@article{remap2020,
    author = {Chèneby, Jeanne and Ménétrier, Zacharie and Mestdagh, Martin and Rosnet, Thomas and Douida, Allyssa and Rhalloussi, Wassim and Bergon, Aurélie and Lopez, Fabrice and Ballester, Benoit},
    title = "{ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments}",
    journal = {Nucleic Acids Research},
    volume = {48},
    number = {D1},
    pages = {D180-D188},
    year = {2019},
    month = {10},
    abstract = "{ReMap (http://remap.univ-amu.fr) aims to provide the largest catalogs of high-quality regulatory regions resulting from a large-scale integrative analysis of hundreds of transcription factors and regulators from DNA-binding experiments in Human and Arabidopsis (Arabidopsis thaliana). In this 2020 update of ReMap we have collected, analyzed and retained after quality control 2764 new human ChIP-seq and 208 ChIP-exo datasets available from public sources. The updated human atlas totalize 5798 datasets covering a total of 1135 transcriptional regulators (TRs) with a catalog of 165 million (M) peaks. This ReMap update comes with two unique Arabidopsis regulatory catalogs. First, a catalog of 372 Arabidopsis TRs across 2.6M peaks as a result of the integration of 509 ChIP-seq and DAP-seq datasets. Second, a catalog of 33 histone modifications and variants across 4.5M peaks from the integration of 286 ChIP-seq datasets. All catalogs are made available through track hubs at Ensembl and UCSC Genome Browsers. Additionally, this update comes with a new web framework providing an interactive user-interface, including improved search features. Finally, full programmatically access to the underlying data is available using a RESTful API together with a new R Shiny interface for a TRs binding enrichment analysis tool.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkz945},
    url = {https://doi.org/10.1093/nar/gkz945},
    eprint = {https://academic.oup.com/nar/article-pdf/48/D1/D180/31697722/gkz945.pdf},
}

@article{leporcq2020tfmotifview,
  title={TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions},
  author={Leporcq, Cl{\'e}mentine and Spill, Yannick and Balaramane, Delphine and Toussaint, Christophe and Weber, Micha{\"e}l and Bardet, Ana{\"\i}s Flore},
  journal={Nucleic acids research},
  volume={48},
  number={W1},
  pages={W208--W217},
  year={2020},
  publisher={Oxford University Press}
}

@article{heinz2010simple,
  title={Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities},
  author={Heinz, Sven and Benner, Christopher and Spann, Nathanael and Bertolino, Eric and Lin, Yin C and Laslo, Peter and Cheng, Jason X and Murre, Cornelis and Singh, Harinder and Glass, Christopher K},
  journal={Molecular cell},
  volume={38},
  number={4},
  pages={576--589},
  year={2010},
  publisher={Elsevier}
}

@article{boeva2016analysis,
  title={Analysis of genomic sequence motifs for deciphering transcription factor binding and transcriptional regulation in eukaryotic cells},
  author={Boeva, Valentina},
  journal={Frontiers in genetics},
  volume={7},
  pages={24},
  year={2016},
  publisher={Frontiers}
}

@article{yao2015inferring,
  title={Inferring regulatory element landscapes and transcription factor networks from cancer methylomes},
  author={Yao, Lijing and Shen, Hui and Laird, Peter W and Farnham, Peggy J and Berman, Benjamin P},
  journal={Genome biology},
  volume={16},
  number={1},
  pages={1--21},
  year={2015},
  publisher={Springer}
}

@article{brodie2016far,
  title={How far from the SNP may the causative genes be?},
  author={Brodie, Aharon and Azaria, Johnathan Roy and Ofran, Yanay},
  journal={Nucleic acids research},
  volume={44},
  number={13},
  pages={6046--6054},
  year={2016},
  publisher={Oxford University Press}
}

@article{williamson2011enhancers,
  title={Enhancers: from developmental genetics to the genetics of common human disease},
  author={Williamson, Iain and Hill, Robert E and Bickmore, Wendy A},
  journal={Developmental cell},
  volume={21},
  number={1},
  pages={17--19},
  year={2011},
  publisher={Elsevier}
}

@article{pennacchio2013enhancers,
  title={Enhancers: five essential questions},
  author={Pennacchio, Len A and Bickmore, Wendy and Dean, Ann and Nobrega, Marcelo A and Bejerano, Gill},
  journal={Nature Reviews Genetics},
  volume={14},
  number={4},
  pages={288--295},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{wang2019identification,
  title={Identification of DNA motifs that regulate DNA methylation},
  author={Wang, Mengchi and Zhang, Kai and Ngo, Vu and Liu, Chengyu and Fan, Shicai and Whitaker, John W and Chen, Yue and Ai, Rizi and Chen, Zhao and Wang, Jun and others},
  journal={Nucleic acids research},
  volume={47},
  number={13},
  pages={6753--6768},
  year={2019},
  publisher={Oxford University Press}
}

@article{grossman2018positional,
  title={Positional specificity of different transcription factor classes within enhancers},
  author={Grossman, Sharon R and Engreitz, Jesse and Ray, John P and Nguyen, Tung H and Hacohen, Nir and Lander, Eric S},
  journal={Proceedings of the National Academy of Sciences},
  volume={115},
  number={30},
  pages={E7222--E7230},
  year={2018},
  publisher={National Acad Sciences}
}



@article{zhu2016transcription,
  title={Transcription factors as readers and effectors of DNA methylation},
  author={Zhu, Heng and Wang, Guohua and Qian, Jiang},
  journal={Nature Reviews Genetics},
  volume={17},
  number={9},
  pages={551--565},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{garcia2019benchmark,
  title={Benchmark and integration of resources for the estimation of human transcription factor activities},
  author={Garcia-Alonso, Luz and Holland, Christian H and Ibrahim, Mahmoud M and Turei, Denes and Saez-Rodriguez, Julio},
  journal={Genome research},
  volume={29},
  number={8},
  pages={1363--1375},
  year={2019},
  publisher={Cold Spring Harbor Lab}
}

@article{10.1093/nar/gkz945,
    author = {Chèneby, Jeanne and Ménétrier, Zacharie and Mestdagh, Martin and Rosnet, Thomas and Douida, Allyssa and Rhalloussi, Wassim and Bergon, Aurélie and Lopez, Fabrice and Ballester, Benoit},
    title = "{ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments}",
    journal = {Nucleic Acids Research},
    volume = {48},
    number = {D1},
    pages = {D180-D188},
    year = {2019},
    month = {10},
    abstract = "{ReMap (http://remap.univ-amu.fr) aims to provide the largest catalogs of high-quality regulatory regions resulting from a large-scale integrative analysis of hundreds of transcription factors and regulators from DNA-binding experiments in Human and Arabidopsis (Arabidopsis thaliana). In this 2020 update of ReMap we have collected, analyzed and retained after quality control 2764 new human ChIP-seq and 208 ChIP-exo datasets available from public sources. The updated human atlas totalize 5798 datasets covering a total of 1135 transcriptional regulators (TRs) with a catalog of 165 million (M) peaks. This ReMap update comes with two unique Arabidopsis regulatory catalogs. First, a catalog of 372 Arabidopsis TRs across 2.6M peaks as a result of the integration of 509 ChIP-seq and DAP-seq datasets. Second, a catalog of 33 histone modifications and variants across 4.5M peaks from the integration of 286 ChIP-seq datasets. All catalogs are made available through track hubs at Ensembl and UCSC Genome Browsers. Additionally, this update comes with a new web framework providing an interactive user-interface, including improved search features. Finally, full programmatically access to the underlying data is available using a RESTful API together with a new R Shiny interface for a TRs binding enrichment analysis tool.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkz945},
    url = {https://doi.org/10.1093/nar/gkz945},
    eprint = {https://academic.oup.com/nar/article-pdf/48/D1/D180/31697722/gkz945.pdf},
}





@article{silva2019elmer,
  title={ELMER v. 2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles},
  author={Silva, Tiago C and Coetzee, Simon G and Gull, Nicole and Yao, Lijing and Hazelett, Dennis J and Noushmehr, Houtan and Lin, De-Chen and Berman, Benjamin P},
  journal={Bioinformatics},
  volume={35},
  number={11},
  pages={1974--1977},
  year={2019},
  publisher={Oxford University Press}
}
@article{reese2019epigenome,
  title={Epigenome-wide meta-analysis of DNA methylation and childhood asthma},
  author={Reese, Sarah E and Xu, Cheng-Jian and Herman, T and Lee, Mi Kyeong and Sikdar, Sinjini and Ruiz-Arenas, Carlos and Merid, Simon K and Rezwan, Faisal I and Page, Christian M and Ullemar, Vilhelmina and others},
  journal={Journal of Allergy and Clinical Immunology},
  volume={143},
  number={6},
  pages={2062--2074},
  year={2019},
  publisher={Elsevier}
}
@article{yin2017impact,
  title={Impact of cytosine methylation on DNA binding specificities of human transcription factors},
  author={Yin, Yimeng and Morgunova, Ekaterina and Jolma, Arttu and Kaasinen, Eevi and Sahu, Biswajyoti and Khund-Sayeed, Syed and Das, Pratyush K and Kivioja, Teemu and Dave, Kashyap and Zhong, Fan and others},
  journal={Science},
  volume={356},
  number={6337},
  year={2017},
  publisher={American Association for the Advancement of Science}
}

 @Manual{motifmatchr,
    title = {motifmatchr: Fast Motif Matching in R},
    author = {Alicia Schep},
    year = {2020},
    note = {R package version 1.10.0},
  }

@article{fornes2022jaspar,
    author = {Castro-Mondragon, Jaime A and Riudavets-Puig, Rafael and Rauluseviciute, Ieva and Berhanu Lemma, Roza and Turchi, Laura and Blanc-Mathieu, Romain and Lucas, Jeremy and Boddie, Paul and Khan, Aziz and Manosalva Pérez, Nicolás and Fornes, Oriol and Leung, Tiffany Y and Aguirre, Alejandro and Hammal, Fayrouz and Schmelter, Daniel and Baranasic, Damir and Ballester, Benoit and Sandelin, Albin and Lenhard, Boris and Vandepoele, Klaas and Wasserman, Wyeth W and Parcy, François and Mathelier, Anthony},
    title = "{JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles}",
    journal = {Nucleic Acids Research},
    volume = {50},
    number = {D1},
    pages = {D165-D173},
    year = {2021},
    month = {11},
    abstract = "{JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19\\% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkab1113},
    url = {https://doi.org/10.1093/nar/gkab1113},
    eprint = {https://academic.oup.com/nar/article-pdf/50/D1/D165/42058061/gkab1113.pdf},
}


  @Manual{JASPAR2022,
    title = {JASPAR2022: Data package for JASPAR database (version 2022)},
    author = {Damir Baranasic},
    year = {2022},
    note = {R package version 0.99.7},
    url = {http://jaspar.genereg.net/},
  }
@article{gomez2019comethdmr,
  title={coMethDMR: accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies with continuous phenotypes},
  author={Gomez, Lissette and Odom, Gabriel J and Young, Juan I and Martin, Eden R and Liu, Lizhong and Chen, Xi and Griswold, Anthony J and Gao, Zhen and Zhang, Lanyu and Wang, Lily},
  journal={Nucleic acids research},
  volume={47},
  number={17},
  pages={e98--e98},
  year={2019},
  publisher={Oxford University Press}
}

@article{bonder2017disease,
  title={Disease variants alter transcription factor levels and methylation of their binding sites},
  author={Bonder, Marc Jan and Luijk, Ren{\'e} and Zhernakova, Daria V and Moed, Matthijs and Deelen, Patrick and Vermaat, Martijn and Van Iterson, Maarten and Van Dijk, Freerk and Van Galen, Michiel and Bot, Jan and others},
  journal={Nature genetics},
  volume={49},
  number={1},
  pages={131},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{banovich2014methylation,
  title={Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels},
  author={Banovich, Nicholas E and Lan, Xun and McVicker, Graham and Van de Geijn, Bryce and Degner, Jacob F and Blischak, John D and Roux, Julien and Pritchard, Jonathan K and Gilad, Yoav},
  journal={PLoS genetics},
  volume={10},
  number={9},
  year={2014},
  publisher={Public Library of Science}
}

@article{yin2017impact,
  title={Impact of cytosine methylation on DNA binding specificities of human transcription factors},
  author={Yin, Yimeng and Morgunova, Ekaterina and Jolma, Arttu and Kaasinen, Eevi and Sahu, Biswajyoti and Khund-Sayeed, Syed and Das, Pratyush K and Kivioja, Teemu and Dave, Kashyap and Zhong, Fan and others},
  journal={Science},
  volume={356},
  number={6337},
  pages={eaaj2239},
  year={2017},
  publisher={American Association for the Advancement of Science}
}

@article{kulakovskiy2016hocomoco,
  title={HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models},
  author={Kulakovskiy, Ivan V and Vorontsov, Ilya E and Yevshin, Ivan S and Soboleva, Anastasiia V and Kasianov, Artem S and Ashoor, Haitham and Ba-Alawi, Wail and Bajic, Vladimir B and Medvedeva, Yulia A and Kolpakov, Fedor A and others},
  journal={Nucleic acids research},
  volume={44},
  number={D1},
  pages={D116--D125},
  year={2016},
  publisher={Oxford University Press}
}

@article{wingender2013tfclass,
  title={TFClass: an expandable hierarchical classification of human transcription factors},
  author={Wingender, Edgar and Schoeps, Torsten and D{\"o}nitz, J{\"u}rgen},
  journal={Nucleic acids research},
  volume={41},
  number={D1},
  pages={D165--D170},
  year={2013},
  publisher={Oxford University Press}
}
