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Showing results 1-26 of 26

2021
1 Aure, Miriam Ragle; Fleischer, Thomas; Bjørklund, Sunniva; Ankill, Jørgen; Castro Mondragón, Jaime Abraham; Børresen-Dale, Anne-Lise; Tost, Jörg; Sahlberg, Kristine Kleivi; Mathelier, Anthony; Tekpli, Xavier; Kristensen, Vessela N..
Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer. Genome Medicine 2021 ;Volume 13. p. -
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2020
2 Khan, Aziz; Riudavets Puig, Rafael; Boddie, Paul; Mathelier, Anthony.
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.. Bioinformatics 2020
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3 Pladsen, Arne Valebjørg; Nilsen, Gro; Rueda, Oscar M.; Aure, Miriam Ragle; Borgan, Ørnulf; Liestøl, Knut; Vitelli, Valeria; Frigessi Di Rattalma, Arnoldo; Langerød, Anita; Mathelier, Anthony; Engebråten, Olav; Kristensen, Vessela N.; Wedge, David C.; Van Loo, Peter; Caldas, Carlos; Børresen-Dale, Anne-Lise; Russnes, Hege Elisabeth Giercksky; Lingjærde, Ole Christian.
DNA copy number motifs are strong and independent predictors of survival in breast cancer. Communications Biology 2020 ;Volume 3. p. -
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2019
4 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.
JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR) 2019 ;Volume 48. p. 87-92
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5 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..
MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Research (NAR) 2019 ;Volume 48.(D1) p. D132-D141
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6 Gheorghe, Marius; Sandve, Geir Kjetil; Khan, Aziz; Cheneby, Jeanne; Ballester, Benoit; Mathelier, Anthony.
A map of direct TF–DNA interactions in the human genome. Nucleic Acids Research (NAR) 2019 ;Volume 47.(4) p. e21-
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7 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.
Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC Genomics 2019 ;Volume 20.(718) p. 1-17
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8 Itkonen, Harri; Urbanucci, Alfonso; Sara ES, Martin; Khan, Aziz; Mathelier, Anthony; Thiede, Bernd; Walker, Suzanne; Mills, Ian Geoffrey.
High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics 2019 ;Volume 9.(8) p. 2183-2197
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9 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.
Twenty-seven tamoxifen-inducible icre-driver mouse strains for eye and brain, including seventeen carrying a new inducible-first constitutive-ready allele. Genetics 2019 ;Volume 211.(4) p. 1155-1177
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10 Salvatore, Stefania; Rand, Knut Dagestad; Grytten, Ivar; Ferkingstad, Egil; Domanska, Diana; Holden, Lars; Gheorghe, Marius; Mathelier, Anthony; Glad, Ingrid Kristine; Sandve, Geir Kjetil.
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics 2019 p. 1-8
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2018
11 Fornes, Oriol; Gheorghe, Marius; Richmond, Phillip A.; Arenillas, David J.; Wasserman, Wyeth W.; Mathelier, Anthony.
MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations. Scientific Data 2018 ;Volume 5:180141. p. 1-7
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12 Khan, Aziz; Mathelier, Anthony; Zhang, Xuegong.
Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. Epigenetics 2018 ;Volume 13.(9) p. 910-922
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13 Khan, Aziz; Montenegro-Montero, Alejandro; Mathelier, Anthony.
Put science first and formatting later. EMBO Reports 2018 p. -
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14 Lecellier, Charles-Henri; Wasserman, Wyeth W.; Mathelier, Anthony.
Human enhancers harboring specific sequence composition, activity, and genome organization are linked to the immune response. Genetics 2018 ;Volume 209.(4) p. 1055-1071
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15 Sugiaman-Trapman, Debora; Vitezic, Morana; Jouhilahti, Eeva-Mari; Mathelier, Anthony; Lauter, Gilbert; Misra, Sougat; Daub, Carsten O.; Kere, Juha; Swoboda, Peter.
Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics 2018 ;Volume 19.(181)
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2017
16 Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi; Severin, Jessica; Mungall, Chris; Arenillas, David; Mathelier, Anthony; Medvedeva, Yulia; Lennartsson, Andreas; Drabløs, Finn Sverre; Ramilowski, Jordan; Rackham, Owen; Gough, Julian; Andersson, Robin; Sandelin, Albin; Ienasescu, Hans; Ono, Hiromasa; Bono, Hidemasa; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R.R.; Kasukawa, Takeya; Kawaji, Hideya.
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Research (NAR) 2017 ;Volume 45.(D1) p. D737-D743
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17 Cheneby, J; Gheorghe, Marius; Artufel, M; Mathelier, Anthony; Ballester, B.
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Research (NAR) 2017 ;Volume 46.(D1) p. D267-D275
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18 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.
An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology 2017 ;Volume 35.(9) p. 872-878
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19 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..
DNA methylation at enhancers identifies distinct breast cancer lineages. Nature Communications 2017 ;Volume 8.(1379)
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20 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.
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research (NAR) 2017 ;Volume 46.(1) p. D260-D266
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21 Khan, Aziz; Mathelier, Anthony.
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics 2017 ;Volume 18.(287)
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22 Khan, Aziz; Mathelier, Anthony.
JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics 2017 ;Volume 34.(9) p. 1612-1614
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2016
23 Arenillas, David J.; Forrest, Alistair R.R.; Kawaji, Hideya; Lassmann, Timo; Wasserman, Wyeth W.; Mathelier, Anthony.
CAGEd-oPOSSUM: Motif enrichment analysis from CAGE-derived TSSs. Bioinformatics 2016 ;Volume 32.(18) p. 2858-2860
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24 Mathelier, Anthony; Xin, Beibei; Chiu, Tsu-Pei; Yang, Lin; Rohs, REmo; Wasserman, Wyeth W..
DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo. Cell Systems 2016 ;Volume 3. p. 278-286
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25 Shi, Wenqiang; Fornes, Oriol; Mathelier, Anthony; Wasserman, Wyeth W..
Evaluating the impact of single nucleotide variants on transcription factor binding. Nucleic Acids Research (NAR) 2016 ;Volume 44.(21) p. 10106-10116
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2014
26 Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J.; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W..
JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR) 2014 ;Volume 42.(1) p. D142-D147
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