Ahmet Sureyya Rifaioglu
Ahmet Sureyya Rifaioglu
Computer Engineering, Middle East Technical University
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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
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
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
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
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
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
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
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
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
FAIR adoption, assessment and challenges at UniProt
L Garcia, J Bolleman, S Gehant, N Redaschi, M Martin
Scientific data 6 (1), 175, 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
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
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
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
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
Deep learning for prediction of drug-target interaction space and protein functions
AS Rifaioğlu
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
Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks
A Ünlü, E Çevrim, A Sarıgün, H Çelikbilek, HA Güvenilir, A Koyaş, ...
arXiv preprint arXiv:2302.07868, 2023
Hnet-DTI: Incorporating heterogeneous information network for drug-target interaction prediction
G Özsarı, AS Rifaioğlu, T Doğan, V Atalay
15th International Symposium on Health Informatics and Bioinformatics HIBIT …, 2022
Disease Centric Large Scale De Novo Design of Drug Candidate Molecules with Graph Generative Deep Adversarial Networks
A Ünlü, E Çevrim, A Sarıgün, H Ataş, A Koyaş, H Çelikbilek, ...
15th International Symposium on Health Informatics and Bioinformatics HIBIT …, 2022
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