%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Robinson:2008p548,
author = {Mark D Robinson and Gordon K Smyth}, 
journal = {Biostatistics (Oxford, England)},
title = {Small-sample estimation of negative binomial dispersion, with applications to SAGE data},
abstract = {We derive a quantile-adjusted conditional maximum likelihood estimator for the dispersion parameter of the negative binomial distribution and compare its performance, in terms of bias, to various other methods. Our estimation scheme outperforms all other methods in very small samples, typical of those from serial analysis of gene expression studies, the motivating data for this study. The impact of dispersion estimation on hypothesis testing is studied. We derive an "exact" test that outperforms the standard approximate asymptotic tests.},
affiliation = {Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, and Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia. mrobinson@wehi.edu.au},
number = {2},
pages = {321--32},
volume = {9},
year = {2008},
month = {Apr},
language = {eng},
keywords = {Weights and Measures, Gene Library, Sample Size, Likelihood Functions, Gene Expression Profiling, RNA: Messenger, Bias (Epidemiology), Research Design, Biometry, Expressed Sequence Tags, Information Storage and Retrieval, Stochastic Processes, Regression Analysis, Binomial Distribution, Humans}, 
date-added = {2009-07-06 17:54:22 -0400},
date-modified = {2010-01-30 23:08:07 -0500},
doi = {10.1093/biostatistics/kxm030},
pii = {kxm030},
pmid = {17728317},
URL = {http://biostatistics.oxfordjournals.org/cgi/content/full/9/2/321},
local-url = {file://localhost/Users/stvjc/Documents/Papers/2008/Robinson/Biostatistics%20(Oxford%20England)%202008%20Robinson.pdf},
uri = {papers://C760FBA3-C68E-4E3E-8645-15A5D6D0F91F/Paper/p548},
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%% This BibTeX bibliography file in UTF-8 format was created using Papers.
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@article{Lee:2008p932,
author = {Albert Lee and Kasper Daniel Hansen and James Bullard and Sandrine Dudoit and Gavin Sherlock and Michael Snyder}, 
journal = {PLoS Genet},
title = {Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High--Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species},
number = {12},
pages = {e1000299},
volume = {4},
year = {2008},
month = {Dec},
date-added = {2009-08-28 06:18:54 -0400},
date-modified = {2009-08-28 06:18:54 -0400},
doi = {10.1371/journal.pgen.1000299.t002},
local-url = {file://localhost/Users/stvjc/Documents/Papers/2008/Lee/PLoS%20Genet%202008%20Lee.pdf},
uri = {papers://C760FBA3-C68E-4E3E-8645-15A5D6D0F91F/Paper/p932},
read = {Yes},
rating = {0}
}


%% This BibTeX bibliography file in UTF-8 format was created using Papers.
%% http://mekentosj.com/papers/

@article{Li:2009p1146,
author = {Heng Li and Bob Handsaker and Alec Wysoker and Tim Fennell and Jue Ruan and Nils Homer and Gabor Marth and Goncalo Abecasis and Richard Durbin and 1000 Genome Project Data Processing Subgroup}, 
journal = {Bioinformatics},
title = {The Sequence Alignment/Map format and SAMtools},
abstract = {SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. AVAILABILITY: http://samtools.sourceforge.net.},
affiliation = {Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.},
number = {16},
pages = {2078--9},
volume = {25},
year = {2009},
month = {Aug},
language = {eng},
date-added = {2009-09-23 14:11:13 -0400},
date-modified = {2009-09-23 14:11:13 -0400},
doi = {10.1093/bioinformatics/btp352},
pii = {btp352},
pmid = {19505943},
local-url = {file://localhost/Users/stvjc/Documents/Papers/2009/Li/Bioinformatics%202009%20Li.pdf},
uri = {papers://C760FBA3-C68E-4E3E-8645-15A5D6D0F91F/Paper/p1146},
read = {Yes},
rating = {0}
}

