@article{Wang2011a,
abstract = {The pre-estimate of the proportion of null hypotheses ($\pi$(0)) plays a critical role in controlling false discovery rate (FDR) in multiple hypothesis testing. However, hidden complex dependence structures of many genomics datasets distort the distribution of p-values, rendering existing $\pi$(0) estimators less effective.},
author = {Wang, Hong-Qiang and Tuominen, Lindsey K and Tsai, Chung-Jui},
doi = {10.1093/bioinformatics/btq650},
file = {:Users/ala2027/Documents/Mendeley Desktop/Wang, Tuominen, Tsai - 2011 - SLIM a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
month = jan,
number = {2},
pages = {225--31},
pmid = {21098430},
title = {{SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21098430},
volume = {27},
year = {2011}
}

@article{Krueger2011,
abstract = {SUMMARY: A combination of bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot of a cell's epigenomic state by revealing its genome-wide cytosine methylation at single base resolution. Bismark is a flexible tool for the time-efficient analysis of BS-Seq data which performs both read mapping and methylation calling in a single convenient step. Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed. Availability and implementation: Bismark is released under the GNU GPLv3+ licence. The source code is freely available from www.bioinformatics.bbsrc.ac.uk/projects/bismark/.},
author = {Krueger, Felix and Andrews, Simon R},
doi = {10.1093/bioinformatics/btr167},
file = {:Users/altuna/Documents/Mendeley Desktop/Krueger, Andrews/Bioinformatics (Oxford, England)/Bioinformatics (Oxford, England) - Bismark a flexible aligner and methylation caller for Bisulfite-Seq applications. - 2011.pdf:pdf},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {Cytosine,Cytosine: metabolism,DNA,DNA Methylation,DNA: chemistry,Sequence Analysis, DNA,Software,Sulfites},
month = jun,
number = {11},
pages = {1571--2},
pmid = {21493656},
title = {{Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3102221\&tool=pmcentrez\&rendertype=abstract},
volume = {27},
year = {2011}
}


@article{Xi2009,
abstract = {Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation.},
author = {Xi, Yuanxin and Li, Wei},
doi = {10.1186/1471-2105-10-232},
issn = {1471-2105},
journal = {BMC bioinformatics},
keywords = {Base Sequence,DNA,DNA Methylation,DNA: chemistry,Genomics,Genomics: methods,Sequence Alignment,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Software,Sulfites,Sulfites: chemistry},
month = jan,
number = {1},
pages = {232},
pmid = {19635165},
title = {{BSMAP: whole genome bisulfite sequence MAPping program.}},
url = {http://www.biomedcentral.com/1471-2105/10/232},
volume = {10},
year = {2009}
}


@article{Li2011,
author = {Li, Heng}, 
title = {Tabix: fast retrieval of sequence features from generic TAB-delimited files},
volume = {27}, 
number = {5}, 
pages = {718-719}, 
year = {2011}, 
doi = {10.1093/bioinformatics/btq671}, 
abstract ={Summary: Tabix is the first generic tool that indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves features overlapping specified regions. Tabix features include few seek function calls per query, data compression with gzip compatibility and direct FTP/HTTP access. Tabix is implemented as a free command-line tool as well as a library in C, Java, Perl and Python. It is particularly useful for manually examining local genomic features on the command line and enables genome viewers to support huge data files and remote custom tracks over networks.Availability and Implementation: http://samtools.sourceforge.net.Contact: hengli@broadinstitute.org}, 
URL = {http://bioinformatics.oxfordjournals.org/content/27/5/718.abstract}, 
eprint = {http://bioinformatics.oxfordjournals.org/content/27/5/718.full.pdf+html}, 
journal = {Bioinformatics} 
}

@Manual{rsamtools,
title = {Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix
file import},
author = {Martin Morgan and Herv\'e Pag\`es and Valerie Obenchain and Nathaniel Hayden},
note = {R package version 1.22.0},
url = {http://bioconductor.org/packages/release/bioc/html/Rsamtools.html},
}

@book{McCullagh1989,
  Author = {P. McCullagh and John A. Nelder},
  Title = {Generalized Linear Models, Second Edition (Chapman \& Hall/CRC Monographs on Statistics \& Applied Probability)},
  Publisher = {Chapman and Hall/CRC},
  Year = {1989},
  ISBN = {0412317605},
  URL = {http://www.amazon.com/Generalized-Chapman-Monographs-Statistics-Probability/dp/0412317605%3FSubscriptionId%3D0JYN1NVW651KCA56C102%26tag%3Dtechkie-20%26linkCode%3Dxm2%26camp%3D2025%26creative%3D165953%26creativeASIN%3D0412317605}
}