
@article{Li2010,
  author = {Li, Jun and Jiang, Hui and Wong, Wing Hung},
  doi = {10.1186/gb-2010-11-5-r50},
  file = {:home/dcjones/papers/2010/Genome Biology/Li, Jiang, Wong/2010 - Li, Jiang, Wong - Modeling non-uniformity in short-read rates in RNA-Seq data(2).pdf:pdf},
  issn = {1465-6906},
  journal = {Genome Biology},
  number = {5},
  pages = {R50},
  title = {{Modeling non-uniformity in short-read rates in RNA-Seq data}},
  url = {http://genomebiology.com/2010/11/5/R50},
  volume = {11},
  year = {2010}
}

@article{Hansen2010,
  abstract = {Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias.},
  author = {Hansen, Kasper and Brenner, Steven and Dudoit, Sandrine},
  doi = {10.1093/nar/gkq224},
  file = {:home/dcjones/papers/2010/Nucleic acids research/Hansen, Brenner, Dudoit/2010 - Hansen, Brenner, Dudoit - Biases in Illumina transcriptome sequencing caused by random hexamer priming.pdf:pdf},
  issn = {1362-4962},
  journal = {Nucleic acids research},
  month = apr,
  pages = {1--7},
  pmid = {20395217},
  title = {{Biases in Illumina transcriptome sequencing caused by random hexamer priming.}},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/20395217},
  year = {2010}
}

@article{Bullard2010,
  title = {Evaluation of Statistical Methods for Normalization and Differential Expression in mRNA-Seq Experiments},
  author = {James Bullard and Elizabeth Purdom and Kasper Hansen and Sandrine Dudoit},
  year = {2010},
  journal = {BMC Bioinformatics},
  volume = {11},
  note = {R package version 1.4.0},
}

@article{Mortazavi2008,
author = {Mortazavi, Ali and Williams, Brian and Mccue, Kenneth and Schaeffer, Lorian and Wold, Barbara},
doi = {10.1038/NMETH.1226},
file = {:home/dcjones/papers/2008/Nature Methods/Mortazavi et al./2008 - Mortazavi et al. - Mapping and quantifying mammalian transcriptomes by RNA-Seq.pdf:pdf},
journal = {Nature Methods},
number = {7},
pages = {1--8},
title = {{Mapping and quantifying mammalian transcriptomes by RNA-Seq}},
volume = {5},
year = {2008}
}

@article{Langmead2009,
abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu).},
author = {Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven},
doi = {10.1186/gb-2009-10-3-r25},
file = {:home/dcjones/papers/2009/Genome biology/Langmead et al./2009 - Langmead et al. - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.pdf:pdf},
issn = {1465-6914},
journal = {Genome biology},
keywords = {Algorithms,Base Sequence,Genome, Human,Genome, Human: genetics,Humans,Sequence Alignment,Sequence Alignment: methods},
number = {3},
pages = {R25},
pmid = {19261174},
title = {{Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19261174},
volume = {10},
year = {2009}
}
