Anthony Mathelier

• Fornes, Oriol; Castro Mondragón, Jaime Abraham; Khan, Aziz; Robin van der, Lee; Zhang, Xi; A. Richmond, Phillip; P. Modi, Bhavi; Correard, Solenne; Gheorghe, Marius; Baranasic, Damir; Santana-Garcia, Walter; Tan, Ge; Cheneby, Jeanne; Ballester, Benoit; Parcy, François; Sandelin, Albin; Lenhard, Boris; Wasserman, Wyeth W. & Mathelier, Anthony (2019). JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research.  ISSN 0305-1048.  48, s 87- 92 . doi: 10.1093/nar/gkz1001 Show summary

  JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles. Moreover, we created a Q&A forum to ease the communication between the user community and JASPAR curators. Finally, we updated the genomic tracks, inference tool, and TF-binding profile similarity clusters. All the data is available through the JASPAR website, its associated RESTful API, and through the JASPAR2020 R/Bioconductor package.

• Fromm, Bastian; Domanska, Diana Ewa; Høye, Eirik; Ovchinnikov, Vladimir; Kang, Wenjing; Aparicio-Puerta, Ernesto; Johansen, Morten; Flatmark, Kjersti; Mathelier, Anthony; Hovig, Eivind; Hackenberg, Michael; Friedländer, Marc R. & Peterson, Kevin J. (2019). MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Research.  ISSN 0305-1048.  48(D1), s D132- D141 . doi: 10.1093/nar/gkz885 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.  ISSN 0305-1048.  47(4), s e21 . doi: 10.1093/nar/gky1210 Full text in Research Archive.
• Ha, Thomas J.; Zhang, Peter G.Y.; Robert, Remi; Yeung, Joanna; Swanson, Douglas J.; Mathelier, Anthony; Wasserman, Wyeth W.; Im, Sujin; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Daub, Carsten O.; Arner, Erik; Carninci, Piero; Hayashizaki, Yoshihide; Forrest, Alistair R.R. & Goldowitz, Daniel (2019). Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC Genomics.  ISSN 1471-2164.  20(718), s 1- 17 . doi: 10.1186/s12864-019-6063-9 Full text in Research Archive.
• Itkonen, Harri; Urbanucci, Alfonso; Sara ES, Martin; Khan, Aziz; Mathelier, Anthony; Thiede, Bernd; Walker, Suzanne & Mills, Ian Geoffrey (2019). High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics.  ISSN 1838-7640.  9(8), s 2183- 2197 . doi: 10.7150/thno.30834 Full text in Research Archive.
• Korecki, Andrea J; Hickmott, Jack W; Lam, Siu Ling; Dreolini, Lisa; Mathelier, Anthony; Baker, Oliver; Kuehne, Claudia; Bonaguro, Russell J; Smith, Jillian; Tan, Chin-Vern; Zhou, Michelle; Goldowitz, Daniel; Deussing, Jan M; Stewart, A. Francis; Wasserman, Wyeth W.; Holt, Robert A & Simpson, Elizabeth M (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), s 1155- 1177 . doi: 10.1534/genetics.119.301984
• Salvatore, Stefania; Rand, Knut Dagestad; Grytten, Ivar; Ferkingstad, Egil; Domanska, Diana; Holden, Lars; Gheorghe, Marius; Mathelier, Anthony; Glad, Ingrid Kristine & Sandve, Geir Kjetil (2019). Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics.  ISSN 1467-5463.  s 1- 8 . doi: 10.1093/bib/bbz083 Show summary

  The generation and systematic collection of genome-wide data is ever-increasing. This vast amount of data has enabled researchers to study relations between a variety of genomic and epigenomic features, including genetic variation, gene regulation and phenotypic traits. Such relations are typically investigated by comparatively assessing genomic co-occurrence. Technically, this corresponds to assessing the similarity of pairs of genome-wide binary vectors. A variety of similarity measures have been proposed for this problem in other fields like ecology. However, while several of these measures have been employed for assessing genomic co-occurrence, their appropriateness for the genomic setting has never been investigated. We show that the choice of similarity measure may strongly influence results and propose two alternative modelling assumptions that can be used to guide this choice. On both simulated and real genomic data, the Jaccard index is strongly altered by dataset size and should be used with caution. The Forbes coefficient (fold change) and tetrachoric correlation are less influenced by dataset size, but one should be aware of increased variance for small datasets. All results on simulated and real data can be inspected and reproduced at https://hyperbrowser.uio.no/sim-measure.

• 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, s 1- 7 . doi: 10.1038/sdata.2018.141 Full text in Research Archive.
• 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), s 910- 922 . doi: 10.1080/15592294.2018.1514231
• 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), s 1055- 1071 . doi: 10.1534/genetics.118.301116
• Sugiaman-Trapman, Debora; Vitezic, Morana; Jouhilahti, Eeva-Mari; Mathelier, Anthony; Lauter, Gilbert; Misra, Sougat; Daub, Carsten O.; Kere, Juha & Swoboda, Peter (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.  ISSN 0305-1048.  46(D1), s 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; Babina, M; Bertin, N; Burroughs, AM; Carlisle, AJ; Daub, CO; Detmar, M; Daviatiiarov, R; Fort, A; Gebhard, C; Goldowitz, D; Guhl, S; Ha, TJ; Harschbager, J; Hasegawa, R; Hashimoto, K; Herlyn, M; Heutink, P; Hitchens, KJ; Hong, CC; Huang, E; Ishizu, Y; Kai, C; Kasukawa, T; Klinken, P; Lassmann, T; Lecellier, CH; Lee, W; Lizio, M; Makeev, V; Mathelier, Anthony; Medvededa, YA; Mejhert, N; Mungall, CJ; Noma, S; Ohshima, M; Okada-Hatakeyama, M; Persson, H; Rizzu, P; Roudnicky, F; Sætrom, Pål; Sato, H; Severin, J; Shin, JW; Swoboda, RK; Tarui, H; Toyoda, H; Vitting-Serup, K; Winterinham, L; Yamaguchi, Y; Yasuzawa, K; Yoneda, M; Yumoto, N; Zabierowsky, S; Zang, PG; Wells, CA; Summers, KM; Kawaii, H; Sandelin, A; Rehli, M; Hayashisaki, Y; Carninci, P; Forrest, ARR; de Hoon, MJL & De Hoon, Michiel J L (2017). An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology.  ISSN 1087-0156.  35(9), s 872- 878 . doi: 10.1038/nbt.3947
• Fleischer, Thomas; Tekpli, Xavier; Mathelier, Anthony; Wang, Shixiong; Nebdal, Daniel J.H.; Dhakal, Hari Prasad; Sahlberg, Kristine Kleivi; Schlichting, Ellen; Børresen-Dale, Anne-Lise; Borgen, Elin; Naume, Bjørn; Eskeland, Ragnhild; Frigessi, Arnoldo; Tost, Jörg; Rodriguez, Antoni Hurtado & Kristensen, Vessela N. (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; Fornes, O; Stigliani, A; Gheorghe, Marius; Castro Mondragón, Jaime Abraham; van der Lee, R; Bessy, A; Cheneby, J; Kulkarni, SR; Tan, G; Baranasic, D; Arenillas, DJ; Sandelin, A; Vandepoele, K; Lenhard, B; Ballester, B; Wassermann, WW; Parcy, F & Mathelier, Anthony (2017). JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research.  ISSN 0305-1048.  46(1), s 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), s 1612- 1614 . doi: 10.1093/bioinformatics/btx804 Full text in Research Archive.
• 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, s 278- 286 . doi: 10.1016/j.cels.2016.07.001
• Shi, Wenqiang; Fornes, Oriol; Mathelier, Anthony & Wasserman, Wyeth W. (2016). Evaluating the impact of single nucleotide variants on transcription factor binding. Nucleic Acids Research.  ISSN 0305-1048.  44(21), s 10106- 10116 . doi: 10.1093/nar/gkw691

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• 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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