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ORCIDBibTeX records: Tunca Dogan
@article{DBLP:journals/cbm/ShojaeiMDACA24,
author = {Mona Shojaei and
Navid Mohammadvand and
Tunca Dogan and
Can Alkan and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Aybar C. Acar},
title = {An integrative framework for clinical diagnosis and knowledge discovery
from exome sequencing data},
journal = {Comput. Biol. Medicine},
volume = {169},
pages = {107810},
year = {2024},
url = {https://doi.org/10.1016/j.compbiomed.2023.107810},
doi = {10.1016/J.COMPBIOMED.2023.107810},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/ShojaeiMDACA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/OzdilekAOAADR23,
author = {A Samet {\"{O}}zdilek and
Ahmet Atakan and
G{\"{o}}khan {\"{O}}zsari and
Aybar C. Acar and
M. Volkan Atalay and
Tunca Dogan and
Ahmet S{\"{u}}reyya Rifaioglu},
title = {ProFAB - open protein functional annotation benchmark},
journal = {Briefings Bioinform.},
volume = {24},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac627},
doi = {10.1093/BIB/BBAC627},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/OzdilekAOAADR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CoudertGCPBNSRBBAAAABBNB23,
author = {Elisabeth Coudert and
Sebastien Gehant and
Edouard De Castro and
Monica Pozzato and
Delphine Baratin and
Teresa Batista Neto and
Christian J. A. Sigrist and
Nicole Redaschi and
Alan Bridge and
Alan J. Bridge and
Lucila Aimo and
Ghislaine Argoud{-}Puy and
Andrea H. Auchincloss and
Kristian B. Axelsen and
Parit Bansal and
Marie{-}Claude Blatter and
Jerven T. Bolleman and
Emmanuel Boutet and
Lionel Breuza and
Blanca Cabrera Gil and
Cristina Casals{-}Casas and
Kamal Chikh Echioukh and
B{\'{e}}atrice A. Cuche and
Anne Estreicher and
Maria Livia Famiglietti and
Marc Feuermann and
Elisabeth Gasteiger and
Pascale Gaudet and
Vivienne Baillie Gerritsen and
Arnaud Gos and
Nadine Gruaz{-}Gumowski and
Chantal Hulo and
Nevila Hyka{-}Nouspikel and
Florence Jungo and
Arnaud Kerhornou and
Philippe Le Mercier and
Damien Lieberherr and
Patrick Masson and
Anne Morgat and
Venkatesh Muthukrishnan and
Salvo Paesano and
Ivo Pedruzzi and
Sandrine Pilbout and
Lucille Pourcel and
Sylvain Poux and
Manuela Pruess and
Catherine Rivoire and
Karin Sonesson and
Shyamala Sundaram and
Alex Bateman and
Maria Jesus Martin and
Sandra E. Orchard and
Michele Magrane and
Shadab Ahmad and
Emanuele Alpi and
Emily H. Bowler{-}Barnett and
Ramona Britto and
Hema Bye{-}A{-}Jee and
Austra Cukura and
Paul Denny and
Tunca Dogan and
Thankgod Ebenezer and
Jun Fan and
Penelope Garmiri and
Leonardo Jose da Costa Gonzales and
Emma Hatton{-}Ellis and
Abdulrahman Hussein and
Alexandr Ignatchenko and
Giuseppe Insana and
Rizwan Ishtiaq and
Vishal Joshi and
Dushyanth Jyothi and
Swaathi Kandasamy and
Antonia Lock and
Aurelien Luciani and
Marija Lugaric and
Jie Luo and
Yvonne Lussi and
Alistair MacDougall and
F{\'{a}}bio Madeira and
Mahdi Mahmoudy and
Alok Mishra and
Katie Moulang and
Andrew Nightingale and
Sangya Pundir and
Guoying Qi and
Shriya Raj and
Pedro Raposo and
Daniel Rice and
Rabie Saidi and
Rafael Santos and
Elena Speretta and
James D. Stephenson and
Prabhat Totoo and
Edward Turner and
Nidhi Tyagi and
Preethi Vasudev and
Kate Warner and
Xavier Watkins and
Rossana Zaru and
Hermann Zellner and
Cathy H. Wu and
Cecilia N. Arighi and
Leslie Arminski and
Chuming Chen and
Yongxing Chen and
Hongzhan Huang and
Kati Laiho and
Peter B. McGarvey and
Darren A. Natale and
Karen Ross and
C. R. Vinayaka and
Qinghua Wang and
Yuqi Wang},
title = {Annotation of biologically relevant ligands in UniProtKB using ChEBI},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac793},
doi = {10.1093/BIOINFORMATICS/BTAC793},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CoudertGCPBNSRBBAAAABBNB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DalkiranARMCADA23,
author = {Alperen Dalkiran and
Ahmet Atakan and
Ahmet S{\"{u}}reyya Rifaioglu and
Maria Jesus Martin and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Aybar C. Acar and
Tunca Dogan and
Volkan Atalay},
title = {Transfer learning for drug-target interaction prediction},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {103--110},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad234},
doi = {10.1093/BIOINFORMATICS/BTAD234},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DalkiranARMCADA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/GuvenilirD23,
author = {Heval Atas G{\"{u}}venilir and
Tunca Dogan},
title = {How to approach machine learning-based prediction of drug/compound-target
interactions},
journal = {J. Cheminformatics},
volume = {15},
number = {1},
pages = {16},
year = {2023},
url = {https://doi.org/10.1186/s13321-023-00689-w},
doi = {10.1186/S13321-023-00689-W},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/GuvenilirD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-07868,
author = {Atabey {\"{U}}nl{\"{u}} and
Elif {\c{C}}evrim and
Ahmet Sarig{\"{u}}n and
Hayriye {\c{C}}elikbilek and
Heval Atas G{\"{u}}venilir and
Altay Koyas and
Deniz Cansen Kahraman and
Abdurrahman Olga{\c{c}} and
Ahmet S{\"{u}}reyya Rifaioglu and
Tunca Dogan},
title = {Target Specific De Novo Design of Drug Candidate Molecules with Graph
Transformer-based Generative Adversarial Networks},
journal = {CoRR},
volume = {abs/2302.07868},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.07868},
doi = {10.48550/ARXIV.2302.07868},
eprinttype = {arXiv},
eprint = {2302.07868},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-07868.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-04662,
author = {Atakan Y{\"{u}}ksel and
Erva Ulusoy and
Atabey {\"{U}}nl{\"{u}} and
Gamze Deniz and
Tunca Dogan},
title = {SELFormer: Molecular Representation Learning via {SELFIES} Language
Models},
journal = {CoRR},
volume = {abs/2304.04662},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.04662},
doi = {10.48550/ARXIV.2304.04662},
eprinttype = {arXiv},
eprint = {2304.04662},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-04662.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OzsariRADMCA22,
author = {G{\"{o}}khan {\"{O}}zsari and
Ahmet S{\"{u}}reyya Rifaioglu and
Ahmet Atakan and
Tunca Dogan and
Maria Jesus Martin and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Volkan Atalay},
title = {SLPred: a multi-view subcellular localization prediction tool for
multi-location human proteins},
journal = {Bioinform.},
volume = {38},
number = {17},
pages = {4226--4229},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac458},
doi = {10.1093/BIOINFORMATICS/BTAC458},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OzsariRADMCA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/natmi/UnsalAATAD22,
author = {Serb{\"{u}}lent {\"{U}}nsal and
Heval Atas and
Muammer Albayrak and
Kemal Turhan and
Aybar C. Acar and
Tunca Dogan},
title = {Learning functional properties of proteins with language models},
journal = {Nat. Mach. Intell.},
volume = {4},
number = {3},
pages = {227--245},
year = {2022},
url = {https://doi.org/10.1038/s42256-022-00457-9},
doi = {10.1038/S42256-022-00457-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/natmi/UnsalAATAD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RifaiogluCKDMA21,
author = {Ahmet S{\"{u}}reyya Rifaioglu and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Deniz Cansen Kahraman and
Tunca Dogan and
Maria Jesus Martin and
Volkan Atalay},
title = {MDeePred: novel multi-channel protein featurization for deep learning-based
binding affinity prediction in drug discovery},
journal = {Bioinform.},
volume = {37},
number = {5},
pages = {693--704},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa858},
doi = {10.1093/BIOINFORMATICS/BTAA858},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RifaiogluCKDMA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BatemanMOMAAABB21,
author = {Alex Bateman and
Maria Jesus Martin and
Sandra E. Orchard and
Michele Magrane and
Rahat Agivetova and
Shadab Ahmad and
Emanuele Alpi and
Emily H. Bowler{-}Barnett and
Ramona Britto and
Borisas Bursteinas and
Hema Bye{-}A{-}Jee and
Ray Coetzee and
Austra Cukura and
Alan W. Sousa da Silva and
Paul Denny and
Tunca Dogan and
Thankgod Ebenezer and
Jun Fan and
Leyla Jael Garc{\'{\i}}a Castro and
Penelope Garmiri and
George E. Georghiou and
Leonardo Gonzales and
Emma Hatton{-}Ellis and
Abdulrahman Hussein and
Alexandr Ignatchenko and
Giuseppe Insana and
Rizwan Ishtiaq and
Petteri Jokinen and
Vishal Joshi and
Dushyanth Jyothi and
Antonia Lock and
Rodrigo Lopez and
Aurelien Luciani and
Jie Luo and
Yvonne Lussi and
Alistair MacDougall and
F{\'{a}}bio Madeira and
Mahdi Mahmoudy and
Manuela Menchi and
Alok Mishra and
Katie Moulang and
Andrew Nightingale and
Carla Susana Oliveira and
Sangya Pundir and
Guoying Qi and
Shriya Raj and
Daniel Rice and
Milagros Rodr{\'{\i}}guez{-}L{\'{o}}pez and
Rabie Saidi and
Joseph Sampson and
Tony Sawford and
Elena Speretta and
Edward Turner and
Nidhi Tyagi and
Preethi Vasudev and
Vladimir Volynkin and
Kate Warner and
Xavier Watkins and
Rossana Zaru and
Hermann Zellner and
Alan J. Bridge and
Sylvain Poux and
Nicole Redaschi and
Lucila Aimo and
Ghislaine Argoud{-}Puy and
Andrea H. Auchincloss and
Kristian B. Axelsen and
Parit Bansal and
Delphine Baratin and
Marie{-}Claude Blatter and
Jerven T. Bolleman and
Emmanuel Boutet and
Lionel Breuza and
Cristina Casals{-}Casas and
Edouard De Castro and
Kamal Chikh Echioukh and
Elisabeth Coudert and
B{\'{e}}atrice A. Cuche and
Mikael Doche and
Dolnide Dornevil and
Anne Estreicher and
Maria Livia Famiglietti and
Marc Feuermann and
Elisabeth Gasteiger and
Sebastien Gehant and
Vivienne Baillie Gerritsen and
Arnaud Gos and
Nadine Gruaz{-}Gumowski and
Ursula Hinz and
Chantal Hulo and
Nevila Hyka{-}Nouspikel and
Florence Jungo and
Guillaume Keller and
Arnaud Kerhornou and
Vicente Lara and
Philippe Le Mercier and
Damien Lieberherr and
Thierry Lombardot and
Xavier Martin and
Patrick Masson and
Anne Morgat and
Teresa Batista Neto and
Salvo Paesano and
Ivo Pedruzzi and
Sandrine Pilbout and
Lucille Pourcel and
Monica Pozzato and
Manuela Pruess and
Catherine Rivoire and
Christian J. A. Sigrist and
Karin Sonesson and
Andre Stutz and
Shyamala Sundaram and
Michael Tognolli and
Laure Verbregue and
Cathy H. Wu and
Cecilia N. Arighi and
Leslie Arminski and
Chuming Chen and
Yongxing Chen and
John S. Garavelli and
Hongzhan Huang and
Kati Laiho and
Peter B. McGarvey and
Darren A. Natale and
Karen Ross and
C. R. Vinayaka and
Qinghua Wang and
Yuqi Wang and
Lai{-}Su Yeh and
Jian Zhang and
Patrick Ruch and
Douglas Teodoro},
title = {UniProt: the universal protein knowledgebase in 2021},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D480--D489},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1100},
doi = {10.1093/NAR/GKAA1100},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/BatemanMOMAAABB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DoganGBKABMC21,
author = {Tunca Dogan and
Ece Akhan G{\"{u}}zelcan and
Marcus Baumann and
Altay Koyas and
Heval Atas and
Ian R. Baxendale and
Maria Jesus Martin and
Reng{\"{u}}l {\c{C}}etin{-}Atalay},
title = {Protein domain-based prediction of drug/compound-target interactions
and experimental validation on {LIM} kinases},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {11},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009171},
doi = {10.1371/JOURNAL.PCBI.1009171},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DoganGBKABMC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DonmezRADCAJ20,
author = {Ataberk Donmez and
Ahmet S{\"{u}}reyya Rifaioglu and
Aybar C. Acar and
Tunca Dogan and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Volkan Atalay and
Wren Jonathan},
title = {iBioProVis: interactive visualization and analysis of compound bioactivity
space},
journal = {Bioinform.},
volume = {36},
number = {14},
pages = {4227--4230},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa496},
doi = {10.1093/BIOINFORMATICS/BTAA496},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DonmezRADCAJ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DonmezRADCA20,
author = {Ataberk Donmez and
Ahmet S{\"{u}}reyya Rifaioglu and
Aybar C. Acar and
Tunca Dogan and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Volkan Atalay},
title = {iBioProVis: interactive visualization and analysis of compound bioactivity
space},
journal = {Bioinform.},
volume = {36},
number = {17},
pages = {4674},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa666},
doi = {10.1093/BIOINFORMATICS/BTAA666},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DonmezRADCA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/RifaiogluAMCAD19,
author = {Ahmet S{\"{u}}reyya Rifaioglu and
Heval Atas and
Maria Jesus Martin and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Volkan Atalay and
Tunca Dogan},
title = {Recent applications of deep learning and machine intelligence on in
silico drug discovery: methods, tools and databases},
journal = {Briefings Bioinform.},
volume = {20},
number = {5},
pages = {1878--1912},
year = {2019},
url = {https://doi.org/10.1093/bib/bby061},
doi = {10.1093/BIB/BBY061},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/RifaiogluAMCAD19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DalkiranRMCAD18,
author = {Alperen Dalkiran and
Ahmet S{\"{u}}reyya Rifaioglu and
Maria Jesus Martin and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
Volkan Atalay and
Tunca Dogan},
title = {ECPred: a tool for the prediction of the enzymatic functions of protein
sequences based on the {EC} nomenclature},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {334:1--334:13},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2368-y},
doi = {10.1186/S12859-018-2368-Y},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DalkiranRMCAD18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DoganMSPBOM16,
author = {Tunca Dogan and
Alistair MacDougall and
Rabie Saidi and
Diego Poggioli and
Alex Bateman and
Claire O'Donovan and
Maria Jesus Martin},
title = {UniProt-DAAC: domain architecture alignment and classification, a
new method for automatic functional annotation in UniProtKB},
journal = {Bioinform.},
volume = {32},
number = {15},
pages = {2264--2271},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw114},
doi = {10.1093/BIOINFORMATICS/BTW114},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DoganMSPBOM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/IsonRMKRCABBBBB16,
author = {Jon C. Ison and
Kristoffer Rapacki and
Herv{\'{e}} M{\'{e}}nager and
Mat{\'{u}}s Kalas and
Emil Rydza and
Piotr Chmura and
Christian Anthon and
Niall Beard and
Karel Berka and
Dan M. Bolser and
Tim Booth and
Anthony Bretaudeau and
Jan Brezovsky and
Rita Casadio and
Gianni Cesareni and
Frederik Coppens and
Michael Cornell and
Gianmauro Cuccuru and
Kristian Davidsen and
Gianluca Della Vedova and
Tunca Dogan and
Olivia Doppelt{-}Azeroual and
Laura Emery and
Elisabeth Gasteiger and
Thomas Gatter and
Tatyana Goldberg and
Marie Grosjean and
Bj{\"{o}}rn A. Gr{\"{u}}ning and
Manuela Helmer{-}Citterich and
Hans Ienasescu and
Vassilios Ioannidis and
Martin Closter Jespersen and
Rafael C. Jim{\'{e}}nez and
Nick S. Juty and
Peter Juvan and
Maximilian Koch and
Camille Laibe and
Jing{-}Woei Li and
Luana Licata and
Fabien Mareuil and
Ivan Micetic and
Rune M{\o}llegaard Friborg and
S{\'{e}}bastien Moretti and
Chris Morris and
Steffen M{\"{o}}ller and
Aleksandra Nenadic and
Hedi Peterson and
Giuseppe Profiti and
Peter M. Rice and
Paolo Romano and
Paola Roncaglia and
Rabie Saidi and
Andrea Schafferhans and
Veit Schw{\"{a}}mmle and
Callum Smith and
Maria Maddalena Sperotto and
Heinz Stockinger and
Radka Svobodov{\'{a}} Varekov{\'{a}} and
Silvio C. E. Tosatto and
Victor de la Torre and
Paolo Uva and
Allegra Via and
Guy Yachdav and
Federico Zambelli and
Gert Vriend and
Burkhard Rost and
Helen E. Parkinson and
Peter L{\o}ngreen and
S{\o}ren Brunak},
title = {Tools and data services registry: a community effort to document bioinformatics
resources},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {38--47},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1116},
doi = {10.1093/NAR/GKV1116},
timestamp = {Thu, 25 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/IsonRMKRCABBBBB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/RifaiogluDC15,
author = {Ahmet S{\"{u}}reyya Rifaioglu and
Tunca Dogan and
Tolga Can},
title = {Unsupervised identification of redundant domain entries in InterPro
database using clustering techniques},
booktitle = {Proceedings of the 6th {ACM} Conference on Bioinformatics, Computational
Biology and Health Informatics, {BCB} 2015, Atlanta, GA, USA, September
9-12, 2015},
pages = {505--506},
publisher = {{ACM}},
year = {2015},
url = {https://doi.org/10.1145/2808719.2811430},
doi = {10.1145/2808719.2811430},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/RifaiogluDC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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