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Ahmet Sureyya Rifaioglu
Ahmet Sureyya Rifaioglu
Computer Engineering, Middle East Technical University
Verified email at ceng.metu.edu.tr
Title
Cited by
Cited by
Year
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
4242019
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
3512019
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
1662020
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
1432018
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
1352019
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
802021
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
622021
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
28*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
182018
FAIR adoption, assessment and challenges at UniProt
L Garcia, J Bolleman, S Gehant, N Redaschi, M Martin
Scientific data 6 (1), 175, 2019
152019
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
112020
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
72023
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
52024
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
5*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
42022
Deep learning for prediction of drug-target interaction space and protein functions
AS Rifaioğlu
12020
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
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
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
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
2022
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