Tunca Dogan

According to our database, Tunca Dogan authored at least 19 papers between 2015 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data.

Mona Shojaei, Navid Mohammadvand, Tunca Dogan, Can Alkan, Rengül Çetin-Atalay, Aybar C. Acar

Comput. Biol. Medicine, February, 2024

2023

How to approach machine learning-based prediction of drug/compound-target interactions.

Heval Atas Güvenilir, Tunca Dogan

J. Cheminformatics, December, 2023

ProFAB - open protein functional annotation benchmark.

A Samet Özdilek, Ahmet Atakan, Gökhan Özsari, Aybar C. Acar, M. Volkan Atalay, Tunca Dogan, Ahmet Süreyya Rifaioglu

Briefings Bioinform., March, 2023

Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Elisabeth Coudert, Sebastien Gehant, Edouard De Castro, Monica Pozzato, Delphine Baratin, Teresa Batista Neto, Christian J. A. Sigrist, Nicole Redaschi, Alan J. Bridge, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Béatrice A. Cuche, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Manuela Pruess, Catherine Rivoire, Karin Sonesson, Shyamala Sundaram, Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Hema Bye-A-Jee, Austra Cukura, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James D. Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang

Bioinform., January, 2023

SELFormer: Molecular Representation Learning via SELFIES Language Models.

Atakan Yüksel, Erva Ulusoy, Atabey Ünlü, Gamze Deniz, Tunca Dogan

CoRR, 2023

Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks.

Atabey Ünlü, Elif Çevrim, Ahmet Sarigün, Hayriye Çelikbilek, Heval Atas Güvenilir, Altay Koyas, Deniz Cansen Kahraman, Abdurrahman Olgaç, Ahmet Süreyya Rifaioglu, Tunca Dogan

CoRR, 2023

Transfer learning for drug-target interaction prediction.

Alperen Dalkiran, Ahmet Atakan, Ahmet Süreyya Rifaioglu, Maria Jesus Martin, Rengül Çetin-Atalay, Aybar C. Acar, Tunca Dogan, Volkan Atalay

Bioinform., 2023

2022

Learning functional properties of proteins with language models.

Serbülent Ünsal, Heval Atas, Muammer Albayrak, Kemal Turhan, Aybar C. Acar, Tunca Dogan

Nat. Mach. Intell., 2022

SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins.

Gökhan Özsari, Ahmet Süreyya Rifaioglu, Ahmet Atakan, Tunca Dogan, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay

Bioinform., 2022

2021

Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases.

Tunca Dogan, Ece Akhan Güzelcan, Marcus Baumann, Altay Koyas, Heval Atas, Ian R. Baxendale, Maria Jesus Martin, Rengül Çetin-Atalay

PLoS Comput. Biol., 2021

UniProt: the universal protein knowledgebase in 2021.

Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan W. Sousa da Silva, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Leyla Jael García Castro, Penelope Garmiri, George E. Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodríguez-López, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan J. Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard De Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Béatrice A. Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, Jian Zhang, Patrick Ruch, Douglas Teodoro

Nucleic Acids Res., 2021

MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery.

Ahmet Süreyya Rifaioglu, Rengül Çetin-Atalay, Deniz Cansen Kahraman, Tunca Dogan, Maria Jesus Martin, Volkan Atalay

Bioinform., 2021

2020

iBioProVis: interactive visualization and analysis of compound bioactivity space.

Ataberk Donmez, Ahmet Süreyya Rifaioglu, Aybar C. Acar, Tunca Dogan, Rengül Çetin-Atalay, Volkan Atalay, Wren Jonathan

Bioinform., 2020

iBioProVis: interactive visualization and analysis of compound bioactivity space.

Ataberk Donmez, Ahmet Süreyya Rifaioglu, Aybar C. Acar, Tunca Dogan, Rengül Çetin-Atalay, Volkan Atalay

Bioinform., 2020

2019

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.

Ahmet Süreyya Rifaioglu, Heval Atas, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay, Tunca Dogan

Briefings Bioinform., 2019

2018

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature.

Alperen Dalkiran, Ahmet Süreyya Rifaioglu, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay, Tunca Dogan

BMC Bioinform., 2018

2016

Tools and data services registry: a community effort to document bioinformatics resources.

Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak

Nucleic Acids Res., 2016

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.

Tunca Dogan, Alistair MacDougall, Rabie Saidi, Diego Poggioli, Alex Bateman, Claire O'Donovan, Maria Jesus Martin

Bioinform., 2016

2015

Unsupervised identification of redundant domain entries in InterPro database using clustering techniques.

Ahmet Süreyya Rifaioglu, Tunca Dogan, Tolga Can

Proceedings of the 6th ACM Conference on Bioinformatics, 2015