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Showing results 1-50 of 53
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2023
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1. |
Fornes, Oriol; Av-Shalom, Tamar V; Korecki, Andrea J; Farkas, Rachelle A; Arenillas, David J; Mathelier, Anthony; Simpson, Elizabeth M; Wasserman, Wyeth W. OnTarget: In silico design of MiniPromoters for targeted delivery of expression. Nucleic Acids Research (NAR) 2023 ;Volume 51.(W1) p. W379-W386 UiO OUS
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Mathelier, Anthony. Insights into the disruption of gene regulatory programs in cancers. Centre de Recherches en Cancérologie de Toulouse seminar; 2023-10-20 UiO
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Mathelier, Anthony. Insights into the disruption of gene regulatory programs in cancers. NORDIC EMBL PARTNERSHIP MEETING 2023; 2023-09-12 - 2023-09-14 UiO
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Rauluseviciute, Ieva; Launay, Timothée; Barzaghi, Guido; Nikumbh, Sarvesh; Lenhard, Boris; Krebs, Arnaud Regis; Castro Mondragon, Jaime Abraham; Mathelier, Anthony. Identification of transcription factor co-binding patterns with non-negative matrix factorization. bioRxiv 2023 UiO
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Rauluseviciute, Ieva; Riudavets-Puig, Rafael; Blanc-Mathieu, Romain; Castro Mondragon, Jaime Abraham; Ferenc, Katalin Terezia; Kumar, Vipin; Lemma, Roza Berhanu; Lucas, Jeremy; Cheneby, Jeanne; Baranasic, Damir; Khan, Aziz; Fornes, Oriol; Gundersen, Sveinung; Johansen, Morten; Hovig, Eivind; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W.; Parcy, François; Mathelier, Anthony. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR) 2023 ;Volume 52.(D1) p. D174-D182 OUS UiO
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2022
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Bjørklund, Sunniva; Aure, Miriam Ragle; Häkkinen, Jari; Vallon-Christersson, Johan; Kumar, Surendra; Bull Evensen, Katrine; Fleischer, Thomas; Tost, Jörg; Sahlberg, Kristine Kleivi; Mathelier, Anthony; Bhanot, Gyan; Ganesan, Shridar; Tekpli, Xavier; Kristensen, Vessela N.; Bathen, Tone Frost; Borgen, Elin; Børresen-Dale, Anne-Lise; Engebråten, Olav; Fritzman, Britt; Hartmann-Johnsen, Olaf Johan; Garred, Øystein; Geisler, Jürgen; Geitvik, Gry; Hofvind, Solveig Sand-Hanssen; Kåresen, Rolf; Langerød, Anita; Lingjærde, Ole Christian; Mælandsmo, Gunhild Mari; Naume, Bjørn; Russnes, Hege Elisabeth Giercksky; Sauer, Torill; Skjerven, Helle; Schlichting, Ellen; Sørlie, Therese. Subtype and cell type specific expression of lncRNAs provide insight into breast cancer. Communications Biology 2022 ;Volume 5.(1) p. 1-14 VV UiT NTNU OSTFSYK KREFTREG AHUS OUS UiO
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Castro Mondragon, Jaime Abraham; Aure, Miriam Ragle; Lingjærde, Ole Christian; Langerød, Anita; Martens, John WM; Børresen-Dale, Anne-Lise; Kristensen, Vessela N.; Mathelier, Anthony. Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers. Nucleic Acids Research (NAR) 2022 ;Volume 50.(21) p. 12131-12148 UiO OUS
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Ferenc, Katalin Terezia; Hsieh, Ping-Han; Mathelier, Anthony; Sandve, Geir Kjetil Ferkingstad. Method development for the identiļ¬cation of cis-regulatory signatures of cell types. Events Norwegian Bioinformatics Days 2022; 2022-09-28 - 2022-09-30 UiO
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Ferenc, Katalin Terezia; Hsieh, Ping-Han; Mathelier, Anthony; Sandve, Geir Kjetil Ferkingstad. Method development for the identification of cis-regulatory signatures of cell types. Nordic AI Meet 2022, Nordic Young Researchers Symposium; 2022-11-14 - 2022-11-15 UiO
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Ferenc, Katalin Terezia; Mathelier, Anthony; Hsieh, Ping-Han; Sandve, Geir Kjetil Ferkingstad. Method development for the identiļ¬cation of cis-regulatory signatures of cell types. EMBL Partnership Conference; 2022-09-21 - 2022-09-23 UiO
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Lemma, Roza Berhanu; Castro-Mondragon, Jaime Abraham; Mathelier, Anthony. Large-scale investigation of noncoding elements associated with transcriptional deregulation involved in carcinogenesis. Norwegian Bioinformatics Days (NDB22); 2022-09-28 - 2022-09-30 UiO
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Lemma, Roza Berhanu; Fleischer, Thomas; Martinsen, Emily; Ledsaak, Marit; Kristensen, Vessela N.; Eskeland, Ragnhild; Gabrielsen, Odd Stokke; Mathelier, Anthony. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics & Chromatin 2022 ;Volume 15. p. - UiO OUS
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Mathelier, Anthony. Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers. Cancer Genomics and Epitranscriptomics: from the bench to the clinic; 2022-11-29 - 2022-12-02 UiO
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Rauluseviciute, Ieva; Castro-Mondragon, Jaime A.; Mathelier, Anthony. Identification of transcription factor co-binding partners with non-negative matrix factorization. 4th EMBL partnership conference; 2022-09-21 - 2022-09-23 UiO
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Rauluseviciute, Ieva; Castro-Mondragon, Jaime A.; Mathelier, Anthony. Identification of transcription factor co-binding patterns with non-negative matrix factorization. Norwegian Bioinformatics Days; 2022-09-28 - 2022-09-30 UiO
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Rauluseviciute, Ieva; Castro-Mondragon, Jaime A.; Mathelier, Anthony. Identification of transcription factor co-binding patterns with non-negative matrix factorization. Norwegian Bioinformatics Days; 2022-09-28 - 2022-09-30 UiO
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Rossini, Roberto; Kumar, Vipin; Mathelier, Anthony; Rognes, Torbjørn; Paulsen, Jonas. MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biology 2022 ;Volume 23.(1) p. - UiO OUS
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Rossini, Roberto; Kumar, Vipin; Rognes, Torbjorn; Mathelier, Anthony; Paulsen, Jonas. MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions. bioRxiv 2022 UiO UiB
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Strømme, Jonas Meier; Johannessen, Bjarne; Kidd, Susanne Gundersen; Bogaard, Mari; Carm, Kristina Totland; Zhang, Xiaokang; Sveen, Anita; Mathelier, Anthony; Lothe, Ragnhild Adelheid; Axcrona, Ulrika; Axcrona, Karol; Skotheim, Rolf I.. Expressed prognostic biomarkers for primary prostate cancer independent of multifocality and transcriptome heterogeneity. Cancer Gene Therapy 2022 ;Volume 29.(8-9) p. 1276-1284 OUS UiO AHUS
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2021
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20. |
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 13:72. p. 1-21 UiO OUS VV AHUS
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21. |
Castro Mondragon, Jaime Abraham; Riudavets Puig, Rafael; Rauluseviciute, Ieva; Lemma, Roza Berhanu; Turchi, Laura; Blanc-Mathieu, Romain; Lucas, Jeremy; Boddie, Paul; Khan, Aziz; Manosalva Perez, Nicolas; Fornes, Oriol; Leung, Tiffany; Aguirre, Alejandro; Hammal, Fayrouz; Schmelter, Daniel; Baranasic, Damir; Ballester, Benoit; Sandelin, Albin; Lenhard, Boris; Vandepoele, Klaas; Wasserman, Wyeth W.; Parcy, François; Mathelier, Anthony. JASPAR 2022: the 9th release of the open-acess database of transcription factor binding profiles. Nucleic Acids Research (NAR) 2021 UiO
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Korecki, Andrea J; Cueva-Vargas, Jorge; Fornes, Oriol; Agostinone, Jessica; Farkas, Rachelle; Hickmott, Jack W; Ling Lam, Siu; Mathelier, Anthony; Zhou, Michelle; Wasserman, Wyeth W.; Di Polo, Adriana; Simpson, Elizabeth M. Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. Gene Therapy 2021 UiO
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Mathelier, Anthony. Insights into the interplay between transcription factor binding and cis-regulatory disruptions in cancers. Nanotumor Bioinformatics webinar series; 2021-12-03 - 2021-12-03 UiO
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24. |
Mileti, Enrichetta; Kwok, Kelvin H.M.; Andersson, Daniel P.; Mathelier, Anthony; Raman, Amitha; Bäckdahl, Jesper; Jalkanen, Jutta; Massier, Lucas; Thorell, Anders; Gao, Hui; Arner, Peter; Mejhert, Niklas; Daub, Carsten O.; Riden, Mikael. Human White Adipose Tissue Displays Selective Insulin Resistance in the Obese State. Diabetes 2021 ;Volume 70.(7) p. 1486-1497 UiO OUS
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25. |
Riudavets Puig, Rafael; Boddie, Paul; Khan, Aziz; Castro Mondragon, Jaime Abraham; Mathelier, Anthony. UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BMC Genomics 2021 UiO
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Riudavets, Rafael; Boddie, Paul; Khan, Aziz; Castro Mondragon, Jaime Abraham; Mathelier, Anthony. UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BMC Genomics 2021 ;Volume 22.(482) p. 1-17 UiO OUS
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2020
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27. |
Fromm, Bastian; Domanska, Diana; 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. Erratum: MirGeneDB 2.0: The metazoan microRNA complement (Nucleic Acids Research (2019) DOI: 10.1093/nar/gkz885). Nucleic Acids Research (NAR) 2020 ;Volume 48.(1) p. D1172- OUS UiO
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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 UiO
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29. |
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. - OUS UiO
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2019
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30. |
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 UiB UiO OUS
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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 OUS UiO
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Gheorghe, Marius; Sandve, Geir Kjetil Ferkingstad; Khan, Aziz; Chèneby, Jeanne; Ballester, Benoit; Mathelier, Anthony. Erratum: A map of direct TF-DNA interactions in the human genome (Nucleic acids research (2019) 47 4 (e21)). Nucleic Acids Research (NAR) 2019 ;Volume 47.(14) p. 7715- UiO
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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- UiO OUS
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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 UiO OUS
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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 UiO OUS
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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 UiO
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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 NR UiO OUS
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2018
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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 UiO OUS
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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 UiO OUS
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40. |
Khan, Aziz; Montenegro-Montero, Alejandro; Mathelier, Anthony. Put science first and formatting later. EMBO Reports 2018 p. - UiO
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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 UiO OUS
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42. |
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) UiO OUS
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2017
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43. |
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 NTNU OUS UiO
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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 UiO
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45. |
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 NTNU
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46. |
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) UiO VV OUS AHUS
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47. |
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 UiO
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48. |
Khan, Aziz; Mathelier, Anthony. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics 2017 ;Volume 18.(287) UiO OUS
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Khan, Aziz; Mathelier, Anthony. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics 2017 ;Volume 34.(9) p. 1612-1614 UiO
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2016
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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 UiO OUS
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