Prof. Dr. MEHMET VOLKAN ATALAY

Yayın Ağı

Makaleler 46

1. Molecular contrastive learning with graph attention network (MoCL-GAT) for enhanced molecular representation

Dalkıran A., RİFAİOĞLU A. S., ATALAY R., ACAR A. C., DOĞAN T., ATALAY M. V.

BMC Bioinformatics , cilt.27, sa.1, 2026 (SCI-Expanded, Scopus)

2. DTA-GNN: a toolkit for constructing target-specific drug–target affinity datasets and training graph neural networks

Özsari G., RİFAİOĞLU A. S., ACAR A. C., DOĞAN T., ATALAY M. V.

SoftwareX , cilt.34, 2026 (SCI-Expanded, Scopus)

3. Hybrid deep learning models with data fusion approach for electricity load forecasting

Özen S., YAZICI A., ATALAY M. V.

Expert Systems , cilt.42, sa.2, 2025 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

4. Drug Repurposing Approach to Identify Candidate Drug Molecules for Hepatocellular Carcinoma

Baser T., Rifaioglu A. S., ATALAY M. V., Atalay R. C.

International Journal of Molecular Sciences , cilt.25, sa.17, 2024 (SCI-Expanded, Scopus)

5. Online embedding and clustering of evolving data streams

Zubaroglu A., Atalay M. V.

STATISTICAL ANALYSIS AND DATA MINING , cilt.16, sa.1, ss.29-44, 2023 (SCI-Expanded, Scopus)

6. POWER CONSUMPTION FORECASTING BY HYBRID DEEP ARCHITECTURES WITH DATA FUSION

Özen S., ATALAY M. V.

Computing and Informatics , cilt.42, sa.1, ss.126-156, 2023 (SCI-Expanded, Scopus)

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

ÖZSARI G., Rifaioglu A. S., ATAKAN A., DOĞAN T., Martin M. J., Atalay R. C., et al.

BIOINFORMATICS , cilt.38, sa.17, ss.4226-4229, 2022 (SCI-Expanded, Scopus)

8. Data Centric Molecular Analysis and Evaluation of Hepatocellular Carcinoma Therapeutics Using Machine Intelligence-Based Tools

Cetin-Atalay R., Kahraman D. C., Nalbat E., Rifaioğlu A. S., Atakan A., Dönmez A., et al.

JOURNAL OF GASTROINTESTINAL CANCER , cilt.52, sa.4, ss.1266-1276, 2021 (ESCI, Scopus)

9. CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations.

DOĞAN T., Atas H., Joshi V., ATAKAN A., Rifaioglu A. S., NALBAT E., et al.

Nucleic acids research , cilt.49, sa.16, 2021 (SCI-Expanded, Scopus)

10. Crowdsourced mapping of unexplored target space of kinase inhibitors

Cichonska A., Ravikumar B., Allaway R. J., Wan F., Park S., Isayev O., et al.

NATURE COMMUNICATIONS , cilt.12, sa.1, 2021 (SCI-Expanded, Scopus)

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

Rifaioglu A., Atalay R. C., KAHRAMAN D. C., DOĞAN T., Martin M., ATALAY M. V.

Bioinformatics , cilt.37, sa.5, ss.693-704, 2021 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

12. Data stream clustering: a review

Zubaroglu A., Atalay V.

ARTIFICIAL INTELLIGENCE REVIEW , cilt.54, sa.2, ss.1201-1236, 2021 (SCI-Expanded, Scopus)

13. iBioProVis: interactive visualization and analysis of compound bioactivity space

Dönmez A., Rifaioğlu A. S., Acar A. C., Doğan T., Cetin-Atalay R., Atalay V.

BIOINFORMATICS , cilt.36, sa.14, ss.4227-4230, 2020 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

14. DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations

RİFAİOĞLU A. S., NALBAT E., Atalay V., Martin M. J., Cetin-Atalay R., DOĞAN T.

CHEMICAL SCIENCE , cilt.11, sa.9, ss.2531-2557, 2020 (SCI-Expanded, Scopus)

15. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou N., Jiang Y., Bergquist T., Lee A., Kacsoh B., Crocker A., et al.

GENOME BIOLOGY , cilt.20, sa.1, 2019 (SCI-Expanded, Scopus)

16. DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

RİFAİOĞLU A. S., Dogan T., Martin M. J., Cetin-Atalay R., Atalay V.

SCIENTIFIC REPORTS , cilt.9, 2019 (SCI-Expanded, Scopus)

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

Dalkıran A., Rifaioğlu A. S., Martin M. J., Cetin-Atalay R., Atalay M. V., Dogan T.

BMC BIOINFORMATICS , cilt.19, 2018 (SCI-Expanded, Scopus)

18. EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes

Danaci H. F., Cetin-Atalay R., ATALAY M. V.

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY , cilt.16, sa.4, 2018 (SCI-Expanded, Scopus)

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

Rifaioglu A. S., Atas H., Martin M., Cetin-Atalay R., Atalay V., Dogan T.

Briefings in bioinformatics , 2018 (SCI-Expanded, Scopus)

20. Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants

RİFAİOĞLU A. S., Dogan T., Sarac O. S., ERSAHİN T., Saidi R., ATALAY M. V., et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.86, sa.2, ss.135-151, 2018 (SCI-Expanded, Scopus)

21. Multi-task Deep Neural Networks in Protein Function Prediction

RİFAİOĞLU A. S., doğan t., Martin M. J., ATALAY R., ATALAY M. V.

arXiv , 2017 (Hakemsiz Dergi)

22. HandVR: a hand-gesture-based interface to a video retrieval system

Genc S., Bastan M., GÜDÜKBAY U., Atalay V., GÜDÜKBAY U.

SIGNAL IMAGE AND VIDEO PROCESSING , cilt.9, sa.7, ss.1717-1726, 2015 (SCI-Expanded, Scopus)

23. Identification of Novel Reference Genes Based on MeSH Categories

Ersahin T., ÇARKACIOĞLU L., CAN T., Konu O., Atalay V., Cetin-Atalay R.

PLOS ONE , cilt.9, sa.3, 2014 (SCI-Expanded, Scopus)

24. A signal transduction score flow algorithm for cyclic cellular pathway analysis, which combines transcriptome and ChIP-seq data

Isik Z., Ersahin T., Atalay V., AYKANAT C., Cetin-Atalay R.

MOLECULAR BIOSYSTEMS , cilt.8, sa.12, ss.3224-3231, 2012 (SCI-Expanded, Scopus)

25. GOPred: GO Molecular Function Prediction by Combined Classifiers

Sarac O. S., Atalay V., Cetin-Atalay R.

PLOS ONE , cilt.5, sa.8, 2010 (SCI-Expanded, Scopus)

26. Prediction of enzyme classes in a hierarchical approach by using SPMap

Yaman A., Atalay V., Atalay R.

NEW BIOTECHNOLOGY , cilt.27, 2010 (SCI-Expanded, Scopus)

27. Bi-k-bi clustering: mining large scale gene expression data using two-level biclustering

Carkacioglu L., Atalay R. C., KONU KARAKAYALI Ö., Atalay V., CAN T.

INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS , cilt.4, sa.6, ss.701-721, 2010 (SCI-Expanded, Scopus)

28. Subsequence-based feature map for protein function classification

Sarac O. S., Guersoy-Yuezueguellue O., Cetin-Atalay R., Atalay V.

COMPUTATIONAL BIOLOGY AND CHEMISTRY , cilt.32, sa.2, ss.122-130, 2008 (SCI-Expanded, Scopus)

29. Experimental study on the sensitivity of autocalibration to projective camera model parameters

Hassanpour R., Atalay V.

OPTICAL ENGINEERING , cilt.45, sa.4, 2006 (SCI-Expanded, Scopus)

30. Implicit motif distribution based hybrid computational kernel for sequence classification

Atalay V., Cetin-Atalay R.

BIOINFORMATICS , cilt.21, sa.8, ss.1429-1436, 2005 (SCI-Expanded, Scopus)

31. Camera auto-calibration using a sequence of 2D images with small rotations

Hassanpour R., Atalay V.

PATTERN RECOGNITION LETTERS , cilt.25, sa.9, ss.989-997, 2004 (SCI-Expanded, Scopus)

32. Almost autonomous training of mixtures of principal component analyzers

Musa M., de Ridder D., Duin R., Atalay V.

PATTERN RECOGNITION LETTERS , cilt.25, sa.9, ss.1085-1095, 2004 (SCI-Expanded, Scopus)

33. Vision-based continuous Graffiti (TM)-like text entry system

Erdem I., Erdem M., Atalay V., Cetin A.

OPTICAL ENGINEERING , cilt.43, sa.3, ss.553-558, 2004 (SCI-Expanded, Scopus)

34. A hierarchical representation of form documents for identification and retrieval

Duygulu P., Atalay V.

International Journal on Document Analysis and Recognition , cilt.5, sa.1, ss.17-27, 2003 (SCI-Expanded, Scopus)

35. Silhouette-based 3-D model reconstruction from multiple images

Mulayim A., Yilmaz U., Atalay V.

IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS , cilt.33, sa.4, ss.582-591, 2003 (SCI-Expanded, Scopus)

36. Ore-age: a hybrid system for assisting and teaching mining method selection

Guray C., Celebi N., Atalay V., Pasamehmetoglu A.

EXPERT SYSTEMS WITH APPLICATIONS , cilt.24, sa.3, ss.261-271, 2003 (SCI-Expanded, Scopus)

37. An Image-Based Inexpensive 3D Scanner

Yilmaz U., Mülayim A. Y., Atalay V.

International Journal of Image and Graphics , cilt.3, sa.2, ss.235-263, 2003 (ESCI, Scopus)

38. Prediction of protein subcellular localization based on primary sequence data

Ozarar M., Atalay V., Atalay R.

COMPUTER AND INFORMATION SCIENCES - ISCIS 2003 , cilt.2869, ss.611-618, 2003 (SCI-Expanded, Scopus)

39. Texture segmentation using the mixtures of principal component analyzers

Musa M., Duin R., de Ridder D., Atalay V.

COMPUTER AND INFORMATION SCIENCES - ISCIS 2003 , cilt.2869, ss.505-512, 2003 (SCI-Expanded, Scopus)

40. Projection based method for segmentation of human face and its evaluation

Baskan S., Bulut M., Atalay V.

PATTERN RECOGNITION LETTERS , cilt.23, sa.14, ss.1623-1629, 2002 (SCI-Expanded, Scopus)

41. Computer vision based mouse

Erdem A., Erdem E., Yardimci Y., Atalay V., Cetin A. E.

ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings , cilt.4, ss.4178, 2002 (Scopus)

42. Vision-based single-stroke character recognition for wearable computing

Ozer O., Ozun O., Tuzel C., Atalay V., Cetin A.

IEEE INTELLIGENT SYSTEMS & THEIR APPLICATIONS , cilt.16, sa.3, ss.33-37, 2001 (SCI-Expanded)

43. Matching algorithm based on Godel coding scheme

Dicle N., Atalay V.

Proceedings of SPIE - The International Society for Optical Engineering , cilt.3974, ss.576-583, 2000 (SCI-Expanded, Scopus)

44. Subband domain coding of binary textual images for document archiving

Gerek O., Cetin A., Tewfik A., Atalay V.

IEEE TRANSACTIONS ON IMAGE PROCESSING , cilt.8, sa.10, ss.1438-1446, 1999 (SCI-Expanded, Scopus)

45. Repulsive attractive network for baseline extraction on document images

Oztop E., Mulayim A., Atalay V., Yarman-Vural F.

SIGNAL PROCESSING , cilt.75, sa.1, ss.1-10, 1999 (SCI-Expanded, Scopus)

46. A matching algorithm based on linear features

Atalay V., Yilmaz M.

PATTERN RECOGNITION LETTERS , cilt.19, sa.9, ss.857-867, 1998 (SCI-Expanded, Scopus)

Hakemli Bilimsel Toplantılarda Yayımlanmış Bildiriler 66

1. Novel isoxazole- piperazine derivatives inhibit the stemness of HCC cells

NALBAT E., İBİŞ K., ÇALIŞKAN B., BANOĞLU E., ATALAY M. V., ATALAY R.

AASLD-TASL Digital Hepatology Meeting, Ankara, Türkiye, 15 Ocak 2022, ss.5-6, (Tam Metin Bildiri)

2. In vitro validation of drug-target interactions revealed in silico by Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC

NALBAT E., RİFAİOĞLU A. S., DOĞAN T., Martin M. J., Cetin-Atalay R., ATALAY M. V.

AACR Annual Meeting, ELECTR NETWORK, 22 - 24 Haziran 2020, cilt.80, (Özet Bildiri)

3. Comparison of predictive models for forecasting timeseries data

Özen S., Atalay V., YAZICI A.

3rd International Conference on Big Data Research, ICBDR 2019, Cergy-Pontoise, Fransa, 20 - 21 Kasım 2019, ss.172-176, (Tam Metin Bildiri) Sürdürülebilir Kalkınma

4. Online embedding and clustering of data streams

Zubaroǧlu A., Atalay V.

3rd International Conference on Big Data Research, ICBDR 2019, Cergy-Pontoise, Fransa, 20 - 21 Kasım 2019, ss.142-146, (Tam Metin Bildiri)

5. Forecasting of Product Quality Through Anomaly DetectionMehmet Dinç,

Dinc M., ERTEKİN BOLELLİ Ş., Ozkan H., Meydanli C., ATALAY M. V.

2nd International Conference on Digital Transformation and Smart Systems, Ankara, Türkiye, 23 - 25 Ekim 2019, (Tam Metin Bildiri)

6. Receptor-Ligand Binding Affinity Prediction via Multi-Channel Deep Chemogenomic Modeling

Atalay M. V., Rifaioğlu A. S., Atalay R., Doğan T., Martin M.

The International Symposium on Health Informatics and Bioinformatics (HIBIT 2019), İzmir, Türkiye, 17 - 18 Ekim 2019, (Yayınlanmadı)

7. Forecasting of Product Quality Through Anomaly Detection

Dinc M., ERTEKİN BOLELLİ Ş., Ozkan H., Meydanli C., ATALAY M. V.

ECML/PKDD 2019 Workshop on Io Stream for Data Driven Predictive Maintenance, Würzburg, Almanya, 16 Eylül 2019, (Tam Metin Bildiri)

8. iBioProVis: Interactive Visualization and Analysis of Compound Bioactivity Space

Dönmez A., RİFAİOĞLU A. S., ACAR A. C., DOĞAN T., Martin M. J., ATALAY R., et al.

27th Conference on Intellient Systems for Molecular Biology and 18th European Conference on Computational Biology, Basel, İsviçre, 21 - 25 Temmuz 2019, (Özet Bildiri)

9. CROssBAR: Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning”, Oral presentation

Atalay M. V., Doğan T., Atalay R., Nalbat E., Rifaioğlu A. S., Ataş H., et al.

27th Conference on Intelligent Systems for Molecular Biology and 18th European Conference on Computational Biology, Basel, İsviçre, 21 - 25 Temmuz 2019, (Yayınlanmadı)

10. Drug-Target Interaction Prediction with Deep Convolutional Neural Networks Using Compound Images

RİFAİOĞLU A. S., ATALAY M. V., Martin M. J., ATALAY R., Doğan T.

26th Conference on Intelligent Systems for Molecular Biology, Chicago, Amerika Birleşik Devletleri, 6 - 10 Temmuz 2018, (Özet Bildiri)

11. Automated Negative Gene Ontology Based Functional Predictions for Proteins with UniGOPred

Doğan T., RİFAİOĞLU A. S., Saidi R., Martin M. J., ATALAY M. V., ATALAY R.

26th Conference on Intelligent Systems for Molecular Biology, Chicago, Amerika Birleşik Devletleri, 6 - 10 Temmuz 2018, (Özet Bildiri)

12. Investigation of Multi-task Deep Neural Networks in Automated Protein Function Prediction

RİFAİOĞLU A. S., Martin M. J., ATALAY R., ATALAY M. V., Doğan T.

ISMB/ECCB 2017: 25th Annual International Conference on Intelligent Systems for Molecular Biology, Prag, Çek Cumhuriyeti, 21 - 25 Temmuz 2017, (Özet Bildiri)

13. Prediction of Enzymatic Properties of Protein Sequences Based on the EC Nomenclature

DALKIRAN A., Doğan T., RİFAİOĞLU A. S., ATALAY M. V., Martin M. J., ATALAY R.

ISMB/ECCB 2017: 25th Annual International Conference on Intelligent Systems for Molecular Biology, Prag, Çek Cumhuriyeti, 21 - 25 Temmuz 2017, (Özet Bildiri)

14. Prediction of Enzymatic Properties of Protein Sequences Based on the EC Nomenclature

DALKIRAN A., RİFAİOĞLU A. S., Doğan T., ATALAY M. V., Martin M. J., ATALAY R.

10th The International Symposium on Health Informatics and Bioinformatics (HIBIT 2017), Kalkanlı, Kıbrıs (Kktc), 28 - 30 Haziran 2017, ss.37, (Özet Bildiri)

15. Investigation of Multitask Deep Neural Networks for Protein Function Prediction

RİFAİOĞLU A. S., Martin M. J., ATALAY R., ATALAY M. V., Doğan T.

10th The International Symposium on Health Informatics and Bioinformatics (HIBIT 2017), Erdemli, Kıbrıs (Kktc), 28 - 30 Haziran 2017, (Özet Bildiri)

16. EClerize: A Customized Force-Directed Layout Algorithm for Biological Networks with EC Attributes

Danacı H. F., ATALAY R., ATALAY M. V.

GLBIO 2017: Great Lakes Bioinformatics Conference, Şikago, Amerika Birleşik Devletleri, 15 - 17 Mayıs 2017, (Özet Bildiri)

17. UniGOPred: A Large Scale Automated GO Term Annotation System for UniProtKB

RİFAİOĞLU A. S., Doğan T., SARAÇ Ö. S., Saidi R., ATALAY M. V., Martin M. J., et al.

GLBIO 2017: Great Lakes Bioinformatics Conference, Şikago, Amerika Birleşik Devletleri, 15 - 17 Mayıs 2017, (Özet Bildiri)

18. ECPred: An Automated Enzymatic Function Prediction Tool Based on Combination of Different Classifiers

DALKIRAN A., RİFAİOĞLU A. S., Doğan T., ATALAY M. V., Martin M. J., ATALAY R.

GLBIO 2017: Great Lakes Bioinformatics Conference, May 15-17, Şikago, Amerika Birleşik Devletleri, 15 - 17 Mayıs 2017, (Özet Bildiri)

19. UniGOPred and ECPred Automated Function Prediction Tools Based on A Combination of Different Classifiers

Rifaioglu A., Dogan T., SARAÇ Ö. S., ATALAY M. V., Martin M., ATALAY R.

ISMB Automated FunctionPrediction-SIG, 11 Temmuz 2015

20. Discriminative Modeling of Cell Signaling as Bayesian Networks

Yaman A. G., ACAR A. F., Atalay V., Cetin-Atalay R.

2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, Nikaragua, 7 - 09 Nisan 2014, ss.1617, (Tam Metin Bildiri)

21. Genetic variants within endotoxin signaling pathway association with asthma and atopy phenotypes

ŞAHİNER Ü. M., YAVUZ S., Buyuktiryaki B., BİRBEN E., Topaloglu E., TUNCER A., et al.

31st Congress of the European-Academy-of-Allergy-and-Clinical-Immunology (EAACI), Geneva, İsviçre, 16 - 20 Haziran 2012, cilt.67, ss.469, (Özet Bildiri)

22. Association of asthma with polymorphisms in the endotoxin signaling pathway

ŞAHİNER Ü. M., YAVUZ S., Buyuktiryaki B., BİRBEN E., Topaloglu E., TUNCER A., et al.

31st Congress of the European-Academy-of-Allergy-and-Clinical-Immunology (EAACI), Geneva, İsviçre, 16 - 20 Haziran 2012, cilt.67, ss.469-470, (Özet Bildiri)

23. Single nucleotide polymorphisms in the endotoxin signaling pathway and their relationship with in vitro IgE synthesis

ŞAHİNER Ü. M., YAVUZ S., Buyuktiryaki B., BİRBEN E., Topaloglu E., Yaman A., et al.

31st Congress of the European-Academy-of-Allergy-and-Clinical-Immunology (EAACI), Geneva, İsviçre, 16 - 20 Haziran 2012, cilt.67, ss.467-468, (Özet Bildiri)