BiB-reproducibility.bib

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%% http://mekentosj.com/papers/

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title = {{The efficiency of pooling mRNA in microarray experiments.}},
journal = {Biostatistics (Oxford, England)},
year = {2003}
}

@article{Brown2011,
author = {Brown, Andrew Anand and Richardson, Sylvia and Whittaker, John},
title = {{Application of the Lasso to Expression Quantitative Trait Loci Mapping}},
journal = {Statistical Applications in Genetics and Molecular Biology},
year = {2011}
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title = {{Statistical significance of quantitative PCR.}},
journal = {BMC Bioinformatics},
year = {2007}
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@article{Lo2008a,
author = {Lo, Kenneth and Brinkman, Ryan Remy and Gottardo, Raphael},
title = {{Automated gating of flow cytometry data via robust model-based clustering.}},
journal = {Cytometry Part A},
year = {2008}
}

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author = {Louis, T.A.},
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title = {{De novo cis-regulatory module elicitation for eukaryotic genomes.}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2005}
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@article{Droit2010,
author = {Droit, Arnaud and Cheung, Charles and Gottardo, Raphael},
title = {{rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments}},
journal = {Bioinformatics},
year = {2010}
}

@article{Rerks-Ngarm2009b,
author = {Rerks-Ngarm, Supachai and Pitisuttithum, Punnee and Nitayaphan, Sorachai and Kaewkungwal, Jaranit and Chiu, Joseph and Paris, Robert and Premsri, Nakorn and Namwat, Chawetsan and de Souza, Mark and Adams, Elizabeth and Benenson, Michael and Gurunathan, Sanjay and Tartaglia, Jim and McNeil, John G and Francis, Donald P and Stablein, Donald and Birx, Deborah L and Chunsuttiwat, Supamit and Khamboonruang, Chirasak and Thongcharoen, Prasert and Robb, Merlin L and Michael, Nelson L and Kunasol, Prayura and Kim, Jerome H},
title = {{Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand.}},
journal = {The New England journal of medicine},
year = {2009}
}

@article{Schmidt2010,
author = {Schmidt, Dominic and Wilson, Michael D and Ballester, Benoit and Schwalie, Petra C and Brown, Gordon D and Marshall, Aileen and Kutter, Claudia and Watt, Stephen and Martinez-Jimenez, Celia P and Mackay, Sarah and Talianidis, Iannis and Flicek, Paul and Odom, Duncan T},
title = {{Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding.}},
journal = {Science (New York, N.Y.)},
year = {2010}
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@article{Skvortsov2007,
author = {Skvortsov, Dmitriy and Abdueva, Diana and Stitzer, Michael E and Finkel, Steven E and Tavar e, Simon},
title = {{Using expression arrays for copy number detection: an example from E. coli.}},
journal = {BMC Bioinformatics},
year = {2007}
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@article{Stylianou2008,
author = {Stylianou, Ioannis M and Affourtit, Jason P and Shockley, Keith R and Wilpan, Robert Y and Abdi, Fadi a and Bhardwaj, Sanjeev and Rollins, Jarod and Churchill, Gary a and Paigen, Beverly},
title = {{Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification.}},
journal = {Genetics},
year = {2008}
}

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author = {Brem, Rachel B and Yvert, Ga\"{e}l and Clinton, Rebecca and Kruglyak, Leonid},
title = {{Genetic dissection of transcriptional regulation in budding yeast.}},
journal = {Science (New York, N.Y.)},
year = {2002}
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@article{Newman2006,
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title = {{Modularity and community structure in networks.}},
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@article{Koup2010,
author = {Koup, R.A. and Graham, B.S. and Douek, D.C.},
title = {{The quest for a T cell-based immune correlate of protection against HIV: a story of trials and errors}},
journal = {Nature Reviews Immunology},
year = {2010}
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@article{Visne2009,
author = {Visne, Ilhami and Dilaveroglu, Erkan and Vierlinger, Klemens and Lauss, Martin and Yildiz, Ahmet and Weinhaeusel, Andreas and Noehammer, Christa and Leisch, Friedrich and Kriegner, Albert},
title = {{RGG: a general GUI Framework for R scripts.}},
journal = {BMC Bioinformatics},
year = {2009}
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author = {McElrath, M Juliana},
title = {{Immune responses to HIV vaccines and potential impact on control of acute HIV-1 infection.}},
journal = {The Journal of infectious diseases},
year = {2010}
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author = {Durinck, Steffen and Bullard, James and Spellman, Paul T and Dudoit, Sandrine},
title = {{GenomeGraphs: integrated genomic data visualization with R.}},
journal = {BMC Bioinformatics},
year = {2009}
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author = {Storey, John D and Akey, Joshua M and Kruglyak, Leonid},
title = {{Multiple locus linkage analysis of genomewide expression in yeast.}},
journal = {PLoS biology},
year = {2005}
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author = {Guillemette, Beno\^{\i}t and Bataille, Alain R and G e vry, Nicolas and Adam, Maryse and Blanchette, Mathieu and Robert, Fran\c{c}ois and Gaudreau, Luc},
title = {{Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning.}},
journal = {PLoS biology},
year = {2005}
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journal = {Nature biotechnology},
year = {2008}
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author = {Ferretti, Vincent and Poitras, Christian and Bergeron, Dominique and Coulombe, Benoit and Robert, Fran\c{c}ois and Blanchette, Mathieu},
title = {{PReMod: a database of genome-wide mammalian cis-regulatory module predictions.}},
journal = {Nucleic Acids Research},
year = {2007}
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author = {Mason, Mike J and Fan, Guoping and Plath, Kathrin and Zhou, Qing and Horvath, Steve},
title = {{Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells.}},
journal = {BMC genomics},
year = {2009}
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journal = {Genome biology},
year = {2004}
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author = {Galbraith, David W},
title = {{Cytometry and plant sciences: a personal retrospective.}},
journal = {Cytometry Part A},
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author = {Irizarry, R. a.},
title = {{Summaries of Affymetrix GeneChip probe level data}},
journal = {Nucleic Acids Research},
year = {2003}
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@article{Sultan2008,
author = {Sultan, Marc and Schulz, Marcel H and Richard, Hugues and Magen, Alon and Klingenhoff, Andreas and Scherf, Matthias and Seifert, Martin and Borodina, Tatjana and Soldatov, Aleksey and Parkhomchuk, Dmitri and Schmidt, Dominic and O'Keeffe, Sean and Haas, Stefan and Vingron, Martin and Lehrach, Hans and Yaspo, Marie-Laure},
title = {{A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.}},
journal = {Science (New York, N.Y.)},
year = {2008}
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author = {Hon, Gary and Ren, Bing and Wang, Wei},
title = {{ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.}},
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year = {2008}
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title = {{rapmad: Robust analysis of peptide microarray data.}},
journal = {BMC Bioinformatics},
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author = {Llamas, Bastien and B e langer, Sonia and Picard, Sylvie and Deschepper, Christian F},
title = {{Cardiac mass and cardiomyocyte size are governed by different genetic loci on either autosomes or chromosome Y in recombinant inbred mice.}},
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title = {{A high-resolution map of transcription in the yeast genome.}},
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title = {{Mapping and quantifying mammalian transcriptomes by RNA-Seq}},
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year = {2008}
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author = {Sotiriou, Christos and Piccart, Martine J},
title = {{Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care?}},
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year = {2007}
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@article{Wang2011,
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title = {{Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells.}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2011}
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@article{Steinbrich-Zollner2008,
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title = {{From transcriptome to cytome: integrating cytometric profiling, multivariate cluster, and prediction analyses for a phenotypical classification of inflammatory diseases.}},
journal = {Cytometry Part A},
year = {2008}
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title = {{Evaluation of the host transcriptional response to human cytomegalovirus infection.}},
journal = {Physiological genomics},
year = {2004}
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@article{Farber2009,
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title = {{Genetic dissection of a major mouse obesity QTL (Carfhg2): integration of gene expression and causality modeling.}},
journal = {Physiological genomics},
year = {2009}
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title = {{Analysis of cell fate from single-cell gene expression profiles in C. elegans.}},
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title = {{Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst}},
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title = {{Transfer Learning for Automatic Gating of Flow Cytometry Data}},
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title = {{Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations}},
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title = {{Fully Bayesian Mixture Model for Differential Gene Expression : Simulations and Model}},
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