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BibTeX 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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