@article{Benjamini1995,
     jstor_articletype = {research-article},
     title = {Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing},
     author = {Benjamini, Yoav and Hochberg, Yosef},
     journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
     jstor_issuetitle = {},
     volume = {57},
     number = {1},
     jstor_formatteddate = {1995},
     pages = {pp. 289-300},
     url = {http://www.jstor.org/stable/2346101},
     ISSN = {00359246},
     abstract = {The common approach to the multiplicity problem calls for controlling the familywise error rate (FWER). This approach, though, has faults, and we point out a few. A different approach to problems of multiple significance testing is presented. It calls for controlling the expected proportion of falsely rejected hypotheses-the false discovery rate. This error rate is equivalent to the FWER when all hypotheses are true but is smaller otherwise. Therefore, in problems where the control of the false discovery rate rather than that of the FWER is desired, there is potential for a gain in power. A simple sequential Bonferroni-type procedure is proved to control the false discovery rate for independent test statistics, and a simulation study shows that the gain in power is substantial. The use of the new procedure and the appropriateness of the criterion are illustrated with examples.},
     language = {English},
     year = {1995},
     publisher = {Wiley for the Royal Statistical Society},
     copyright = {Copyright © 1995 Royal Statistical Society},
    }

@article{benjamini2001,
    author = "Benjamini, Yoav and Yekutieli, Daniel",
    doi = "10.1214/aos/1013699998",
    fjournal = "The Annals of Statistics",
    journal = "Ann. Statist.",
    month = "08",
    number = "4",
    pages = "1165--1188",
    publisher = "The Institute of Mathematical Statistics",
    title = "The control of the false discovery rate in multiple testing under dependency",
    url = "http://dx.doi.org/10.1214/aos/1013699998",
    volume = "29",
    year = "2001"
}

@article{Durinck2005,
author = {Durinck, Steffen and Moreau, Yves and Kasprzyk, Arek and Davis, Sean and De Moor, Bart and Brazma, Alvis and Huber, Wolfgang}, 
title = {BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis},
volume = {21}, 
number = {16}, 
pages = {3439-3440}, 
year = {2005}, 
doi = {10.1093/bioinformatics/bti525}, 
abstract ={Summary: biomaRt is a new Bioconductor package that integrates BioMart data resources with data analysis software in Bioconductor. It can annotate a wide range of gene or gene product identifiers (e.g. Entrez-Gene and Affymetrix probe identifiers) with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Furthermore biomaRt enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. Fast and up-to-date data retrieval is possible as the package executes direct SQL queries to the BioMart databases (e.g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.Availability: http://www.bioconductor.org. LGPLContact: steffen.durinck@esat.kuleuven.ac.be}, 
URL = {http://bioinformatics.oxfordjournals.org/content/21/16/3439.abstract}, 
eprint = {http://bioinformatics.oxfordjournals.org/content/21/16/3439.full.pdf+html}, 
journal = {Bioinformatics} 
}

@Article{Gentleman2004,
AUTHOR = {Gentleman, Robert and Carey, Vincent and Bates, Douglas and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean and Zhang, Jianhua},
TITLE = {Bioconductor: open software development for computational biology and bioinformatics},
JOURNAL = {Genome Biology},
VOLUME = {5},
YEAR = {2004},
NUMBER = {10},
PAGES = {R80},
URL = {http://genomebiology.com/2004/5/10/R80},
DOI = {10.1186/gb-2004-5-10-r80},
PubMedID = {15461798},
ISSN = {1465-6906},
ABSTRACT = {The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.},
}

@article{dudoit2003,
author = "Dudoit, Sandrine and Shaffer, Juliet Popper and Boldrick, Jennifer C.",
doi = "10.1214/ss/1056397487",
fjournal = "Statistical Science",
journal = "Statist. Sci.",
month = "02",
number = "1",
pages = "71--103",
publisher = "The Institute of Mathematical Statistics",
title = "Multiple Hypothesis Testing in Microarray Experiments",
url = "http://dx.doi.org/10.1214/ss/1056397487",
volume = "18",
year = "2003"
}

@article{Hochberg1988,
author = {Hochberg, Yosef}, 
title = {A sharper Bonferroni procedure for multiple tests of significance},
volume = {75}, 
number = {4}, 
pages = {800-802}, 
year = {1988}, 
doi = {10.1093/biomet/75.4.800}, 
abstract ={A simple procedure for multiple tests of significance based on individual p-values is derived. This simple procedure is sharper than Holm's (1979) sequentially rejective procedure. Both procedures contrast the ordered p- values with the same set of critical values. Holm's procedure rejects an hypothesis only if its p-value and each of the smaller p-values are less than their corresponding critical-values. The new procedure rejects all hypotheses with smaller or equal p-values to that of any one found less than its critical value.}, 
URL = {http://biomet.oxfordjournals.org/content/75/4/800.abstract}, 
eprint = {http://biomet.oxfordjournals.org/content/75/4/800.full.pdf+html}, 
journal = {Biometrika} 
}

@article{Holm1979,
     jstor_articletype = {research-article},
     title = {A Simple Sequentially Rejective Multiple Test Procedure},
     author = {Holm, Sture},
     journal = {Scandinavian Journal of Statistics},
     jstor_issuetitle = {},
     volume = {6},
     number = {2},
     jstor_formatteddate = {1979},
     pages = {pp. 65-70},
     url = {http://www.jstor.org/stable/4615733},
     ISSN = {03036898},
     abstract = {This paper presents a simple and widely applicable multiple test procedure of the sequentially rejective type, i.e. hypotheses are rejected one at a time until no further rejections can be done. It is shown that the test has a prescribed level of significance protection against error of the first kind for any combination of true hypotheses. The power properties of the test and a number of possible applications are also discussed.},
     language = {English},
     year = {1979},
     publisher = {Wiley on behalf of Board of the Foundation of the Scandinavian Journal of Statistics},
     copyright = {Copyright © 1979 Board of the Foundation of the Scandinavian Journal of Statistics},
    }

@book{johnson2005,
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}

@article{lieberman2009comprehensive,
  title={Comprehensive mapping of long-range interactions reveals folding principles of the human genome},
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}

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  publisher={Nature Publishing Group}
}

@article{zhu2010,
  title={ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data},
  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},
  journal={BMC bioinformatics},
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  year={2010},
  publisher={BioMed Central Ltd}
}

@incollection{zhu2013,
  title={Integrative analysis of ChIP-chip and ChIP-seq dataset},
  author={Zhu, Lihua Julie},
  booktitle={Tiling Arrays},
  pages={105--124},
  year={2013},
  publisher={Springer}
}

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  journal={Genome Biol},
  volume={13},
  number={9},
  pages={R48},
  year={2012}
}

@article{encode2012integrated,
  title={An integrated encyclopedia of DNA elements in the human genome},
  author={ENCODE Project Consortium and others},
  journal={Nature},
  volume={489},
  number={7414},
  pages={57--74},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{leung1996over,
  title={Over-and underrepresentation of short DNA words in herpesvirus genomes},
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  pages={345--360},
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}

@article{van2000statistical,
  title={Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals},
  author={van Helden, Jacques and l{\'\i} del Olmo, Marcel and P{\'e}rez-Ort{\'\i}n, Jos{\'e} E},
  journal={Nucleic Acids Research},
  volume={28},
  number={4},
  pages={1000--1010},
  year={2000},
  publisher={Oxford Univ Press}
}

@article{johnson2007,
   author = {Johnson, D. S. and Mortazavi, A. and Myers, R. M. and Wold, B.},
   title = {Genome-wide mapping of in vivo protein-DNA interactions},
   journal = {Science},
   volume = {316},
   number = {5830},
   pages = {1497-502},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Linking)},
   DOI = {10.1126/science.1141319},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/17540862},
   year = {2007},
   type = {Journal Article}
}

@article{barski2007,
   author = {Barski, A. and Cuddapah, S. and Cui, K. and Roh, T. Y. and Schones, D. E. and Wang, Z. and Wei, G. and Chepelev, I. and Zhao, K.},
   title = {High-resolution profiling of histone methylations in the human genome},
   journal = {Cell},
   volume = {129},
   number = {4},
   pages = {823-37},
   ISSN = {0092-8674 (Print)
0092-8674 (Linking)},
   DOI = {10.1016/j.cell.2007.05.009},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/17512414},
   year = {2007},
   type = {Journal Article}
}

@article{blat1999,
   author = {Blat, Y. and Kleckner, N.},
   title = {Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region},
   journal = {Cell},
   volume = {98},
   number = {2},
   pages = {249-59},
   ISSN = {0092-8674 (Print)
0092-8674 (Linking)},
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}

@article{skene2017,
   author = {Skene, P. J. and Henikoff, S.},
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   journal = {Elife},
   volume = {6},
   ISSN = {2050-084X (Electronic)
2050-084X (Linking)},
   DOI = {10.7554/eLife.21856},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/28079019},
   year = {2017},
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}

@article{thomas2017,
   author = {Thomas, R. and Thomas, S. and Holloway, A. K. and Pollard, K. S.},
   title = {Features that define the best ChIP-seq peak calling algorithms},
   journal = {Brief Bioinform},
   volume = {18},
   number = {3},
   pages = {441-450},
   ISSN = {1477-4054 (Electronic)
1467-5463 (Print)
1467-5463 (Linking)},
   DOI = {10.1093/bib/bbw035},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/27169896},
   year = {2017},
   type = {Journal Article}
}

@article{zhang2008,
   author = {Zhang, Y. and Liu, T. and Meyer, C. A. and Eeckhoute, J. and Johnson, D. S. and Bernstein, B. E. and Nusbaum, C. and Myers, R. M. and Brown, M. and Li, W. and Liu, X. S.},
   title = {Model-based analysis of ChIP-Seq (MACS)},
   journal = {Genome Biol},
   volume = {9},
   number = {9},
   pages = {R137},
   ISSN = {1474-760X (Electronic)
1465-6906 (Print)
1474-7596 (Linking)},
   DOI = {10.1186/gb-2008-9-9-r137},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/18798982},
   year = {2008},
   type = {Journal Article}
}

@article{encode2012,
   author = {Consortium, Encode Project},
   title = {An integrated encyclopedia of DNA elements in the human genome},
   journal = {Nature},
   volume = {489},
   number = {7414},
   pages = {57-74},
   note = {eng
R01HG003143/HG/NHGRI NIH HHS/
RC2 HG005573/HG/NHGRI NIH HHS/
U54HG004592/HG/NHGRI NIH HHS/
RC2 HG005679/HG/NHGRI NIH HHS/
R01 HG003143/HG/NHGRI NIH HHS/
ZIA HG200341/ImNIH/Intramural NIH HHS/
U41HG004568/HG/NHGRI NIH HHS/
U54 HG004557/HG/NHGRI NIH HHS/
U01HG004695/HG/NHGRI NIH HHS/
U54 HG004570/HG/NHGRI NIH HHS/
R37 DK044746/DK/NIDDK NIH HHS/
U54 HG004576/HG/NHGRI NIH HHS/
R01HG003988/HG/NHGRI NIH HHS/
U54 HG004592/HG/NHGRI NIH HHS/
U54HG004576/HG/NHGRI NIH HHS/
R01 HG003988/HG/NHGRI NIH HHS/
R01 HG003541/HG/NHGRI NIH HHS/
R01HG004456-03/HG/NHGRI NIH HHS/
R01HG003541/HG/NHGRI NIH HHS/
U54HG004558/HG/NHGRI NIH HHS/
RC2HG005591/HG/NHGRI NIH HHS/
RC2 HG005591/HG/NHGRI NIH HHS/
K99 HG006698/HG/NHGRI NIH HHS/
U54 HG004558/HG/NHGRI NIH HHS/
P30 CA016086/CA/NCI NIH HHS/
R01 DK054369/DK/NIDDK NIH HHS/
ZIA HG200323/ImNIH/Intramural NIH HHS/
U54HG004557/HG/NHGRI NIH HHS/
U54 HG004563/HG/NHGRI NIH HHS/
U01HG004561/HG/NHGRI NIH HHS/
U54HG004563/HG/NHGRI NIH HHS/
R01 HG005085/HG/NHGRI NIH HHS/
U01 HG004571/HG/NHGRI NIH HHS/
U41 HG004568/HG/NHGRI NIH HHS/
R01HG003700/HG/NHGRI NIH HHS/
T32 GM007205/GM/NIGMS NIH HHS/
095908/WT_/Wellcome Trust/United Kingdom
R01 DK065806/DK/NIDDK NIH HHS/
P30 CA045508/CA/NCI NIH HHS/
RC2HG005679/HG/NHGRI NIH HHS/
WT_/Wellcome Trust/United Kingdom
U54HG004570/HG/NHGRI NIH HHS/
R01 HG003700/HG/NHGRI NIH HHS/
U01 HG004695/HG/NHGRI NIH HHS/
U54HG004555/HG/NHGRI NIH HHS/
U01 HG004561/HG/NHGRI NIH HHS/
U01HG004571/HG/NHGRI NIH HHS/
U54 HG004555/HG/NHGRI NIH HHS/
R01 HG004456/HG/NHGRI NIH HHS/
Research Support, American Recovery and Reinvestment Act
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, U.S. Gov't, Non-P.H.S.
England
2012/09/08
Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.},
   abstract = {The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.},
   keywords = {Alleles
Animals
Binding Sites/genetics
Chromatin/genetics/metabolism
Chromatin Immunoprecipitation
Chromosomes, Human/genetics/metabolism
DNA/*genetics
DNA Footprinting
DNA Methylation/genetics
DNA-Binding Proteins/metabolism
Deoxyribonuclease I/metabolism
*Encyclopedias as Topic
Exons/genetics
Genetic Predisposition to Disease/genetics
Genetic Variation/genetics
Genome, Human/*genetics
Genome-Wide Association Study
*Genomics
Histones/chemistry/metabolism
Humans
Mammals/genetics
*Molecular Sequence Annotation
Neoplasms/genetics
Polymorphism, Single Nucleotide/genetics
Promoter Regions, Genetic/genetics
Proteins/genetics
Regulatory Sequences, Nucleic Acid/*genetics
Sequence Analysis, RNA
Transcription Factors/metabolism
Transcription, Genetic/genetics},
   ISSN = {1476-4687 (Electronic)
0028-0836 (Print)
0028-0836 (Linking)},
   DOI = {10.1038/nature11247},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/22955616},
   year = {2012},
   type = {Journal Article}
}

@article{lieberman2009,
   author = {Lieberman-Aiden, E. and van Berkum, N. L. and Williams, L. and Imakaev, M. and Ragoczy, T. and Telling, A. and Amit, I. and Lajoie, B. R. and Sabo, P. J. and Dorschner, M. O. and Sandstrom, R. and Bernstein, B. and Bender, M. A. and Groudine, M. and Gnirke, A. and Stamatoyannopoulos, J. and Mirny, L. A. and Lander, E. S. and Dekker, J.},
   title = {Comprehensive mapping of long-range interactions reveals folding principles of the human genome},
   journal = {Science},
   volume = {326},
   number = {5950},
   pages = {289-93},
   note = {Lieberman-Aiden, Erez
van Berkum, Nynke L
Williams, Louise
Imakaev, Maxim
Ragoczy, Tobias
Telling, Agnes
Amit, Ido
Lajoie, Bryan R
Sabo, Peter J
Dorschner, Michael O
Sandstrom, Richard
Bernstein, Bradley
Bender, M A
Groudine, Mark
Gnirke, Andreas
Stamatoyannopoulos, John
Mirny, Leonid A
Lander, Eric S
Dekker, Job
eng
R37DK44746/DK/NIDDK NIH HHS/
HG003143/HG/NHGRI NIH HHS/
U54HG004592/HG/NHGRI NIH HHS/
R01 HG003143/HG/NHGRI NIH HHS/
T32 HG002295/HG/NHGRI NIH HHS/
R37 DK044746/DK/NIDDK NIH HHS/
R01HL06544/HL/NHLBI NIH HHS/
U54 HG004592/HG/NHGRI NIH HHS/
R01 HG003143-06/HG/NHGRI NIH HHS/
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
2009/10/10
Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.},
   abstract = {We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonl
y used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.},
   keywords = {Biotin
Cell Line, Transformed
Cell Nucleus/*ultrastructure
Chromatin/*chemistry
Chromatin Immunoprecipitation
*Chromosomes, Human/chemistry/ultrastructure
Computational Biology
DNA/*chemistry
Gene Library
*Genome, Human
Humans
In Situ Hybridization, Fluorescence
Models, Molecular
Monte Carlo Method
Nucleic Acid Conformation
Principal Component Analysis
Protein Conformation
Sequence Analysis, DNA},
   ISSN = {1095-9203 (Electronic)
0036-8075 (Print)
0036-8075 (Linking)},
   DOI = {10.1126/science.1181369},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/19815776},
   year = {2009},
   type = {Journal Article}
}

@article{adachi2002,
   author = {Adachi, N. and Lieber, M. R.},
   title = {Bidirectional gene organization: a common architectural feature of the human genome},
   journal = {Cell},
   volume = {109},
   number = {7},
   pages = {807-9},
   note = {Adachi, Noritaka
Lieber, Michael R
eng
Letter
2002/07/12
Cell. 2002 Jun 28;109(7):807-9. doi: 10.1016/s0092-8674(02)00758-4.},
   keywords = {Animals
DNA Repair
Gene Order/*genetics
*Genome, Human
Humans
Promoter Regions, Genetic/genetics
Transcription, Genetic/*genetics},
   ISSN = {0092-8674 (Print)
0092-8674 (Linking)},
   DOI = {10.1016/s0092-8674(02)00758-4},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/12110178},
   year = {2002},
   type = {Journal Article}
}

