@article{bacher2012multilineage,
	Author = {Bacher, Ulrike and Schnittger, Susanne and Macijewski, Katja and Grossmann, Vera and Kohlmann, Alexander and Alpermann, Tamara and Kowarsch, Andreas and Nadarajah, Niroshan and Kern, Wolfgang and Haferlach, Claudia and others},
	Date-Added = {2017-01-17 21:36:14 +0000},
	Date-Modified = {2017-01-17 21:36:21 +0000},
	Journal = {Blood},
	Number = {20},
	Pages = {4719--4722},
	Publisher = {Am Soc Hematology},
	Title = {{Multilineage dysplasia does not influence prognosis in CEBPA-mutated AML, supporting the WHO proposal to classify these patients as a unique entity}},
	Volume = {119},
	Year = {2012}}

@article{abdul2010vitro,
	Author = {Abdul-Nabi, Anmaar M and Yassin, Enas R and Varghese, Nobish and Deshmukh, Hrishikesh and Yaseen, Nabeel R},
	Date-Added = {2017-01-17 21:32:52 +0000},
	Date-Modified = {2017-01-17 21:32:58 +0000},
	Journal = {PLoS One},
	Number = {8},
	Pages = {e12464},
	Publisher = {Public Library of Science},
	Title = {{In vitro transformation of primary human CD34+ cells by AML fusion oncogenes: early gene expression profiling reveals possible drug target in AML}},
	Volume = {5},
	Year = {2010}}

@article{majeti2009dysregulated,
	Author = {Majeti, Ravindra and Becker, Michael W and Tian, Qiang and Lee, Tsung-Lu Michael and Yan, Xiaowei and Liu, Rui and Chiang, Jung-Hsien and Hood, Leroy and Clarke, Michael F and Weissman, Irving L},
	Date-Added = {2017-01-17 21:28:58 +0000},
	Date-Modified = {2017-01-17 21:28:58 +0000},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {9},
	Pages = {3396--3401},
	Publisher = {National Acad Sciences},
	Title = {Dysregulated gene expression networks in human acute myelogenous leukemia stem cells},
	Volume = {106},
	Year = {2009}}

@article{LeDieu:2009,
	Abstract = {Understanding how the immune system in patients with cancer interacts with malignant cells is critical for the development of successful immunotherapeutic strategies. We studied peripheral blood from newly diagnosed patients with acute myeloid leukemia ({AML}) to assess the impact of this disease on the patients' T cells. The absolute number of peripheral blood T cells is increased in {AML} compared with healthy controls. An increase in the absolute number of {CD}3+56+ cells was also noted. Gene expression profiling on T cells from {AML} patients compared with healthy donors demonstrated global differences in transcription suggesting aberrant T-cell activation patterns. These gene expression changes differ from those observed in chronic lymphocytic leukemia ({CLL}), indicating the heterogeneous means by which different tumors evade the host immune response. However, in common with {CLL}, differentially regulated genes involved in actin cytoskeletal formation were identified, and therefore the ability of T cells from {AML} patients to form immunologic synapses was assessed. Although {AML} T cells could form conjugates with autologous blasts, their ability to form immune synapses and recruit phosphotyrosine signaling molecules to the synapse was significantly impaired. These findings identify T-cell dysfunction in {AML} that may contribute to the failure of a host immune response against leukemic blasts.},
	Author = {Le Dieu, Rifca and Taussig, David C. and Ramsay, Alan G. and Mitter, Richard and Miraki-Moud, Faridah and Fatah, Rewas and Lee, Abigail M. and Lister, T. Andrew and Gribben, John G.},
	Date-Added = {2017-01-17 21:28:08 +0000},
	Date-Modified = {2017-01-17 21:28:08 +0000},
	Doi = {10.1182/blood-2009-02-206946},
	Issn = {1528-0020},
	Journal = {Blood},
	Keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Antigens, {CD}3, Antigens, {CD}36, Blast Crisis, Gene Expression Profiling, Gene Expression Regulation, Leukemic, Genotype, Humans, Immunological Synapses, Leukemia, Myeloid, Acute, Lymphocyte Count, Male, Middle Aged, T-Lymphocytes},
	Language = {eng},
	Month = oct,
	Number = {18},
	Pages = {3909--3916},
	Pmcid = {PMC2773481},
	Pmid = {19710498},
	Title = {Peripheral blood {T} cells in acute myeloid leukemia ({AML}) patients at diagnosis have abnormal phenotype and genotype and form defective immune synapses with {AML} blasts},
	Volume = {114},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1182/blood-2009-02-206946}}

@article{Tavazoie:1999,
	Author = {Tavazoie, Saeed and Hughes, Jason D. and Campbell, Michael J. and Cho, Raymond J. and Church, George M.},
	Date-Added = {2017-01-15 00:36:50 +0000},
	Date-Modified = {2017-01-15 00:36:50 +0000},
	Journal = {Nature Genetics},
	Pages = {281--285},
	Title = {{Systematic determination of genetic network architecture}},
	Volume = {22},
	Year = {1999}}

@manual{simpleaffy2.38.0,
	Author = {Crispin J Miller},
	Date-Added = {2017-01-14 05:34:09 +0000},
	Date-Modified = {2017-01-14 05:34:09 +0000},
	Note = {{R package version 2.38.0}},
	Title = {simpleaffy: Very simple high level analysis of Affymetrix data},
	Url = {http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/},
	Year = {2013},
	Bdsk-Url-1 = {http://www.bioconductor.org,%20http://bioinformatics.picr.man.ac.uk/simpleaffy/}}

@incollection{limma,
	Address = {New York},
	Author = {Gordon K Smyth},
	Booktitle = {Bioinformatics and Computational Biology Solutions Using {R} and Bioconductor},
	Date-Added = {2017-01-14 05:28:27 +0000},
	Date-Modified = {2017-01-14 05:28:27 +0000},
	Editor = {R. Gentleman and V. Carey and S. Dudoit and R. Irizarry and W. Huber},
	Pages = {397--420},
	Publisher = {Springer},
	Title = {Limma: linear models for microarray data},
	Year = {2005}}

@article{brettschneider2008quality,
	Author = {Brettschneider, Julia and Collin, Fran{\c{c}}ois and Bolstad, Benjamin M and Speed, Terence P},
	Date-Added = {2017-01-14 05:28:07 +0000},
	Date-Modified = {2017-01-14 05:28:07 +0000},
	Journal = {Technometrics},
	Number = {3},
	Title = {Quality assessment for short oligonucleotide microarray data},
	Volume = {50},
	Year = {2008}}

@incollection{bolstad2005quality,
	Address = {New York},
	Author = {Bolstad, Benjamin M and Collin, Fran{\c{c}}ois and Brettschneider, Julia and Simpson, K and Cope, L and Irizarry, RA and Speed, Terence P},
	Booktitle = {Bioinformatics and computational biology solutions using {R} and {B}ioconductor},
	Date-Added = {2017-01-14 05:28:02 +0000},
	Date-Modified = {2017-01-14 05:28:02 +0000},
	Pages = {33--47},
	Publisher = {Springer},
	Title = {Quality assessment of {Affymetrix GeneChip} data},
	Year = {2005}}

@phdthesis{bolstad2004low,
	Author = {Bolstad, Benjamin Milo},
	Date-Added = {2017-01-14 05:27:51 +0000},
	Date-Modified = {2017-01-14 05:27:51 +0000},
	School = {University of California},
	Title = {Low-level analysis of high-density oligonucleotide array data: background, normalization and summarization},
	Year = {2004}}

@article{draghici2007systems,
	Author = {Dr\v{a}ghici, Sorin and Khatri, Purvesh and Tarca, Adi L and Amin, Kashyap and Done, Arina and Voichi\c{t}a, C\u{a}lin and Georgescu, Constantin and Romero, Roberto},
	Date-Added = {2017-01-14 05:27:36 +0000},
	Date-Modified = {2017-01-14 05:27:36 +0000},
	Journal = {Genome Research},
	Number = {10},
	Pages = {1537--1545},
	Pmcid = {PMC1987343},
	Pmid = {17785539},
	Publisher = {Cold Spring Harbor Lab},
	Title = {A systems biology approach for pathway level analysis},
	Volume = {17},
	Year = {2007}}

@article{Tarca2012down,
	Author = {Tarca, Adi L and Dr\v{a}ghici, Sorin and Bhatti, Gaurav and Romero, Roberto},
	Date-Added = {2017-01-14 05:27:29 +0000},
	Date-Modified = {2017-01-14 05:27:29 +0000},
	Journal = {BMC Bioinformatics},
	Number = {1},
	Pages = {136},
	Pmcid = {PMC3443069},
	Pmid = {22713124},
	Publisher = {BioMed Central Ltd},
	Title = {Down-weighting overlapping genes improves gene set analysis},
	Volume = {13},
	Year = {2012}}

@article{Efron:2007,
	Author = {Efron, Bradley and Tibshirani, Robert},
	Date-Added = {2017-01-14 05:27:21 +0000},
	Date-Modified = {2017-01-14 05:27:21 +0000},
	Journal = {The Annals of Applied Statistics},
	Number = {1},
	Pages = {107--129},
	Publisher = {JSTOR},
	Title = {{On testing the significance of sets of genes}},
	Volume = {1},
	Year = {2007}}

@article{Draghici:2003a,
	Author = {Dr\v{a}ghici, Sorin and Khatri, Purvesh and Martins, Rui P and Ostermeier, G Charles and Krawetz, Stephen A},
	Date-Added = {2017-01-14 05:27:12 +0000},
	Date-Modified = {2017-01-14 05:27:12 +0000},
	Journal = {Genomics},
	Number = {2},
	Pages = {98--104},
	Pmid = {12620386},
	Title = {Global functional profiling of gene expression},
	Volume = {81},
	Year = {2003}}

@article{pearson1976biometrika,
	Author = {Pearson, E and Haetlet, H},
	Date-Added = {2017-01-14 05:26:45 +0000},
	Date-Modified = {2017-01-14 05:32:01 +0000},
	Journal = {Biometrika Trust},
	Title = {Biometrika tables for statisticians},
	Year = {1976}}

@article{Gossett:1908,
	Author = {Gosset, William Sealy},
	Date-Added = {2017-01-14 05:26:37 +0000},
	Date-Modified = {2017-01-14 05:26:37 +0000},
	Journal = {Biometrika},
	Pages = {1--25},
	Title = {{The Probable Error of a Mean}},
	Volume = {6},
	Year = {1908}}

@book{kallenberg2002foundations,
	Address = {New York},
	Author = {Kallenberg, Olav},
	Date-Added = {2017-01-14 05:26:25 +0000},
	Date-Modified = {2017-01-14 05:26:25 +0000},
	Publisher = {Springer-Verlag},
	Title = {Foundations of modern probability},
	Year = {2002}}

@article{edgington1972additive,
	Author = {Edgington, Eugene S},
	Date-Added = {2017-01-14 05:26:18 +0000},
	Date-Modified = {2017-01-14 05:26:18 +0000},
	Journal = {The Journal of Psychology},
	Number = {2},
	Pages = {351--363},
	Publisher = {Taylor \& Francis},
	Title = {An additive method for combining probability values from independent experiments},
	Volume = {80},
	Year = {1972}}

@article{irwin1927frequency,
	Author = {Irwin, Joseph Oscar},
	Date-Added = {2017-01-14 05:26:12 +0000},
	Date-Modified = {2017-01-14 05:26:12 +0000},
	Journal = {Biometrika},
	Number = {3-4},
	Pages = {225--239},
	Publisher = {JSTOR},
	Title = {On the frequency distribution of the means of samples from a population having any law of frequency with finite moments, with special reference to {Pearson's Type II}},
	Volume = {19},
	Year = {1927}}

@article{philip1927distribution,
	Author = {Hall, Philip},
	Date-Added = {2017-01-14 05:26:06 +0000},
	Date-Modified = {2017-01-14 05:26:06 +0000},
	Journal = {Biometrika},
	Number = {3-4},
	Pages = {240--244},
	Publisher = {Biometrika Trust},
	Title = {The distribution of means for samples of size n drawn from a population in which the variate takes values between 0 and 1, all such values being equally probable},
	Volume = {19},
	Year = {1927}}

@article{wilkinson1951statistical,
	Author = {Wilkinson, Bryan},
	Date-Added = {2017-01-14 05:25:49 +0000},
	Date-Modified = {2017-01-14 05:25:49 +0000},
	Journal = {Psychological Bulletin},
	Number = {2},
	Pages = {156},
	Publisher = {American Psychological Association},
	Title = {A statistical consideration in psychological research.},
	Volume = {48},
	Year = {1951}}

@book{tippett1931methods,
	Address = {London},
	Author = {Tippett, Leonard Henry Caleb},
	Date-Added = {2017-01-14 05:25:43 +0000},
	Date-Modified = {2017-01-14 05:25:43 +0000},
	Publisher = {Williams \& Norgate},
	Title = {The methods of statistics},
	Year = {1931}}

@book{stouffer1949the,
	Address = {Princeton},
	Author = {Stouffer, SA and Suchman, EA and DeVinney, LC and Star, SA and Williams, RM, Jr.},
	Date-Added = {2017-01-14 05:25:36 +0000},
	Date-Modified = {2017-01-14 05:25:36 +0000},
	Publisher = {Princeton University Press},
	Title = {The American Soldier: Adjustment during army life},
	Volume = {1},
	Year = {1949}}

@book{fisher1925statistical,
	Address = {Edinburgh},
	Author = {Fisher, Ronald Aylmer},
	Date-Added = {2017-01-14 05:25:25 +0000},
	Date-Modified = {2017-01-14 05:25:25 +0000},
	Publisher = {Oliver \& Boyd},
	Title = {Statistical methods for research workers},
	Year = {1925}}

@article{nguyen2015DANUBE,
	Author = {Nguyen, Tin and Mitrea, Cristina and Tagett, Rebecca and Dr\u{a}ghici, Sorin},
	Date-Added = {2017-01-14 05:25:03 +0000},
	Date-Modified = {2017-01-14 05:25:03 +0000},
	Doi = {10.1109/JPROC.2015.2507119},
	Journal = {Proceedings of the IEEE},
	Month = {March},
	Number = {99},
	Pages = {1--20},
	Publisher = {IEEE},
	Title = {{DANUBE: Data-driven meta-ANalysis using UnBiased Empirical distributions - applied to biological pathway analysis}},
	Volume = {PP},
	Year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/JPROC.2015.2507119}}

@article{nguyen2015novel,
	Author = {Nguyen, Tin and Tagett, Rebecca and Donato, Michele and Mitrea, Cristina and Dr\u{a}ghici, Sorin},
	Date-Added = {2017-01-14 05:25:03 +0000},
	Date-Modified = {2017-01-14 05:25:03 +0000},
	Journal = {Bioinformatics},
	Number = {3},
	Pages = {409--416},
	Publisher = {Oxford University Press},
	Title = {A novel bi-level meta-analysis approach-applied to biological pathway analysis},
	Volume = {32},
	Year = {2016}}

@article{nguyen2016overcoming,
	Author = {Nguyen, Tin and Diaz, Diana and Tagett, Rebecca and Draghici, Sorin},
	Date-Added = {2017-01-14 05:25:03 +0000},
	Date-Modified = {2017-01-14 05:25:03 +0000},
	Doi = {DOI:10.1038/srep29251},
	Journal = {Nature Scientific Reports},
	Pages = {29251},
	Publisher = {Nature Publishing Group},
	Title = {Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data},
	Volume = {6},
	Year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/srep29251}}

@inproceedings{nguyen2016tomas,
	Author = {Nguyen, Tin and Diaz, Diana and Draghici, Sorin},
	Booktitle = {Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
	Date-Added = {2017-01-14 05:25:03 +0000},
	Date-Modified = {2017-01-14 05:25:03 +0000},
	Organization = {ACM},
	Pages = {13--22},
	Title = {{TOMAS: A novel TOpology-aware Meta-Analysis approach applied to System biology}},
	Year = {2016}}
	
@article{nguyen2020nbia,
  title={NBIA: a network-based integrative analysis framework – applied to pathway analysis},
  author={Nguyen, Tin and Shafi, Adib and Nguyen, Tuan-Minh and Schissler, A Grant and Draghici, Sorin},
  journal={Scientific reports},
  volume={10},
  number={1},
  pages={1--11},
  year={2020},
  publisher={Nature Publishing Group}
}
