Anthony Mathelier

• Bjørklund, Sunniva; Aure, Miriam Ragle; Häkkinen, Jari; Vallon-Christersson, Johan; Kumar, Surendra & Evensen, Katrine Bull [Show all 14 contributors for this article] (2022). Subtype and cell type specific expression of lncRNAs provide insight into breast cancer. Communications Biology. ISSN 2399-3642. 5(1). doi: 10.1038/s42003-022-03559-7.
• Strømme, Jonas Meier; Johannessen, Bjarne; Kidd, Susanne Gundersen; Bogaard, Mari; Carm, Kristina Totland & Zhang, Xiaokang [Show all 12 contributors for this article] (2022). Expressed prognostic biomarkers for primary prostate cancer independent of multifocality and transcriptome heterogeneity. Cancer Gene Therapy. ISSN 0929-1903. p. 1–9. doi: 10.1038/s41417-022-00444-7.
• Lemma, Roza Berhanu; Fleischer, Thomas; Martinsen, Emily; Ledsaak, Marit; Kristensen, Vessela N. & Eskeland, Ragnhild [Show all 8 contributors for this article] (2022). Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics & Chromatin. ISSN 1756-8935. 15. doi: 10.1186/s13072-022-00444-9.
• Korecki, Andrea J; Cueva-Vargas, Jorge; Fornes, Oriol; Agostinone, Jessica; Farkas, Rachelle & Hickmott, Jack W [Show all 12 contributors for this article] (2021). Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. Gene Therapy. ISSN 0969-7128. doi: 10.1038/s41434-021-00227-z. Full text in Research Archive
• Mileti, Enrichetta; Kwok, Kelvin H.M.; Andersson, Daniel P.; Mathelier, Anthony; Raman, Amitha & Bäckdahl, Jesper [Show all 14 contributors for this article] (2021). Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State. Diabetes. ISSN 0012-1797. 70(7), p. 1486–1497. doi: 10.2337/db21-0001.
• Castro Mondragon, Jaime Abraham; Riudavets Puig, Rafael; Rauluseviciute, Ieva; Lemma, Roza Berhanu; Turchi, Laura & Blanc-Mathieu, Romain [Show all 23 contributors for this article] (2021). JASPAR 2022: the 9th release of the open-acess database of transcription factor binding profiles. Nucleic Acids Research (NAR). ISSN 0305-1048. doi: 10.1093/nar/gkab1113. Full text in Research Archive
• Riudavets, Rafael; Boddie, Paul; Khan, Aziz; Castro Mondragon, Jaime Abraham & Mathelier, Anthony (2021). UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BMC Genomics. ISSN 1471-2164. 22(482), p. 1–17. doi: 10.1186/s12864-021-07760-6. Full text in Research Archive
• Aure, Miriam Ragle; Fleischer, Thomas; Bjørklund, Sunniva; Ankill, Jørgen; Castro Mondragón, Jaime Abraham & Børresen-Dale, Anne-Lise [Show all 11 contributors for this article] (2021). Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer. Genome Medicine. ISSN 1756-994X. 13:72, p. 1–21. doi: 10.1186/s13073-021-00880-4. Full text in Research Archive
• Khan, Aziz; Riudavets Puig, Rafael; Boddie, Paul & Mathelier, Anthony (2020). BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btaa928. Full text in Research Archive
• Pladsen, Arne Valebjørg; Nilsen, Gro; Rueda, Oscar M.; Aure, Miriam Ragle; Borgan, Ørnulf & Liestøl, Knut [Show all 18 contributors for this article] (2020). DNA copy number motifs are strong and independent predictors of survival in breast cancer. Communications Biology. ISSN 2399-3642. 3. doi: 10.1038/s42003-020-0884-6. Full text in Research Archive
• Fromm, Bastian; Domanska, Diana Ewa; Høye, Eirik; Ovchinnikov, Vladimir; Kang, Wenjing & Aparicio-Puerta, Ernesto [Show all 13 contributors for this article] (2019). MirGeneDB 2.0: the metazoan microRNA complement . Nucleic Acids Research (NAR). ISSN 0305-1048. 48(D1), p. D132–D141. doi: 10.1093/nar/gkz885. Full text in Research Archive
• Salvatore, Stefania; Rand, Knut Dagestad; Grytten, Ivar; Ferkingstad, Egil; Domanska, Diana & Holden, Lars [Show all 10 contributors for this article] (2019). Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics. ISSN 1467-5463. p. 1–8. doi: 10.1093/bib/bbz083.
• Ha, Thomas J.; Zhang, Peter G.Y.; Robert, Remi; Yeung, Joanna; Swanson, Douglas J. & Mathelier, Anthony [Show all 17 contributors for this article] (2019). Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC Genomics. ISSN 1471-2164. 20(718), p. 1–17. doi: 10.1186/s12864-019-6063-9. Full text in Research Archive
• Korecki, Andrea J; Hickmott, Jack W; Lam, Siu Ling; Dreolini, Lisa; Mathelier, Anthony & Baker, Oliver [Show all 17 contributors for this article] (2019). Twenty-seven tamoxifen-inducible icre-driver mouse strains for eye and brain, including seventeen carrying a new inducible-first constitutive-ready allele. Genetics. ISSN 0016-6731. 211(4), p. 1155–1177. doi: 10.1534/genetics.119.301984.
• Fornes, Oriol; Castro Mondragón, Jaime Abraham; Khan, Aziz; Robin van der, Lee; Zhang, Xi & A. Richmond, Phillip [Show all 19 contributors for this article] (2019). JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR). ISSN 0305-1048. 48, p. 87–92. doi: 10.1093/nar/gkz1001. Full text in Research Archive
• Itkonen, Harri; Urbanucci, Alfonso; Sara ES, Martin; Khan, Aziz; Mathelier, Anthony & Thiede, Bernd [Show all 8 contributors for this article] (2019). High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics. ISSN 1838-7640. 9(8), p. 2183–2197. doi: 10.7150/thno.30834. Full text in Research Archive
• Gheorghe, Marius; Sandve, Geir Kjetil; Khan, Aziz; Cheneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). A map of direct TF–DNA interactions in the human genome. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(4). doi: 10.1093/nar/gky1210. Full text in Research Archive
• Fornes, Oriol; Gheorghe, Marius; Richmond, Phillip A.; Arenillas, David J.; Wasserman, Wyeth W. & Mathelier, Anthony (2018). MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations. Scientific Data. ISSN 2052-4463. 5:180141, p. 1–7. doi: 10.1038/sdata.2018.141. Full text in Research Archive
• Lecellier, Charles-Henri; Wasserman, Wyeth W. & Mathelier, Anthony (2018). Human enhancers harboring specific sequence composition, activity, and genome organization are linked to the immune response. Genetics. ISSN 0016-6731. 209(4), p. 1055–1071. doi: 10.1534/genetics.118.301116.
• Khan, Aziz; Mathelier, Anthony & Zhang, Xuegong (2018). Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. Epigenetics. ISSN 1559-2294. 13(9), p. 910–922. doi: 10.1080/15592294.2018.1514231.
• Sugiaman-Trapman, Debora; Vitezic, Morana; Jouhilahti, Eeva-Mari; Mathelier, Anthony; Lauter, Gilbert & Misra, Sougat [Show all 9 contributors for this article] (2018). Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics. ISSN 1471-2164. 19(181). doi: 10.1186/s12864-018-4564-6. Full text in Research Archive
• Cheneby, J; Gheorghe, Marius; Artufel, M; Mathelier, Anthony & Ballester, B (2017). ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Research (NAR). ISSN 0305-1048. 46(D1), p. D267–D275. doi: 10.1093/nar/gkx1092. Full text in Research Archive
• de rie, D; Abugesaissa, I; Alam, T; Arner, E; Ashoor, H & Åström, G [Show all 70 contributors for this article] (2017). An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology. ISSN 1087-0156. 35(9), p. 872–878. doi: 10.1038/nbt.3947.
• Khan, Aziz; Fornes, O; Stigliani, A; Gheorghe, Marius; Castro Mondragón, Jaime Abraham & van der Lee, R [Show all 19 contributors for this article] (2017). JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research (NAR). ISSN 0305-1048. 46(1), p. D260–D266. doi: 10.1093/nar/gkx1126. Full text in Research Archive
• Khan, Aziz & Mathelier, Anthony (2017). JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics. ISSN 1367-4803. 34(9), p. 1612–1614. doi: 10.1093/bioinformatics/btx804. Full text in Research Archive
• Fleischer, Thomas; Tekpli, Xavier; Mathelier, Anthony; Wang, Shixiong; Nebdal, Daniel J.H. & Dhakal, Hari Prasad [Show all 16 contributors for this article] (2017). DNA methylation at enhancers identifies distinct breast cancer lineages. Nature Communications. ISSN 2041-1723. 8(1379). doi: 10.1038/s41467-017-00510-x. Full text in Research Archive
• Khan, Aziz & Mathelier, Anthony (2017). Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics. ISSN 1471-2105. 18(287). doi: 10.1186/s12859-017-1708-7. Full text in Research Archive
• Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi & Severin, Jessica [Show all 25 contributors for this article] (2017). Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Research (NAR). ISSN 0305-1048. 45(D1), p. D737–D743. doi: 10.1093/nar/gkw995. Full text in Research Archive
• Shi, Wenqiang; Fornes, Oriol; Mathelier, Anthony & Wasserman, Wyeth W. (2016). Evaluating the impact of single nucleotide variants on transcription factor binding. Nucleic Acids Research (NAR). ISSN 0305-1048. 44(21), p. 10106–10116. doi: 10.1093/nar/gkw691.
• Mathelier, Anthony; Xin, Beibei; Chiu, Tsu-Pei; Yang, Lin; Rohs, REmo & Wasserman, Wyeth W. (2016). DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo. Cell Systems. ISSN 2405-4712. 3, p. 278–286. doi: 10.1016/j.cels.2016.07.001.
• Arenillas, David J.; Forrest, Alistair R.R.; Kawaji, Hideya; Lassmann, Timo; Wasserman, Wyeth W. & Mathelier, Anthony (2016). CAGEd-oPOSSUM: Motif enrichment analysis from CAGE-derived TSSs. Bioinformatics. ISSN 1367-4803. 32(18), p. 2858–2860. doi: 10.1093/bioinformatics/btw337.
• Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca & Arenillas, David J. [Show all 17 contributors for this article] (2014). JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR). ISSN 0305-1048. 42(1), p. D142–D147. doi: 10.1093/nar/gkt997. Full text in Research Archive

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• Fromm, Bastian; Domanska, Diana; Høye, Eirik; Ovchinnikov, Vladimir; Kang, Wenjing & Aparicio-Puerta, Ernesto [Show all 13 contributors for this article] (2020). Erratum: MirGeneDB 2.0: The metazoan microRNA complement (Nucleic Acids Research (2019) DOI: 10.1093/nar/gkz885). Nucleic Acids Research (NAR). ISSN 0305-1048. 48(1). doi: 10.1093/nar/gkz1016.
• Gheorghe, Marius; Sandve, Geir Kjetil Ferkingstad; Khan, Aziz; Chèneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). Erratum: A map of direct TF-DNA interactions in the human genome (Nucleic acids research (2019) 47 4 (e21)). Nucleic Acids Research (NAR). ISSN 0305-1048. 47(14). doi: 10.1093/nar/gkz582.
• Khan, Aziz; Montenegro-Montero, Alejandro & Mathelier, Anthony (2018). Put science first and formatting later. EMBO Reports. ISSN 1469-221X. doi: 10.15252/embr.201845731.

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