@article{diffReps,
    author = {Shen, , Li AND Shao, , Ning-Yi AND Liu, , Xiaochuan AND Maze, , Ian AND Feng, , Jian AND Nestler, , Eric J.},
    journal = {PLoS ONE},
    publisher = {Public Library of Science},
    title = {diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates},
    year = {2013},
    month = {06},
    volume = {8},
    url = {http://dx.doi.org/10.1371%2Fjournal.pone.0065598},
    pages = {e65598},
    number = {6},
    doi = {10.1371/journal.pone.0065598}
}        

@Article{Bowtie,
AUTHOR = {Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven},
TITLE = {Ultrafast and memory-efficient alignment of short DNA sequences to the human genome},
JOURNAL = {Genome Biology},
VOLUME = {10},
YEAR = {2009},
NUMBER = {3},
PAGES = {R25},
URL = {http://genomebiology.com/2009/10/3/R25},
DOI = {10.1186/gb-2009-10-3-r25},
PubMedID = {19261174},
ISSN = {1465-6906},
}

@article{Tophat,
author = {Trapnell, Cole and Pachter, Lior and Salzberg, Steven L.}, 
title = {TopHat: discovering splice junctions with RNA-Seq},
volume = {25}, 
number = {9}, 
pages = {1105-1111}, 
year = {2009}, 
doi = {10.1093/bioinformatics/btp120}, 
URL = {http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract}, 
eprint = {http://bioinformatics.oxfordjournals.org/content/25/9/1105.full.pdf+html}, 
journal = {Bioinformatics} 
}

@article{Cufflinks,
   author = {Trapnell, Cole and Williams, Brian A. and Pertea, Geo and Mortazavi, Ali and Kwan, Gordon and van Baren, Marijke J. and Salzberg, Steven L. and Wold, Barbara J. and Pachter, Lior},
   title = {Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation},
   journal = {Nat Biotech},
   volume = {28},
   number = {5},
   pages = {511-515},
   note = {10.1038/nbt.1621},
   year = {2010}
}

@ONLINE{ENCODE,
author = {{ENCODE Consortium}},
title = {The Encyclopedia of DNA Elements (http://encodeproject.org/ENCODE/)},
url = {http://encodeproject.org/ENCODE/}
}

