Unsupervised identification of redundant domain entries in InterPro database using clustering techniques. - Ahmet Süreyya Rifaioglu; Tunca Dogan; Tolga Can (BCB, 2015)

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)

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; et al. (Nucleic Acids Res., 2016)

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)

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)

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)

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)

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)

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; et al. (Nucleic Acids Res., 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)

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)

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)

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)

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)

SELFormer: Molecular Representation Learning via SELFIES Language Models. - Atakan Yüksel; Erva Ulusoy; Atabey Ünlü; Gamze Deniz; Tunca Dogan (CoRR, 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; et al. (Bioinform., 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., 2023)

How to approach machine learning-based prediction of drug/compound-target interactions. - Heval Atas Güvenilir; Tunca Dogan (J. Cheminformatics, 2023)

Multi-modal Representation Learning Enables Accurate Protein Function Prediction in Low-Data Setting. - Serbülent Ünsal; Sinem Özdemir; Bünyamin Kasap; M. Ersan Kalayci; Kemal Turhan; Tunca Dogan; Aybar C. Acar (CoRR, 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, 2024)

ChemPile: A 250GB Diverse and Curated Dataset for Chemical Foundation Models. - Adrian Mirza; Nawaf Alampara; Martiño Ríos-García; Mohamed Abdelalim; Jack Butler; Bethany Connolly; Tunca Dogan; Marianna Nezhurina; Bünyamin Sen; Santosh Tirunagari; Mark Worrall; Adamo Young; et al. (CoRR, 2025)