@article{lemeurFQ,
  title =	 {Bioconductor package flow\uppercase{Q}},
  author =	 {Gentleman, R. and Hahne, F. and Kettman, J. and Le Meur, N.},
  url = {http://www.bioconductor.org},
}

@Article{BIOC,
  author = {Robert C Gentleman and Vincent
J. Carey and Douglas M. Bates and 
Ben Bolstad and Marcel
Dettling and Sandrine Dudoit and Byron Ellis and
Laurent Gautier
and Yongchao Ge and Jeff Gentry and Kurt Hornik and 
Torsten
Hothorn and Wolfgang Huber and Stefano Iacus and  Rafael
Irizarry
and Friedrich Leisch and Cheng Li and Martin Maechler and Anthony J. Rossini
and Gunther Sawitzki and Colin Smith and Gordon Smyth and Luke Tierney
and Jean Y. H. Yang and  Jianhua Zhang},
  title = {Bioconductor: Open software development for 
computational biology and bioinformatics},
  journal = {Genome Biology},
  volume = {5},
  year = {2004},
  pages = {R80},
  url = {http://genomebiology.com/2004/5/10/R80}
}

@article{lemeur2007,
  title =	 {Quality Assessment of Ungated Flow Cytometry data in High Throughput experiments},
  author =	 {Le Meur, N. and Rossini, A. and Gasparetto, M and Smith, C and Brinkman, R.R. and Gentleman, R.},
  journal =	 {Cytometry A},
  volume =	 {71},
  pages =	 {393-403},
  year =	 {2007}
}

@article{Bottino2003,
  title =	 {Identification of PVR (CD155) and Nectin-2 (CD112) as Cell Surface Ligands for the Human DNAM-1 (CD226) Activating Molecule},
  author =	 {Cristina Bottino and Roberta Castriconi and
  Daniela Pende and Paola Rivera and Marina Nanni and Barbara Carnemolla and Claudia Cantoni and
  Jessica Grassi and Stefania Marcenaro and Nicolas Reymond and Massimo Vitale and Lorenzo Moretta and
  Marc Lopez and Alessandro Moretta},
  journal =	 {The Journal of Experimental Medicine},
  volume =	 {198},
  pages =	 {557-567},
  year =	 {2003}
}

@article{Critchley2007,
  title =	 {Down-regulation of the interferon signaling pathway in \uppercase{T} lymphocytes from patients with metastatic melanoma},
  author =	 {Critchley-Thorne, RJ. and Yan, N. and Nacu, S. and Weber, J. and Holmes, SP. and Lee, PP.},
  journal =	 {PLoS Med},
  volume =	 {4},
  pages =	 {e176},
  year =	 {2007 }
}


@article{lo2008,
  title =	 {Automated gating of flow cytometry data via robust model-based clustering},
  author =	 {K. Lo and R. R. Brinkman and R. Gottardo},
  journal =	 {Cytometry A},
  volume =	 {73A},
  pages =	 {321-332},
  year =	 {2008}
}

@article{hahne2009,
  title =	 {flowCore a Bioconductor package for high throughput flow cytometry},
  author =	 {Hahne, F. and LeMeur, N. and Brinkman, R.R. and Ellis, B. and Haaland, P. and Sarkar, D. and
  Spidlen, J. and Strain, E. and Gentleman, R.},
  journal =	 {BMC Bioinformatics},
  year =	 {2009}
}

@article{Appay,
	author  = {Appay, V and van Lier, R A W and Sallusto, F and Roederer, M}, 
	title   = {Phenotype and Function of Human T Lymphocyte Subsets: Consensus and Issues},
	journal = {Cytometry A}, 
	year  = {2008},
		  volume= {73A}, 
	 	  pages = {975-983},
}		


@ARTICLE{Maecker2005,
  author =	 {Holden T Maecker and Aline Rinfret and Patricia
                  D'Souza and Janice Darden and Eva Roig and Claire
                  Landry and Peter Hayes and Josephine Birungi and Omu
                  Anzala and Miguel Garcia and Alexandre Harari and
                  Ian Frank and Ruth Baydo and Megan Baker and
                  Jennifer Holbrook and Janet Ottinger and Laurie
                  Lamoreaux and C. Lorrie Epling and Elizabeth
                  Sinclair and Maria A Suni and Kara Punt and Sandra
                  Calarota and Sophia El-Bahi and Gailet Alter and
                  Hazel Maila and Ellen Kuta and Josephine Cox and
                  Clive Gray and Marcus Altfeld and Nolwenn Nougarede
                  and Jean Boyer and Lynda Tussey and Timothy Tobery
                  and Barry Bredt and Mario Roederer and Richard Koup
                  and Vernon C Maino and Kent Weinhold and Giuseppe
                  Pantaleo and Jill Gilmour and Helen Horton and
                  Rafick P Sekaly},
  title =	 {Standardization of cytokine flow cytometry assays.},
  journal =	 {BMC Immunol},
  year =	 2005,
  volume =	 6,
  pages =	 13,
  abstract =	 {BACKGROUND: Cytokine flow cytometry (CFC) or
                  intracellular cytokine staining (ICS) can quantitate
                  antigen-specific T cell responses in settings such
                  as experimental vaccination. Standardization of ICS
                  among laboratories performing vaccine studies would
                  provide a common platform by which to compare the
                  immunogenicity of different vaccine candidates
                  across multiple international organizations
                  conducting clinical trials. As such, a study was
                  carried out among several laboratories involved in
                  HIV clinical trials, to define the inter-lab
                  precision of ICS using various sample types, and
                  using a common protocol for each experiment (see
                  additional files online). RESULTS: Three sample
                  types (activated, fixed, and frozen whole blood;
                  fresh whole blood; and cryopreserved PBMC) were
                  shipped to various sites, where ICS assays using
                  cytomegalovirus (CMV) pp65 peptide mix or control
                  antigens were performed in parallel in 96-well
                  plates. For one experiment, antigens and antibody
                  cocktails were lyophilised into 96-well plates to
                  simplify and standardize the assay setup. Results
                  ((CD4+)cytokine+ cells and (CD8+)cytokine+ cells)
                  were determined by each site. Raw data were also
                  sent to a central site for batch analysis with a
                  dynamic gating template. Mean inter-laboratory
                  coefficient of variation (C.V.)  ranged from 17-44\%
                  depending upon the sample type and analysis method.
                  Cryopreserved peripheral blood mononuclear cells
                  (PBMC) yielded lower inter-lab C.V.'s than whole
                  blood. Centralized analysis (using a dynamic gating
                  template) reduced the inter-lab C.V. by 5-20\%,
                  depending upon the experiment. The inter-lab
                  C.V. was lowest (18-24\%) for samples with a mean of
                  > 0.5\% IFNgamma + T cells, and highest (57-82\%)
                  for samples with a mean of < 0.1\% IFNgamma +
                  cells. CONCLUSION: ICS assays can be performed by
                  multiple laboratories using a common protocol with
                  good inter-laboratory precision, which improves as
                  the frequency of responding cells
                  increases. Cryopreserved PBMC may yield slightly
                  more consistent results than shipped whole blood.
                  Analysis, particularly gating, is a significant
                  source of variability, and can be reduced by
                  centralized analysis and/or use of a standardized
                  dynamic gating template. Use of pre-aliquoted
                  lyophilized reagents for stimulation and staining
                  can provide further standardization to these
                  assays.},
  doi =		 {10.1186/1471-2172-6-13},
  institution =	 {BD Biosciences, San Jose,
                  USA. holden_maecker@bd.com},
  keywords =	 {Blood Preservation; Cryopreservation; Cytokines;
                  Cytomegalovirus Infections; Enzyme-Linked
                  Immunosorbent Assay; Flow Cytometry; Freeze Drying;
                  Humans; Indicators and Reagents; Laboratories;
                  Lymphocytes; Phosphoproteins; Reproducibility of
                  Results; Specimen Handling; T-Lymphocytes; Viral
                  Matrix Proteins},
  owner =	 {fhahne},
  pii =		 {1471-2172-6-13},
  pmid =	 15978127,
  timestamp =	 {2008.08.15},
  url =		 {http://dx.doi.org/10.1186/1471-2172-6-13}
}

@Manual{Rmain,
  title =	 {R: A Language and Environment for Statistical
                  Computing},
  author =	 {{R Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address =	 {Vienna, Austria},
  year =	 2008,
  note =	 {{ISBN} 3-900051-07-0},
  url =		 {http://www.R-project.org}
}

@misc{Rweb,
  url =		 {http://www.r-project.org},
  year =	 2008
}

@ARTICLE{SpidlenInPressCytometryA,
  title =	 {{Gating-ML: XML-based Gating Descriptions in Flow
                  Cytometry.}},
  author =	 {Spidlen Josef and  Leif Robert and Moore Wayne and Roederer
                  Mario and International Society for the Advancement of
                  Cytometry Data Standards Task Force and Brinkman Ryan},
  journal =	 {Cytometry A (in press)},
  year =	 2008
}

@misc{biocweb,
  url =		 {http://www.bioconductor.org},
  year =	 2008
}

@article{brinkman2007hcf,
  title =	 {{High-Content Flow Cytometry and Temporal Data
                  Analysis for Defining a Cellular Signature of
                  Graft-Versus-Host Disease}},
  author =	 {Brinkman, R.R. and Gasparetto, M. and Lee,
                  S.J.J. and Ribickas, A.J. and Perkins, J. and
                  Janssen, W. and Smiley, R. and Smith, C.},
  journal =	 {Biology of Blood and Marrow Transplantation},
  volume =	 13,
  number =	 6,
  pages =	 {691--700},
  year =	 2007,
  publisher =	 {Elsevier}
}

@misc{flowcoreweb,
  url =
                  {http://bioconductor.org/packages/2.2/bioc/html/flowCore.html},
  year =	 2008
}

@article{gasparetto2004ice,
  title =	 {{Identification of compounds that enhance the
                  anti-lymphoma activity of rituximab using flow
                  cytometric high-content screening}},
  author =	 {Gasparetto, M. and Gentry, T. and Sebti, S. and
                  O'Bryan, E. and Nimmanapalli, R. and Blaskovich,
                  M.A. and Bhalla, K. and Rizzieri, D. and Haaland,
                  P. and Dunne, J. and others},
  journal =	 {Journal of Immunological Methods},
  volume =	 292,
  number =	 {1-2},
  pages =	 {59--71},
  year =	 2004,
  publisher =	 {Elsevier}
}

@article{gentleman2006bos,
  title =	 {{Bioconductor: open software development for
                  computational biology and bioinformatics}},
  author =	 {Gentleman, R.C. and Carey, V.J. and Bates, D.M. and
                  Bolstad, B. and Dettling, M. and Dudoit, S. and
                  Ellis, B. and Gautier, L. and Ge, Y. and Gentry,
                  J. and others},
  journal =	 {feedback},
  year =	 2006
}

@book{lattice,
  author =	 {Deepayan Sarkar},
  title =	 {Lattice: Multivariate Data Visualization With R},
  publisher =	 {Springer},
  year =	 2008
}

@article{lizard2007fca,
  title =	 {{Flow cytometry analyses and bioinformatics:
                  interest in new softwares to optimize novel
                  technologies and to favor the emergence of
                  innovative concepts in cell research.}},
  author =	 {Lizard, G.},
  journal =	 {Cytometry A},
  volume =	 71,
  number =	 9,
  pages =	 {646--7},
  year =	 2007
}



@article{sarkar2008ufv,
  title =	 {{Using flowViz to visualize flow cytometry data}},
  author =	 {Sarkar, D. and Le Meur, N. and Gentleman, R.},
  journal =	 {Bioinformatics},
  volume =	 24,
  number =	 6,
  pages =	 878,
  year =	 2008,
  publisher =	 {Oxford Univ Press}
}

@article{seamer1997pnd,
  title =	 {{Proposed new data file standard for flow cytometry,
                  version FCS 3. 0}},
  author =	 {Seamer, LC and Bagwell, CB and Barden, L. and
                  Redelman, D. and Salzman, GC and Wood, JCS and
                  Murphy, RF},
  journal =	 {Cytometry},
  volume =	 28,
  number =	 2,
  pages =	 {118--122},
  year =	 1997
}

@article{wand2008,
  title =	 {{Feature Significance for Multivariate Kernel
                  Density Estimation.}},
  author =	 {Duong, T. and Cowling, A. and Koch, I. and Wand,
                  M.P.},
  journal =	 {Computational Statistics and Data Analysis},
  volume =	 52,
  number =	 9,
  pages =	 {4225-4242},
  year =	 2008,
  publisher =	 {Elsevier}
}

@article{wand2008_2,
  title =	 {{Highest Density Difference Region Estimation with
                  Application to Flow Cytometric Data.}},
  author =	 {Duong, T. and Cowling, A. and Koch, I. and Wand,
                  M.P.},
  journal =	 {under review},
  year =	 2008
}


@article{mahnke2007omi,
  title={{Optimizing a Multicolor Immunophenotyping Assay}},
  author={Mahnke, Y.D. and Roederer, M.},
  journal={Clinics in Laboratory Medicine},
  volume={27},
  number={3},
  pages={469--485},
  year={2007},
  publisher={Elsevier}
}
