| Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases AS Rifaioglu, H Atas, MJ Martin, R Cetin-Atalay, V Atalay, T Doğan Briefings in bioinformatics 20 (5), 1878-1912, 2019 | 474 | 2019 |
| The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome biology 20, 1-23, 2019 | 388 | 2019 |
| DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations AS Rifaioglu, E Nalbat, V Atalay, MJ Martin, R Cetin-Atalay, T Doğan Chemical science 11 (9), 2531-2557, 2020 | 190 | 2020 |
| ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature A Dalkiran, AS Rifaioglu, MJ Martin, R Cetin-Atalay, V Atalay, T Doğan BMC bioinformatics 19, 1-13, 2018 | 152 | 2018 |
| DEEPred: automated protein function prediction with multi-task feed-forward deep neural networks A Sureyya Rifaioglu, T Doğan, M Jesus Martin, R Cetin-Atalay, V Atalay Scientific reports 9 (1), 7344, 2019 | 148 | 2019 |
| MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery AS Rifaioglu, R Cetin Atalay, D Cansen Kahraman, T Doğan, M Martin, ... Bioinformatics 37 (5), 693-704, 2021 | 94 | 2021 |
| Crowdsourced mapping of unexplored target space of kinase inhibitors A Cichońska, B Ravikumar, RJ Allaway, F Wan, S Park, O Isayev, S Li, ... Nature communications 12 (1), 3307, 2021 | 69 | 2021 |
| Multimodal single cell data integration challenge: results and lessons learned C Lance, MD Luecken, DB Burkhardt, R Cannoodt, P Rautenstrauch, ... BioRxiv, 2022.04. 11.487796, 2022 | 57 | 2022 |
| CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations T Doğan, H Atas, V Joshi, A Atakan, AS Rifaioglu, E Nalbat, A Nightingale, ... Nucleic acids research 49 (16), e96-e96, 2021 | 30* | 2021 |
| Transfer learning for drug–target interaction prediction A Dalkıran, A Atakan, AS Rifaioğlu, MJ Martin, RÇ Atalay, AC Acar, ... Bioinformatics 39 (Supplement_1), i103-i110, 2023 | 21 | 2023 |
| Large‐scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants AS Rifaioglu, T Doğan, ÖS Saraç, T Ersahin, R Saidi, MV Atalay, ... Proteins: Structure, Function, and Bioinformatics 86 (2), 135-151, 2018 | 18 | 2018 |
| FAIR adoption, assessment and challenges at UniProt L Garcia, J Bolleman, S Gehant, N Redaschi, M Martin Scientific data 6 (1), 175, 2019 | 15 | 2019 |
| iBioProVis: interactive visualization and analysis of compound bioactivity space A Donmez, AS Rifaioglu, A Acar, T Doğan, R Cetin-Atalay, V Atalay Bioinformatics 36 (14), 4227-4230, 2020 | 11 | 2020 |
| Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage DR Ghasemi, K Okonechnikov, A Rademacher, S Tirier, KK Maass, ... Nature Communications 15 (1), 269, 2024 | 7 | 2024 |
| Predicting the specificity-determining positions of receptor tyrosine kinase Axl T Karakulak, AS Rifaioglu, JP Rodrigues, E Karaca Frontiers in Molecular Biosciences 8, 658906, 2021 | 7* | 2021 |
| SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins G Özsarı, AS Rifaioglu, A Atakan, T Doğan, MJ Martin, R Çetin Atalay, ... Bioinformatics 38 (17), 4226-4229, 2022 | 6 | 2022 |
| Multi-mask aggregators for graph neural networks A Sarıgün, AS Rifaioglu The First Learning on Graphs Conference, 2022 | 6 | 2022 |
| Deep learning for prediction of drug-target interaction space and protein functions AS Rifaioğlu | 2 | 2020 |
| Drug Repurposing Approach to Identify Candidate Drug Molecules for Hepatocellular Carcinoma T Baser, AS Rifaioglu, MV Atalay, RC Atalay International Journal of Molecular Sciences 25 (17), 9392, 2024 | | 2024 |
| ProFAB—open protein functional annotation benchmark AS Özdilek, A Atakan, G Özsarı, A Acar, MV Atalay, T Doğan, AS Rifaioğlu Briefings in bioinformatics 24 (2), bbac627, 2023 | | 2023 |
