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@article{Mak:2010iv,
	Author = {Mak, Anthony B and Ni, Zuyao and Hewel, Johannes A and Chen, Ginny I and Zhong, Guoqing and Karamboulas, Konstantina and Blakely, Kim and Smiley, Sandra and Marcon, Edyta and Roudeva, Denitza and Li, Joyce and Olsen, Jonathan B and Wan, Cuihong and Punna, Thanuja and Isserlin, Ruth and Chetyrkin, Sergei and Gingras, Anne-Claude and Emili, Andrew and Greenblatt, Jack and Moffat, Jason},
	Date-Added = {2012-08-31 13:27:13 +0000},
	Date-Modified = {2012-08-31 13:27:13 +0000},
	Journal = {Molecular {\&} cellular proteomics : MCP},
	Month = may,
	Number = {5},
	Pages = {811--823},
	Title = {{A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency.}},
	Volume = {9},
	Year = {2010}}

@manual{Pages:fk,
	Author = {H. Pages and P. Aboyoun and M. Lawrence},
	Date-Added = {2012-08-29 14:21:33 +0000},
	Date-Modified = {2012-08-29 14:21:36 +0000},
	Note = {R package version 1.14.4},
	Title = {IRanges: Infrastructure for manipulating intervals on sequences}}

@article{Roberts:2012kp,
	Author = {Roberts, Adam and Goff, Loyal and Pertea, Geo and Kim, Daehwan and Kelley, David R and Pimentel, Harold and Salzberg, Steven L and Rinn, John L and Pachter, Lior and Trapnell, Cole},
	Date-Added = {2012-08-24 20:51:07 +0000},
	Date-Modified = {2012-08-24 20:51:07 +0000},
	Journal = {Nature Protocols},
	Month = mar,
	Number = {3},
	Pages = {562--578},
	Title = {{Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks}},
	Volume = {7},
	Year = {2012}}

@article{DOrso:2010fc,
	Author = {D'Orso, Iv{\'a}n and Frankel, Alan D},
	Date-Added = {2012-08-13 15:58:14 +0000},
	Date-Modified = {2012-08-13 15:58:14 +0000},
	Journal = {Nature structural {\&} molecular biology},
	Month = jul,
	Number = {7},
	Pages = {815--821},
	Title = {{RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation.}},
	Volume = {17},
	Year = {2010}}

@article{Michels:2003jz,
	Author = {Michels, Annemieke A and Nguyen, Van Trung and Fraldi, Alessandro and Labas, Val{\'e}rie and Edwards, Mia and Bonnet, Fran{\c c}ois and Lania, Luigi and Bensaude, Olivier},
	Date-Added = {2012-08-13 15:12:13 +0000},
	Date-Modified = {2012-08-13 15:12:13 +0000},
	Journal = {Molecular and cellular biology},
	Month = jul,
	Number = {14},
	Pages = {4859--4869},
	Title = {{MAQ1 and 7SK RNA interact with CDK9/cyclin T complexes in a transcription-dependent manner.}},
	Volume = {23},
	Year = {2003}}

@manual{Carlson:uq,
	Author = {M. Carlson and H. Pages and P. Aboyoun and S. Falcon and M. Morgan and D. Sarkar and M. Lawrence},
	Date-Added = {2012-08-03 19:05:07 +0000},
	Date-Modified = {2012-08-03 19:05:09 +0000},
	Note = {R package version 1.8.2},
	Title = {GenomicFeatures: Tools for making and manipulating transcript centric annotations}}

@manual{Aboyoun:fk,
	Author = {P. Aboyoun and H. Pages and M. Lawrence},
	Date-Added = {2012-08-03 18:49:56 +0000},
	Date-Modified = {2012-08-03 18:49:58 +0000},
	Note = {R package version 1.8.9},
	Title = {GenomicRanges: Representation and manipulation of genomic intervals}}

@article{Durinck:2005bb,
	Author = {Durinck, Steffen and Moreau, Yves and Kasprzyk, Arek and Davis, Sean and De Moor, Bart and Brazma, Alvis and Huber, Wolfgang},
	Date-Added = {2012-07-24 17:38:43 +0000},
	Date-Modified = {2012-07-24 17:38:43 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = aug,
	Number = {16},
	Pages = {3439--3440},
	Title = {{BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.}},
	Volume = {21},
	Year = {2005}}

@article{Durinck:2009uf,
	Author = {Durinck, S and Spellman, PT and Birney, E},
	Date-Added = {2012-07-24 17:38:08 +0000},
	Date-Modified = {2012-07-24 17:48:22 +0000},
	Journal = {Nature protocols},
	Number = {8},
	Pages = {1184-1191},
	Title = {{Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt}},
	Volume = {4},
	Year = {2009}}

@manual{Lawrence:fk,
	Author = {Michael Lawrence and Vince Carey and Robert Gentleman},
	Date-Added = {2012-07-24 16:48:32 +0000},
	Date-Modified = {2012-07-24 16:48:47 +0000},
	Note = {R package version 1.16.1},
	Title = {rtracklayer: R interface to genome browsers and their annotation tracks}}

@article{Benjamini:1995ws,
	Author = {Benjamini, Y and Hochberg, Y},
	Date-Added = {2012-07-24 16:20:15 +0000},
	Date-Modified = {2012-07-24 16:22:35 +0000},
	Journal = {Journal of the Royal Statistical Society. Series B {\ldots}},
	Number = {1},
	Pages = {289-300},
	Title = {{Controlling the false discovery rate: a practical and powerful approach to multiple testing}},
	Volume = {57},
	Year = {1995}}

@article{Hafner:2010kr,
	Author = {Hafner, Markus and Landthaler, Markus and Burger, Lukas and Khorshid, Mohsen and Hausser, Jean and Berninger, Philipp and Rothballer, Andrea and Ascano, Manuel and Jungkamp, Anna-Carina and Munschauer, Mathias and Ulrich, Alexander and Wardle, Greg S and Dewell, Scott and Zavolan, Mihaela and Tuschl, Thomas},
	Date-Added = {2012-07-20 22:19:21 +0000},
	Date-Modified = {2012-07-20 22:19:21 +0000},
	Journal = {Cell},
	Month = apr,
	Number = {1},
	Pages = {129--141},
	Title = {{Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP}},
	Volume = {141},
	Year = {2010}}

@article{Song:2011fk,
	Author = {Song, Q and Smith, A D},
	Date-Added = {2012-07-02 07:53:16 +0000},
	Date-Modified = {2012-07-02 07:53:16 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = mar,
	Number = {6},
	Pages = {870--871},
	Title = {{Identifying dispersed epigenomic domains from ChIP-Seq data}},
	Volume = {27},
	Year = {2011}}

@article{Shimazaki:2007ho,
	Author = {Shimazaki, Hideaki and Shinomoto, Shigeru},
	Date-Added = {2012-07-02 07:48:28 +0000},
	Date-Modified = {2012-07-02 07:48:28 +0000},
	Journal = {Neural computation},
	Month = jun,
	Number = {6},
	Pages = {1503--1527},
	Title = {{A method for selecting the bin size of a time histogram.}},
	Volume = {19},
	Year = {2007}}

@article{Guttman:2011bo,
	Author = {Guttman, Mitchell and Donaghey, Julie and Carey, Bryce W. and Garber, Manuel and Grenier, Jennifer K and Munson, Glen and Young, Geneva and Lucas, Anne Bergstrom and Ach, Robert and Bruhn, Laurakay and Yang, Xiaoping and Amit, Ido and Meissner, Alexander and Regev, Aviv and Rinn, John L and Root, David E and Lander, Eric S},
	Date-Added = {2012-06-27 14:20:33 +0000},
	Date-Modified = {2012-06-27 14:51:41 +0000},
	Journal = {Nature},
	Month = aug,
	Pages = {1--11},
	Title = {{lincRNAs act in the circuitry controlling pluripotency and differentiation}},
	Volume = {000},
	Year = {2011}}

@article{Amaral:2010ib,
	Author = {Amaral, P P and Clark, M B and Gascoigne, D K and Dinger, M E and Mattick, J. S.},
	Date-Added = {2011-12-30 03:09:53 +0000},
	Date-Modified = {2011-12-30 03:09:53 +0000},
	Journal = {Nucleic Acids Research},
	Month = dec,
	Number = {Database},
	Pages = {D146--D151},
	Title = {{lncRNAdb: a reference database for long noncoding RNAs}},
	Volume = {39},
	Year = {2010}}

@article{Bischoff:2009hn,
	Author = {Bischoff, Steve R and Tsai, Shengdar and Hardison, Nicholas and Motsinger-Reif, Alison A and Freking, Brad A and Nonneman, Dan and Rohrer, Gary and Piedrahita, Jorge A},
	Date-Added = {2011-11-24 15:03:13 +0000},
	Date-Modified = {2011-11-24 15:03:13 +0000},
	Journal = {Biology of reproduction},
	Month = nov,
	Number = {5},
	Pages = {906--920},
	Title = {{Characterization of conserved and nonconserved imprinted genes in swine.}},
	Volume = {81},
	Year = {2009}}

@article{Zhang:2008wp,
	Author = {Zhang, Yong and Liu, Tao and Meyer, Clifford A and Eeckhoute, J{\'e}r{\^o}me and Johnson, David S and Bernstein, Bradley E and Nusbaum, Chad and Myers, Richard M and Brown, Myles and Li, Wei and Liu, X Shirley},
	Date-Added = {2011-11-24 03:30:38 +0000},
	Date-Modified = {2011-11-24 03:30:38 +0000},
	Journal = {Genome Biology},
	Number = {9},
	Pages = {R137},
	Title = {{Model-based analysis of ChIP-Seq (MACS).}},
	Volume = {9},
	Year = {2008}}

@article{Boyer:2006ev,
	Author = {Boyer, Laurie A and Plath, Kathrin and Zeitlinger, Julia and Brambrink, Tobias and Medeiros, Lea A and Lee, Tong Ihn and Levine, Stuart S and Wernig, Marius and Tajonar, Adriana and Ray, Mridula K and Bell, George W and Otte, Arie P and Vidal, Miguel and Gifford, David K and Young, Richard A and Jaenisch, Rudolf},
	Date-Added = {2011-11-23 22:13:55 +0000},
	Date-Modified = {2011-11-23 22:13:55 +0000},
	Journal = {Nature},
	Month = apr,
	Number = {7091},
	Pages = {349--353},
	Title = {{Polycomb complexes repress developmental regulators in murine embryonic stem cells}},
	Volume = {441},
	Year = {2006}}

@article{ENCODEProjectConsortium:2007fu,
	Author = {{ENCODE Project Consortium}},
	Date-Added = {2011-11-16 15:37:08 +0000},
	Date-Modified = {2011-11-16 15:37:35 +0000},
	Journal = {Nature},
	Month = jun,
	Number = {7146},
	Pages = {799--816},
	Title = {{Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.}},
	Volume = {447},
	Year = {2007}}

@inproceedings{Rabiner:1989hs,
	Author = {Rabiner, L.R},
	Booktitle = {Proceedings of the IEEE},
	Date-Added = {2011-11-05 15:11:25 +0000},
	Date-Modified = {2011-11-05 15:11:25 +0000},
	Pages = {257--286},
	Title = {{A tutorial on hidden Markov models and selected applications in speech recognition}},
	Year = {1989}}

@article{Sanger:1977vp,
	Author = {Sanger, F. and Nicklen, S. and Coulson, A. R.},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Proceedings of the National Academy of Sciences of the United States of America},
	Month = dec,
	Number = {12},
	Pages = {5463--5467},
	Title = {{DNA sequencing with chain-terminating inhibitors.}},
	Volume = {74},
	Year = {1977}}

@article{Meng:1993uq,
	Author = {Meng, XL},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2012-07-24 01:20:01 +0000},
	Journal = {Biometrika},
	Number = {2},
	Pages = {267-78},
	Title = {{Maximum likelihood estimation via the ECM algorithm: A general framework}},
	Volume = {80},
	Year = {1993}}

@book{Russo:1996ut,
	Author = {Russo, Vincenzo E a},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Month = dec,
	Publisher = {Cold Spring Harbor Laboratory Press},
	Title = {{Epigenetic Mechanisms of Gene Regulation (Cold Spring Harbor Monograph)}},
	Year = {1996}}

@article{Ewing:1998uq,
	Author = {Ewing, B and Green, P},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Genome Research},
	Month = mar,
	Number = {3},
	Pages = {186--194},
	Title = {{Base-calling of automated sequencer traces using phred. II. Error probabilities.}},
	Volume = {8},
	Year = {1998}}

@article{Pruitt:2001wx,
	Author = {Pruitt, KD and Maglott, DR},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nucleic Acids Research},
	Number = {1},
	Pages = {137--140},
	Title = {{RefSeq and LocusLink: NCBI gene-centered resources}},
	Volume = {29},
	Year = {2001}}

@article{Plath:2003ff,
	Author = {Plath, Kathrin and Fang, Jia and Mlynarczyk-Evans, Susanna K and Cao, Ru and Worringer, Kathleen A and Wang, Hengbin and de la Cruz, Cecile C and Otte, Arie P and Panning, Barbara and Zhang, Yi},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Science (New York, NY)},
	Month = apr,
	Number = {5616},
	Pages = {131--135},
	Title = {{Role of histone H3 lysine 27 methylation in X inactivation.}},
	Volume = {300},
	Year = {2003}}

@article{Bracken:2003ei,
	Author = {Bracken, Adrian P and Pasini, Diego and Capra, Maria and Prosperini, Elena and Colli, Elena and Helin, Kristian},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {The EMBO journal},
	Month = oct,
	Number = {20},
	Pages = {5323--5335},
	Title = {{EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer.}},
	Volume = {22},
	Year = {2003}}

@article{Kohlmaier:2004kt,
	Author = {Kohlmaier, Alexander and Savarese, Fabio and Lachner, Monika and Martens, Joost and Jenuwein, Thomas and Wutz, Anton},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {PLoS Biology},
	Month = jul,
	Number = {7},
	Pages = {E171--1003},
	Title = {{A chromosomal memory triggered by Xist regulates histone methylation in X inactivation.}},
	Volume = {2},
	Year = {2004}}

@article{Abouelhoda:2004hw,
	Author = {Abouelhoda, Mohamed Ibrahim and Kurtz, Stefan and Ohlebusch, Enno},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Journal of Discrete Algorithms},
	Number = {1},
	Pages = {53--86},
	Title = {{Replacing suffix trees with enhanced suffix arrays}},
	Volume = {2},
	Year = {2004}}

@article{2005Sci...309.1559F,
	Author = {Consortium, The FANTOM and Group, RIKEN Genome Exploration Research and Genome Network Project Core Group, Genome Science Group and Carninci, P. and Kasukawa, T. and Katayama, S. and Gough, J. and Frith, M. C. and Maeda, N. and Oyama, R. and Ravasi, T. and Lenhard, B. and Wells, C. and Kodzius, R. and Shimokawa, K. and Bajic, V. B. and Brenner, S E and Batalov, S. and Forrest, A. R. R. and Zavolan, M. and Davis, M. J. and Wilming, L. G. and Aidinis, V. and Allen, J. E. and Ambesi-Impiombato, A. and Apweiler, R. and Aturaliya, R. N. and Bailey, T. L. and Bansal, M. and Baxter, L. and others},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Science (New York, NY)},
	Month = sep,
	Number = {5},
	Pages = {1559--1563},
	Title = {{The Transcriptional Landscape of the Mammalian Genome}},
	Volume = {309},
	Year = {2005}}

@article{Wu:2005bl,
	Author = {Wu, TD and Watanabe, CK},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Number = {9},
	Pages = {1859--1875},
	Title = {{GMAP: a genomic mapping and alignment program for mRNA and EST sequences}},
	Volume = {21},
	Year = {2005}}

@book{MBishop:2006uc,
	Author = {Bishop, Christopher},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-16 20:39:05 +0000},
	Number = {605--631},
	Pages = {605--631},
	Publisher = {Springer Science},
	Series = {Information Science and Statisitcs},
	Title = {{Pattern recognition and machine learning}},
	Year = {2006}}

@article{Bernstein:2006vh,
	Author = {Bernstein, BE and Mikkelsen, TS and Xie, X and Kamal, M and Huebert, DJ and Cuff, J and Fry, B and Meissner, A and Wernig, M and Plath, K},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Cell},
	Number = {2},
	Pages = {315--326},
	Title = {{A bivalent chromatin structure marks key developmental genes in embryonic stem cells}},
	Volume = {125},
	Year = {2006}}

@article{Schulze:2007cy,
	Author = {Schulze, Uta and Hepp, Bettina and Ong, Cheng Soon and R{\"a}tsch, Gunnar},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = aug,
	Number = {15},
	Pages = {1892--1900},
	Title = {{PALMA: mRNA to genome alignments using large margin algorithms.}},
	Volume = {23},
	Year = {2007}}

@article{Mikkelsen:2007fk,
	Abstract = {We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.},
	Author = {Mikkelsen, Tarjei S and Ku, Manching and Jaffe, David B and Issac, Biju and Lieberman, Erez and Giannoukos, Georgia and Alvarez, Pablo and Brockman, William and Kim, Tae-Kyung and Koche, Richard P and Lee, William and Mendenhall, Eric and O'Donovan, Aisling and Presser, Aviva and Russ, Carsten and Xie, Xiaohui and Meissner, Alexander and Wernig, Marius and Jaenisch, Rudolf and Nusbaum, Chad and Lander, Eric S and Bernstein, Bradley E},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Doi = {10.1038/nature06008},
	Journal = {Nature},
	Journal-Full = {Nature},
	Mesh = {Alleles; Animals; Cell Lineage; Chromatin; CpG Islands; Fibroblasts; Gene Expression Regulation, Developmental; Genome; Genomic Imprinting; Histones; Male; Methylation; Mice; Pluripotent Stem Cells; Promoter Regions, Genetic; Transcription, Genetic},
	Month = {Aug},
	Number = {7153},
	Pages = {553-60},
	Pmc = {PMC2921165},
	Pmid = {17603471},
	Pst = {ppublish},
	Title = {Genome-wide maps of chromatin state in pluripotent and lineage-committed cells},
	Volume = {448},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature06008}}

@article{Li:2008in,
	Author = {Li, Ruiqiang and Li, Yingrui and Kristiansen, Karsten and Wang, Jun},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = mar,
	Number = {5},
	Pages = {713--714},
	Title = {{SOAP: short oligonucleotide alignment program}},
	Volume = {24},
	Year = {2008}}

@article{Chamberlain:2008gh,
	Author = {Chamberlain, Stormy J and Yee, Della and Magnuson, Terry},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {STEM CELLS},
	Month = jun,
	Number = {6},
	Pages = {1496--1505},
	Title = {{Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency.}},
	Volume = {26},
	Year = {2008}}

@article{Mortazavi:2008jj,
	Author = {Mortazavi, Ali and Williams, Brian A and Mccue, Kenneth and Schaeffer, Lorian and Wold, Barbara},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Methods},
	Month = jul,
	Number = {7},
	Pages = {621--628},
	Title = {{Mapping and quantifying mammalian transcriptomes by RNA-Seq}},
	Volume = {5},
	Year = {2008}}

@article{Cloonan:2008ge,
	Author = {Cloonan, Nicole and Forrest, Alistair R R and Kolle, Gabriel and Gardiner, Brooke B A and Faulkner, Geoffrey J and Brown, Mellissa K and Taylor, Darrin F and Steptoe, Anita L and Wani, Shivangi and Bethel, Graeme and Robertson, Alan J and Perkins, Andrew C and Bruce, Stephen J and Lee, Clarence C and Ranade, Swati S and Peckham, Heather E and Manning, Jonathan M and Mckernan, Kevin J and Grimmond, Sean M},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Methods},
	Month = jul,
	Note = {Strand specific protocol},
	Number = {7},
	Pages = {613--619},
	Title = {{Stem cell transcriptome profiling via massive-scale mRNA sequencing}},
	Volume = {5},
	Year = {2008}}

@article{Valouev:2008wz,
	Author = {Valouev, Anton and Johnson, David S and Sundquist, Andreas and Medina, Catherine and Anton, Elizabeth and Batzoglou, Serafim and Myers, Richard M and Sidow, Arend},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Methods},
	Month = aug,
	Number = {9},
	Pages = {829--834},
	Title = {{Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data}},
	Volume = {5},
	Year = {2008}}

@article{Pandey:2008gv,
	Author = {Pandey, Radha Raman and Mondal, Tanmoy and Mohammad, Faizaan and Enroth, Stefan and Redrup, Lisa and Komorowski, Jan and Nagano, Takashi and Mancini-Dinardo, Debora and Kanduri, Chandrasekhar},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Molecular Cell},
	Month = oct,
	Number = {2},
	Pages = {232--246},
	Title = {{Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation}},
	Volume = {32},
	Year = {2008}}

@article{Bentley:2008uv,
	Author = {Bentley, David R and Balasubramanian, Shankar and Swerdlow, Harold P and Smith, Geoffrey P and Milton, John and Brown, Clive G and Hall, Kevin P and Evers, Dirk J and Barnes, Colin L and Bignell, Helen R and Boutell, Jonathan M and Bryant, Jason and Carter, Richard J and Cheetham, R Keira and Cox, Anthony J and Ellis, Darren J and Flatbush, Michael R and Gormley, Niall A and Humphray, Sean J and Irving, Leslie J and Karbelashvili, Mirian S and Kirk, Scott M and Li, Heng and Liu, Xiaohai and Maisinger, Klaus S and Murray, Lisa J and Obradovic, Bojan and Ost, Tobias and Parkinson, Michael L and Pratt, Mark R and others},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature},
	Month = nov,
	Number = {7218},
	Pages = {53--59},
	Title = {{Accurate whole human genome sequencing using reversible terminator chemistry}},
	Volume = {456},
	Year = {2008}}

@article{Shen:2008hz,
	Author = {Shen, Xiaohua and Liu, Yingchun and Hsu, Yu-Jung and Fujiwara, Yuko and Kim, Jonghwan and Mao, Xiaohong and Yuan, Guo-Cheng and Orkin, Stuart H},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Molecular cell},
	Month = nov,
	Number = {4},
	Pages = {491--502},
	Title = {{EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency.}},
	Volume = {32},
	Year = {2008}}

@inproceedings{DeBona:2008gr,
	Author = {De Bona, Fabio and Ossowski, Stephan and Schneeberger, Korbinian and Raetsch, Gunnar},
	Booktitle = {Bmc Bioinformatics},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Organization = {Friedrich Miescher Lab, Max Planck Soc, D-72076 Tubingen, Germany},
	Pages = {--},
	Title = {{Optimal spliced alignments of short sequence reads}},
	Year = {2008}}

@article{Zerbino:2008bm,
	Author = {Zerbino, Daniel R and Birney, Ewan},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Genome Research},
	Number = {5},
	Pages = {821--829},
	Title = {{Velvet: Algorithms for de novo short read assembly using de Bruijn graphs}},
	Volume = {18},
	Year = {2008}}

@article{Li:2008ip,
	Author = {Li, Heng and Ruan, Jue and Durbin, Richard},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Genome Research},
	Number = {11},
	Pages = {1851--1858},
	Title = {{Mapping short DNA sequencing reads and calling variants using mapping quality scores}},
	Volume = {18},
	Year = {2008}}

@article{Bock:2008gu,
	Author = {Bock, Christoph and Lengauer, Thomas},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Number = {1},
	Pages = {1--10},
	Title = {{Computational epigenetics}},
	Volume = {24},
	Year = {2008}}

@article{Jiang:2009bw,
	Author = {Jiang, H and Wong, W H},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = feb,
	Number = {8},
	Pages = {1026--1032},
	Title = {{Statistical inferences for isoform expression in RNA-Seq}},
	Volume = {25},
	Year = {2009}}

@article{Guttman:2009gwa,
	Author = {Guttman, Mitchell and Amit, Ido and Garber, Manuel and French, Courtney and Lin, Michael F. and Feldser, David and Huarte, Maite and Zuk, Or and Carey, Bryce W. and Cassady, John P. and Cabili, Moran N. and Jaenisch, Rudolf and Mikkelsen, Tarjei S and Jacks, Tyler and Hacohen, Nir and Bernstein, Bradley E and Kellis, Manolis and Regev, Aviv and Rinn, John L and Lander, Eric S},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature},
	Month = mar,
	Number = {7235},
	Pages = {223--227},
	Title = {{Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals}},
	Volume = {457},
	Year = {2009}}

@webpage{picard,
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Month = {May},
	Title = {Picard},
	Url = {http://picard.sourceforge.net},
	Year = {2009},
	Bdsk-Url-1 = {http://picard.sourceforge.net}}

@article{Trapnell:2009dp,
	Author = {Trapnell, C and Pachter, L and Salzberg, S L},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = may,
	Number = {9},
	Pages = {1105--1111},
	Title = {{TopHat: discovering splice junctions with RNA-Seq}},
	Volume = {25},
	Year = {2009}}

@article{Kim:2009ic,
	Author = {Kim, H and Kang, K and Kim, J},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nucleic Acids Research},
	Month = may,
	Number = {9},
	Pages = {2940--2950},
	Title = {{AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2}},
	Volume = {37},
	Year = {2009}}

@article{Li:2009fi,
	Author = {Li, Heng and Durbin, Richard},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = jul,
	Number = {14},
	Pages = {1754--1760},
	Title = {{Fast and accurate short read alignment with Burrows-Wheeler transform.}},
	Volume = {25},
	Year = {2009}}

@article{Li:2009ka,
	Author = {Li, H and Handsaker, B and Wysoker, A and Fennell, T and Ruan, J and Homer, N and Marth, G and Abecasis, G and Durbin, R and {1000 Genome Project Data Processing Subgroup}},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = aug,
	Number = {16},
	Pages = {2078--2079},
	Title = {{The Sequence Alignment/Map format and SAMtools}},
	Volume = {25},
	Year = {2009}}

@article{Li:2009cx,
	Author = {Li, Ruiqiang and Yu, Chang and Li, Yingrui and Lam, Tak-Wah and Yiu, Siu-Ming and Kristiansen, Karsten and Wang, Jun},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = aug,
	Number = {15},
	Pages = {1966--1967},
	Title = {{SOAP2: an improved ultrafast tool for short read alignment}},
	Volume = {25},
	Year = {2009}}

@article{Simon:2009eh,
	Author = {Simon, Jeffrey A and Kingston, Robert E},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature reviews. Molecular cell biology},
	Month = oct,
	Number = {10},
	Pages = {697--708},
	Title = {{Mechanisms of polycomb gene silencing: knowns and unknowns.}},
	Volume = {10},
	Year = {2009}}

@article{Laajala:2009ij,
	Author = {Laajala, Teemu D and Raghav, Sunil and Tuomela, Soile and Lahesmaa, Riitta and Aittokallio, Tero and Elo, Laura L},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {BMC Genomics},
	Number = {1},
	Pages = {618},
	Title = {{A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments}},
	Volume = {10},
	Year = {2009}}

@article{Langmead:2009fv,
	Author = {Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven L},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Genome Biology},
	Number = {3},
	Pages = {R25},
	Title = {{Ultrafast and memory-efficient alignment of short DNA sequences to the human genome}},
	Volume = {10},
	Year = {2009}}

@article{Wang:2009di,
	Author = {Wang, Zhong and Gerstein, Mark and Snyder, Michael},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature reviews Genetics},
	Number = {1},
	Pages = {57--63},
	Title = {{RNA-Seq: a revolutionary tool for transcriptomics}},
	Volume = {10},
	Year = {2009}}

@article{Khalil:2009vv,
	Author = {Khalil, AM and Guttman, M and Huarte, M and Garber, M and Raj, A and Rivea Morales, D and Thomas, K and Presser, A and Bernstein, BE and van Oudenaarden, A},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {28},
	Pages = {11667},
	Title = {{Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression}},
	Volume = {106},
	Year = {2009}}

@article{Peng:2009hc,
	Author = {Peng, Jamy C and Valouev, Anton and Swigut, Tomek and Zhang, Junmei and Zhao, Yingming and Sidow, Arend and Wysocka, Joanna},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Cell},
	Month = dec,
	Number = {7},
	Pages = {1290--1302},
	Title = {{Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells}},
	Volume = {139},
	Year = {2009}}

@article{Shen:2009iw,
	Author = {Shen, Xiaohua and Kim, Woojin and Fujiwara, Yuko and Simon, Matthew D and Liu, Yingchun and Mysliwiec, Matthew R and Yuan, Guo-Cheng and Lee, Youngsook and Orkin, Stuart H},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Cell},
	Month = dec,
	Number = {7},
	Pages = {1303--1314},
	Title = {{Jumonji Modulates Polycomb Activity and Self-Renewal versus Differentiation of Stem Cells}},
	Volume = {139},
	Year = {2009}}

@article{Harris:2010dw,
	Author = {Harris, Elena Y and Ponts, Nadia and Levchuk, Aleksandr and Roch, Karine Le and Lonardi, Stefano},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = feb,
	Number = {4},
	Pages = {572--573},
	Title = {{BRAT: bisulfite-treated reads analysis tool.}},
	Volume = {26},
	Year = {2010}}

@webpage{fastxtoolkit,
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Month = {February},
	Title = {FASTX-Toolkit: FASTQ/A short-reads pre-processing tools},
	Url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
	Year = {2010},
	Bdsk-Url-1 = {http://hannonlab.cshl.edu/fastx_toolkit/index.html}}

@article{Li:2010cl,
	Author = {Li, Bo and Ruotti, Victor and Stewart, Ron M and Thomson, James A and Dewey, Colin N},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = feb,
	Number = {4},
	Pages = {493--500},
	Title = {{RNA-Seq gene expression estimation with read mapping uncertainty}},
	Volume = {26},
	Year = {2010}}

@article{Trapnell:2010kd,
	Author = {Trapnell, Cole and Williams, Brian A and Pertea, Geo and Mortazavi, Ali and Kwan, Gordon and Baren, Marijke J van and Salzberg, Steven L and Wold, Barbara J and Pachter, Lior},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Biotechnology},
	Month = feb,
	Number = {5},
	Pages = {516--520},
	Title = {{Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation}},
	Volume = {28},
	Year = {2010}}

@article{Li:2010kq,
	Author = {Li, G and Margueron, R and Ku, M and Chambon, P and Bernstein, B E and Reinberg, D},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Genes {\&} Development},
	Month = feb,
	Number = {4},
	Pages = {368--380},
	Title = {{Jarid2 and PRC2, partners in regulating gene expression}},
	Volume = {24},
	Year = {2010}}

@article{Quinlan:2010km,
	Author = {Quinlan, Aaron R and Hall, Ira M},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = mar,
	Number = {6},
	Pages = {841--842},
	Title = {{BEDTools: a flexible suite of utilities for comparing genomic features.}},
	Volume = {26},
	Year = {2010}}

@article{Gupta:2010fi,
	Author = {Gupta, Rajnish A and Shah, Nilay and Wang, Kevin C and Kim, Jeewon and Horlings, Hugo M and Wong, David J and Tsai, Miao-Chih and Hung, Tiffany and Argani, Pedram and Rinn, John L and Wang, Yulei and Brzoska, Pius and Kong, Benjamin and Li, Rui and West, Robert B and Vijver, Marc J van de and Sukumar, Saraswati and Chang, Howard Y},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature},
	Month = apr,
	Number = {7291},
	Pages = {1071--1076},
	Title = {{Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis}},
	Volume = {464},
	Year = {2010}}

@article{Guttman:2010io,
	Author = {Guttman, Mitchell and Garber, Manuel and Levin, Joshua Z and Donaghey, Julie and Robinson, James and Adiconis, Xian and Fan, Lin and Koziol, Magdalena J and Gnirke, Andreas and Nusbaum, Chad and Rinn, John L and Lander, Eric S and Regev, Aviv},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Biotechnology},
	Month = may,
	Number = {5},
	Pages = {503--510},
	Title = {{Ab initio reconstruction of cell type--specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs}},
	Volume = {28},
	Year = {2010}}

@article{Kircher:2010jq,
	Author = {Kircher, Martin and Kelso, Janet},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {BioEssays},
	Month = may,
	Number = {6},
	Pages = {524--536},
	Title = {{High-throughput DNA sequencing - concepts and limitations}},
	Volume = {32},
	Year = {2010}}

@article{Yap:2010em,
	Author = {Yap, Kyoko L and Li, Side and Mu{\~n}oz-Cabello, Ana M and Raguz, Selina and Zeng, Lei and Mujtaba, Shiraz and Gil, Jes{\'u}s and Walsh, Martin J and Zhou, Ming-Ming},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Molecular Cell},
	Month = jun,
	Number = {5},
	Pages = {662--674},
	Title = {{Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a}},
	Volume = {38},
	Year = {2010}}

@article{Kanhere:2010ev,
	Author = {Kanhere, Aditi and Viiri, Keijo and Ara{\'u}jo, Carla C and Rasaiyaah, Jane and Bouwman, Russell D and Whyte, Warren A and Pereira, C Filipe and Brookes, Emily and Walker, Kimberly and Bell, George W and Pombo, Ana and Fisher, Amanda G and Young, Richard A and Jenner, Richard G},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Molecular Cell},
	Month = jun,
	Number = {5},
	Pages = {675--688},
	Title = {{Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2}},
	Volume = {38},
	Year = {2010}}

@article{Fiume:2010cl,
	Author = {Fiume, M and Williams, V and Brook, A and Brudno, M},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = aug,
	Number = {16},
	Pages = {1938--1944},
	Title = {{Savant: genome browser for high-throughput sequencing data}},
	Volume = {26},
	Year = {2010}}

@article{Anders:2010fu,
	Author = {Anders, Simon and Huber, Wolfgang},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Genome Biology},
	Month = oct,
	Number = {10},
	Pages = {R106},
	Title = {{Differential expression analysis for sequence count data}},
	Volume = {11},
	Year = {2010}}

@article{Zhu:2010uc,
	Author = {Zhu, Lihua J and Gazin, Claude and Lawson, Nathan D and Pag{\`e}s, Herv{\'e} and Lin, Simon M and Lapointe, David S and Green, Michael R},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {BMC Bioinformatics},
	Pages = {--},
	Title = {{ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data}},
	Volume = {11},
	Year = {2010}}

@article{Qin:2010gt,
	Author = {Qin, Zhaohui S and Yu, Jianjun and Shen, Jincheng and Maher, Christopher A and Hu, Ming and Kalyana-Sundaram, Shanker and Yu, Jindan and Chinnaiyan, Arul M},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {BMC Bioinformatics},
	Pages = {369},
	Title = {{HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data}},
	Volume = {11},
	Year = {2010}}

@article{2010PLoSO...511471W,
	Author = {Wilbanks, Elizabeth G and Facciotti, Marc T},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {PloS one},
	Number = {7},
	Pages = {e11471--},
	Title = {{Evaluation of algorithm performance in ChIP-seq peak detection.}},
	Volume = {5},
	Year = {2010}}

@article{Walker:2010gy,
	Author = {Walker, Emily and Chang, Wing Y. and Hunkapiller, Julie and Cagney, Gerard and Garcha, Kamal and Torchia, Joseph and Krogan, Nevan J. and Reiter, Jeremy F. and Stanford, William L.},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Cell Stem Cell},
	Note = {PCL2 or MTF2},
	Number = {2},
	Pages = {153--166},
	Title = {{Polycomb-like 2 Associates with PRC2 and Regulates Transcriptional Networks during Mouse Embryonic Stem Cell Self-Renewal and Differentiation}},
	Volume = {6},
	Year = {2010}}

@article{Flicek:2010cu,
	Author = {Flicek, P and Amode, M R and Barrell, D and Beal, K and Brent, S and Chen, Y and Clapham, P and Coates, G and Fairley, S and Fitzgerald, S and Gordon, L and Hendrix, M and Hourlier, T and Johnson, N and Kahari, A and Keefe, D and Keenan, S and Kinsella, R and Kokocinski, F and Kulesha, E and Larsson, P and Longden, I and McLaren, W and Overduin, B and Pritchard, B and Riat, H S and Rios, D and Ritchie, G R S and Ruffier, M and Schuster, M and others},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nucleic Acids Research},
	Month = dec,
	Number = {Database},
	Pages = {D800--D806},
	Title = {{Ensembl 2011}},
	Volume = {39},
	Year = {2010}}

@article{Jones:2010jz,
	Author = {Jones, Amanda and Wang, Hengbin},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Protein {\&} Cell},
	Month = dec,
	Number = {12},
	Pages = {1056--1062},
	Title = {{Polycomb repressive complex 2 in embryonic stem cells: an overview}},
	Volume = {1},
	Year = {2010}}

@article{Zhao:2010du,
	Author = {Zhao, Jing and Ohsumi, Toshiro K and Kung, Johnny T and Ogawa, Yuya and Grau, Daniel J and Sarma, Kavitha and Song, Ji Joon and Kingston, Robert E and Borowsky, Mark and Lee, Jeannie T},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Molecular Cell},
	Month = dec,
	Number = {6},
	Pages = {939--953},
	Title = {{Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq}},
	Volume = {40},
	Year = {2010}}

@article{Margueron:2011ie,
	Author = {Margueron, Rapha{\"e}l and Reinberg, Danny},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature},
	Month = jan,
	Number = {7330},
	Pages = {343--349},
	Title = {{The Polycomb complex PRC2 and its mark in life}},
	Volume = {469},
	Year = {2011}}

@article{Wu:2011ed,
	Author = {Wu, Zhengpeng and Wang, Xi and Zhang, Xuegong},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = feb,
	Number = {4},
	Pages = {502--508},
	Title = {{Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq}},
	Volume = {27},
	Year = {2011}}

@article{Zhang:2011fz,
	Author = {Zhang, Zhuo and Jones, Amanda and Sun, Chiao-Wang and Li, Chao and Chang, Chia-Wei and Joo, Heui-Yun and Dai, Qian and Mysliwiec, Matthew R and Wu, Li-Chen and Guo, Yahong and Yang, Wei and Liu, Kaimao and Pawlik, Kevin M and Erdjument-Bromage, Hediye and Tempst, Paul and Lee, Youngsook and Min, Jinrong and Townes, Tim M and Wang, Hengbin},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {STEM CELLS},
	Month = feb,
	Number = {2},
	Pages = {229--240},
	Title = {{PRC2 Complexes with JARID2, MTF2, and esPRC2p48 in ES Cells to Modulate ES Cell Pluripotency and Somatic Cell Reprograming}},
	Volume = {29},
	Year = {2011}}

@article{Roberts:2011kf,
	Author = {Roberts, Adam and Trapnell, Cole and Donaghey, Julie and Rinn, John L and Pachter, Lior},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Genome Biology},
	Month = mar,
	Number = {3},
	Pages = {R22},
	Title = {{Improving RNA-Seq expression estimates by correcting for fragment bias.}},
	Volume = {12},
	Year = {2011}}

@article{Mak:2011cy,
	Author = {Mak, H Craig},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Publishing Group},
	Month = apr,
	Number = {4},
	Pages = {331--333},
	Title = {{John Storey}},
	Volume = {29},
	Year = {2011}}

@article{rom:2011gf,
	Author = {Ulf, Orom Andersson and Shiekhattar, Ramin},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-16 15:55:09 +0000},
	Journal = {Current Opinion in Genetics {\&} Development},
	Month = apr,
	Number = {2},
	Pages = {194--198},
	Title = {{Long non-coding RNAs and enhancers}},
	Volume = {21},
	Year = {2011}}

@article{Garber:2011gp,
	Author = {Garber, Manuel and Grabherr, Manfred G and Guttman, Mitchell and Trapnell, Cole},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Publishing Group},
	Month = may,
	Number = {6},
	Pages = {469--477},
	Title = {{Computational methods for transcriptome annotation and quantification using RNA-seq}},
	Volume = {8},
	Year = {2011}}

@article{Lienert:2011hg,
	Author = {Lienert, Florian and Mohn, Fabio and Tiwari, Vijay K and Baubec, Tuncay and Roloff, Tim C and Gaidatzis, Dimos and Stadler, Michael B and Sch{\"u}beler, Dirk},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {PLoS Genetics},
	Month = jun,
	Number = {6},
	Pages = {e1002090},
	Title = {{Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells}},
	Volume = {7},
	Year = {2011}}

@article{Roberts:2011hw,
	Author = {Roberts, Adam and Pimentel, Harold and Trapnell, Cole and Pachter, Lior},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Bioinformatics (Oxford, England)},
	Month = jun,
	Title = {{Identification of novel transcripts in annotated genomes using RNA-Seq.}},
	Year = {2011}}

@article{Hung:2011hz,
	Author = {Hung, Tiffany and Wang, Yulei and Lin, Michael F. and Koegel, Ashley K and Kotake, Yojiro and Grant, Gavin D and Horlings, Hugo M and Shah, Nilay and Umbricht, Christopher and Wang, Pei and Wang, Yu and Kong, Benjamin and Langer{\o}d, Anita and B{\o}rresen-Dale, Anne-Lise and Kim, Seung K and van de Vijver, Marc and Sukumar, Saraswati and Whitfield, Michael L and Kellis, Manolis and Xiong, Yue and Wong, David J and Chang, Howard Y},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Genetics},
	Month = jun,
	Number = {7},
	Pages = {621--629},
	Title = {{Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters}},
	Volume = {43},
	Year = {2011}}

@webpage{fastqc,
	Author = {Simon Andrews},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Month = {September},
	Title = {FastQC},
	Url = {http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/},
	Year = {2011},
	Bdsk-Url-1 = {http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/}}

@article{Martin:2011em,
	Author = {Martin, Jeffrey A and Wang, Zhong},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature reviews Genetics},
	Month = sep,
	Number = {10},
	Pages = {671--682},
	Title = {{Next-generation transcriptome assembly}},
	Volume = {12},
	Year = {2011}}

@webpage{geneimprint,
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Month = {October},
	Title = {Geneimprint},
	Url = {http://geneimprint.org},
	Year = {2011},
	Bdsk-Url-1 = {http://geneimprint.org}}

@article{Martin:2011va,
	Author = {Martin, M},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {EMBnet journal},
	Title = {{Cutadapt removes adapter sequences from high-throughput sequencing reads}},
	Year = {2011}}

@article{Robinson:2011ii,
	Author = {Robinson, James T and Thorvaldsd{\'o}ttir, Helga and Winckler, Wendy and Guttman, Mitchell and Lander, Eric S and Getz, Gad and Mesirov, Jill P},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {Nature Publishing Group},
	Number = {1},
	Pages = {24--26},
	Title = {{Integrative genomics viewer}},
	Volume = {29},
	Year = {2011}}

@article{Feng:2011ci,
	Author = {Feng, Xin and Grossman, Robert and Stein, Lincoln},
	Date-Added = {2011-11-04 14:39:51 +0000},
	Date-Modified = {2011-11-04 14:39:51 +0000},
	Journal = {BMC Bioinformatics},
	Pages = {139},
	Title = {{PeakRanger: A cloud-enabled peak caller for ChIP-seq data}},
	Volume = {12},
	Year = {2011}}
