D.D. Sener, H. Ogul, S. Basak, (2022), Text-based experiment retrieval in genomic databases. Journal of Information Science (in press). https://doi.org/10.1177/01655515221118670

R. Assidicky, U.M. Tokat, I.O. Tarman, O. Saatci, P.G. Ersan, U. Raza, H. Ogul, Y. Riazalhosseini, T. Can, O. Sahin, (2022), Targeting HIF1-alpha/miR-326/ITGA5 axis potentiates chemotherapy response in triple-negative breast cancer, Breast Cancer Research and Treatment 193, 331-348.

T. Bayrak, Z. Çetin, E. Saygılı, H. Ogul, (2022), Identifying the tumor location-associated candidate genes in development of new drugs for colorectal cancer using machine-learning-based approach. Medical and Biological Engineering and Computing 60, 2877–2897.

T. Aşuroglu, H. Ogul, (2022), A deep learning approach for Parkinson’s Disease severity assessment, Health and Technology 12 (5), 943-953.




T. Asuroglu, H. Ogul, (2021), A Deep Learning Approach for Sepsis Monitoring via Severity Score Estimation, Computer Methods and Programs in Biomedicine 198, 105816.


T. Bayrak, H. Ogul, (2021). Computer-aided diagnosis of sleep apnea using gene expression. Health and Technology 11, p. 941–952.


Z. Çetin, T. Bayrak, H. Ogul, E.I. Saygili, E.K. Akkol, (2021), Predicted SARS-CoV-2 miRNAs associated with epigenetic viral pathogenesis and the detection of new possible drugs for Covid-19, Current Drug Delivery 18 (10), 1595-1610.


A. Paker, H. Ogul, (2021). A Deep Learning Model for MicroRNA-Target Binding. In Elloumi, Mourad (Eds.), Deep Learning for Biomedical Data Analysis: Techniques, Approaches, and Applications. Springer. ISSN 978-3-030-71675-2. p. 61–79.


D. Chand, H. Ogul, (2021), A Framework for Lecture Video Segmentation from Extracted Speech Content, 19th IEEE World Symposium on Applied Machine Intelligence and Informatics (SAMI'2021), Herl’any.

T. Balci, H. Ogul, (2021). Predicting Bank Return on Equity (ROE) using Neural Networks. 19th IEEE World Symposium on Applied Machine Intelligence and Informatics (SAMI'2021), Herl’any.




A. Baldominos, H. Oğul, R. Colomo-Palacios, J. Sanz-Morenoc, J. Gómez-Pulidod, (2020), Infection prediction using physiological and social data in social environments, Information Processing and Management 57, 3, 102213.

A. Baldominos, A. Puello, H. Oğul, T. Aşuroğlu and R. Colomo-Palacios, (2020), Predicting Infections Using Computational Intelligence – A Systematic Review, IEEE Access, vol. 8, pp. 31083-31102, 2020.


C. Cabıoğlu, H. Oğul (2020), Computer-Aided Breast Cancer Diagnosis from Thermal Images using Transfer Learning, 8th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO'2020), Granada, Lecture Notes in Computer Science 12108, 716-726.

B. Erdoğan, H. Oğul, (2020), Objective pain assessment using vital signs, 10th International Symposium on Frontiers in Ambient and Mobile Systems (FAMS'2020), Warsaw, Procedia Computer Science 170, 947-952.


S. Agziyagli, H. Ogul, (2020), Multi-level lecture video classification using text content, 14th IEEE International Conference on Application of Information and Communication Technologies (AICT2020), Tashkent.


D. Chand, H. Oğul, (2020), Content-Based Search in Lecture Video: A Systematic Literature Review, 3rd International Conference on Information and Computer Technologies, San Jose.



I. Haberal, H. Oğul, (2019), Prediction of protein metal binding sites using deep neural networks, Molecular Informatics 38(7).

T. Bayrak, H. Oğul,  (2019), A new approach for predicting the exact value of gene expression: Two-way collaborative filtering, Current Bioinformatics 14(6), s 480- 490 .

K. Acici, T.Asuroglu, C. B. Erdas, H. Ogul (2019). T4SS Effector Protein Prediction with Deep Learning. Data 4(1). 


H. Ogul, A. Baldominos, T. Asuroglu, R. Colomo-Palacios, (2019), On computer-aided prognosis of septic shock from vital signs, 32rd IEEE International Symposium on Computer-Based Medical Systems (IEEE-CBMS'19), Cordoba.

A. Baldominos, H. Ogul, R. Colomo-Palacios, (2019), Infection diagnosis using biomedical signals in small data scenarios, 32rd IEEE International Symposium on Computer-Based Medical Systems (IEEE-CBMS'19), Cordoba.


A. Paker, H. Ogul (2019). mirLSTM: A Deep Sequential Approach to MicroRNA Target Binding Site Prediction. Communications in Computer and Information Science  1062, s 38- 44 




K. Açıcı, Ç.B. Erdaş, T. Aşuroğlu, H. Oğul, (2018), HANDY: A benchmark dataset for context-awareness via wrist-worn motion sensors, Data 3, 24.

T. Aşuroğlu, K. Açıcı, Ç. B. Erdaş, M. K. Toprak, H. Erdem, H. Oğul, (2018), Parkinson's disease monitoring from gait analysis via foot-worn sensors, Biocybernetics and Biomedical Engineering 38, 760-772.

D.D.Şener, D.Santoni, G.Fellici, H.Oğul, (2018), A content-based retrieval framework for whole metagenome sequencing samples, Journal of Integrative Bioinformatics 15(4).

E.Sümer, S.Sümer, H.Oğul, (2018), A novel computer vision-based advertisement system for individual marketing, Technical Gazette 25, 5(2018), 1485-1491.

H. Ogul. (2018), ALoT: A time-series similarity measure based on alignment of textures. 19th Int Conf on Intelligent Data Engineering and Automated Learning (IDEAL'18), Madrid.

E. Sümer, M. Engin, M. Ağıldere, H. Oğul, (2018), Monitoring Nodule Progression in Chest X-ray Images, Pamukkale University Journal of Engineering Sciences 24, 934 - 941.

C.B. Erdaş, T. Asuroglu, K. Acici, H. Ogul, (2018), Aktivite Tanımada Yapay Sinir Ağları ve Genetik Programlama Yöntemlerinin Karşılaştırılması. Akıllı Sistemler ve Uygulamaları Dergisi 1(1):62-66.

T. Bayrak, H. Ogul, (2018), Data Integration for gene expression prediction, 3rd Int Conf on Artificial Intelligence and Data Processing (IDAP 2018), Malatya.

N. Yardim, S. Kocadag, S. Akgun, G. Pekcan, G. Kiziltan, E. Aksoydan, E. Karaagaoglu, H. Ogul, (2018), Gaziantep Beslenme ve Sağlik Araştirmasi (GBSA) – 2017, 2. International Public Health Congress, Antalya.


E.E.Özkoç, H.Oğul, (2017), Content-based search on time-series microarray databases using clustering-based fingerprints, Current Bioinformatics 12, 398-405.

K.Açıcı, Ç.B.Erdaş, T.Aşuroğlu, M.K.Toprak, H.Erdem, H.Oğul,  (2017), A Random Forest method to detect Parkinson's Disease via gait analysis, 6th Mining Humanistic Data Workshop (at EANN'17), Athens.

E.Corapcioglu, H.Oğul, (2017), Exploiting active microRNA interactions for diagnosis from expression profiling experiments. 30th IEEE International Symposium on Computer-Based Medical Systems (IEEE-CBMS'17), Thessaloniki.

İ.Haberal, H.Oğul, (2017) DeepMBS: Prediction of protein metal binding-site using deep learning networks, 4th International Conference on Mathematics and Computers in Sciences and Industry (MCSI 2017), Corfu Island, Greece.

H.Oğul, Ç.B.Erdaş, K.Açıcı, T.Aşuroğlu, (2017) HANDY: A benchmark set for mobile context-awareness. 7th ACM Conference on Digital Health, London.

K. Açıcı, C.B. Erdaş, T. Aşuroğlu, M.K. Toprak, H. Erdem, H. Oğul, (2017), Wearable Solutions for Parkinson's Disease Monitoring. 10th Int Sym on Health Informatics and Bioinformatics (HIBIT'17), Kıbrıs.

T.Bayrak, H.Oğul, (2017) Microarray missing data imputation using regression, 13th IASTED International Conference on Biomedical Engineering (BIOMED'17), Innsbruck.

K.Acici, T.Asuroglu, H.Oğul (2017), Information retrieval in metal music subgenres, 25th IEEE Signal Processing and Communications Applications Conference (SIU 2017), Antalya.

N.Çelik, H.Oğul (2017), A web application for content-based geographic image retrieval, 25th IEEE Signal Processing and Communications Applications Conference (SIU 2017), Antalya.

E.Corapcioglu, H.Oğul (2017), A medical decision support system proposal supported by genomic analysis, 25th IEEE Signal Processing and Communications Applications Conference (SIU 2017), Antalya.


H.Oğul, (2016), Content-Based Retrieval of Microarray Experiments, in Pattern Recognition in Computational Molecular Biology: Techniques and Approaches (eds M. Elloumi, C. S. Iliopoulos, J. T. L. Wang and A. Y. Zomaya), John Wiley & Sons, Inc, Hoboken, NJ, USA. 

H.Ogul , B.B.Ogul, A.M.Agildere, T.Bayrak,  E. Sumer (2016) Eliminating rib shadows in chest radiographic images providing diagnostic assistance, Computer Methods and Programs in Biomedicine 27, 174-184.

D.Dede, H.Oğul, (2016), Retrieving relevant time-course experiment: A study on Arabidopsis microarrays, IET Systems Biology 10, 87-93.

H.Ogul, E.Tuncer, (2016), MicroRNA expression prediction: regression from regulatory elements, Biocybernetics and Biomedical Engineering 36, 89-94. 

T.Asuroglu, K. Acici, C.B. Erdas, H. Ogul, (2016), Texture of Activities: Exploiting Local Binary Patterns for Accelerometer Data Analysis, 12th International Conference on Signal-Image Technology and Internet-Based Systems (SITIS 2016), Naples.

H.Ogul, B.Kirmaci, (2016) Lyrics mining for music meta-data estimation, 5th Mining Humanistic Data Workshop (at AIAI'16) Thessaloniki.

C.B.Erdas, I.Atasoy, K.Acici, H.Ogul, (2016) Integrating features for accelerometer-based activity recognition, 7th International Conference on Emerging Ubiquitous Systems and Pervasive Networks (EUSPN 2016), London.

M.Igdeli, A.Yilmaz, H.Ogul, (2016), Sequence analysis to predict microRNA chemotherapy resistance, 8th IEEE International Conference on Intelligent Systems (IEEE-IS'16) Sofia.

K.Narci, H.Oğul, M.Akkaya, (2016), Sequence-based microRNA clustering, International Conference on Bioinformatics Models, Methods and Algorithms, (BIOSTEC'16) Roma.

B.B.Oğul, H.Oğul, E.Sümer, (2016), Context-sensitive model learning for lung nodule detection, 24th IEEE Signal Processing and Communications Applications Conference (SIU 2015), Zonguldak.

M. Dikmen, K. Açıcı, H. Oğul (2016), Bakteriyel Tip IV Protein Efektörlerin Tespiti için İşlemsel Yaklaşımlar, Akıllı Sistemlerde Yenilikler ve Uygulamaları Sempozyumu (ASYU'16), Duzce.


K.Açıcı, Y.K.Terzi, H.Oğul, (2015), Retrieving relevant experiments: the case of microRNA microarrays, Biosystems 134, 71-78.

E.Corapcioglu, H.Oğul, (2015), miSEA: microRNA set enrichment analysis, Biosystems 134, 37-42.

B.B. Oğul, E. Sümer and H. Oğul, (2015), Unsupervised Rib Delineation In Chest Radiographs By An Integrative Approach, 11th International Conference on Computer Vision Theory and Applications (VISAPP'15), Berlin.

B.Kırmacı, H. Oğul, (2015) Evaluating text features for lyrics-based songwriter prediction, IEEE 19th International Conference on Intelligent Engineering Systems (INES'15), Bratislava.

M.Engin, H.Ogul, E.Sümer, (2015), An Evaluation of Image Registration Methods for Chest Radiographs, SAI Intelligent Systems Conference (IntelliSys'15), London, UK.

K.Açıcı, H.Oğul, (2015), Inferring Microarray Relevance By Enrichment Of Chemotherapy Resistance-Based microRNA sets. IEEE 19th International Conference on Intelligent Engineering Systems (INES'15). Bratislava.

D.Dede, H.Oğul, (2015), Inferring Similarity between Time-Series Microarrays: A Content-based Approach, 2nd IEEE International Conference on Cybernetics (CYBCONF 2015), Gdynia, Poland.

S.Kucukbay, H. Oğul, (2015), Predicting Metal-Binding Sites of Protein Residues, 1st International Workshop on Biological, Chemical and Physical Computations (FedCIS'15), Lodz, Poland.

E.E.Ozkoc, H.Ogul, (2015), Effect of feature selection on time-series microarray experiment search, Bionengineering Conferece, (BIOENG'15), İstanbul.

H.Oğul, M.E.Tuncer (2015), Predicting microRNA expression from sequence. IFMBE Proceedings 45, 602-604

K.Açıcı, H.Oğul, (2015), Comparison of Similarity Metrics in Microarray Experiment Retrieval, 23rd IEEE Signal Processing and Communications Applications Conference (SIU 2015), Malatya.

B.Kırmacı, H.Oğul, (2015), Author Recognition from Lyrics, 23rd IEEE Signal Processing and Communications Applications Conference (SIU 2015), Malatya.


D.Dede, H.Oğul, (2014), TriClust: A tool for cross-species analysis of gene regulation,
Molecular Informatics 33, 382 – 387.


H.Oğul, (2014), Computational Prediction of MicroRNA Function and Activity, Book Chapter in "miRNomics: MicroRNA Biology and Computational Analysis" Series: Methods in Molecular Biology, Vol. 1107, 243-256, Springer. [link]


İ.Cüceloğlu, H.Oğul, (2014), Automated categorization of scanned bank documents from extracted text content, 10th International Conference on Knowledge Management, November 24-26, Antalya, Turkey. [pdf]


İ.Cüceloğlu, H.Oğul, (2014), Detecting handwritten signatures in scanned documents, Computer Vision Winter Workshop (CVWW'14), Krtiny, Czech Republic. [pdf]


A.Hayran, E.E.Özkoç, H.Oğul, (2014), Content-based search in time-series microarray databases. 5th International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD'14), Munich, Germany. [pdf]


K.Açıcı, D.D.Şener, H.Oğul, (2014) Sensitive Prediction of Bacterial Type IV Effectors, 18th Annual Biomedical Engineering Conference (BIYOMUT'14), İstanbul.

T.Bayrak, H.Oğul, (2014) Classification of Patients with Heart Failure, 18th Annual Biomedical Engineering Conference (BIYOMUT'14), İstanbul.


İ.Haberal, H.Oğul, (2014), Detection of microRNA clusters associated with prostate cancer. 22nd IEEE Signal Processing and Communications Applications Conference (SIU 2014), Trabzon. [pdf]


H.Oğul, (2014), Functional landscape of public gene expression repositories, 3. International Workshop on Translational Bioinformatics and Health Informatics, İzmir. [pdf]




H.Oğul, A.Kalkan, S.U.Umu, M.S.Akkaya, (2013), TRAINER: A general-purpose trainable short biosequence classifier, Protein & Peptide Letters 20, 1108-1114. [link]


M.Engin, H.Oğul, (2013), Analysis of the EEG Signals to Infer Whether the Brain Is in Planning or Relaxing State, 13th National Congress on Medical Technologies (TIPTEKNO'13), Antalya, Turkey. [pdf]


E.Yalnız, H.Oğul, (2013), A pattern classification application for bank marketing, 8th International Statistics Congress (ISTKON'13), Antalya, Turkey. [pdf]


H.Oğul, G.S.Özcan (2013), A framework for integrative analysis of transcriptional and post-transcriptional gene regulation, 7th IEEE International Conference on Application of Information and Communication Technologies (AICT'13), Baku, Azerbeycan. [pdf]


D.Dede, H.Oğul, (2013), A three-way clustering approach to cross-species gene regulation analysis, 7th IEEE International Symposium on INnovations in Intelligent SysTems and Applications (INISTA'13), Albena, Bulgaria. [pdf]


D.Ölçer, H.Oğul, (2013), Clustering microRNAs from sequence and time-series expression, 5th International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies (BIOTECHNO'13), Lisboa, Portugal. [pdf]


H.Oğul, O.Altındağ, (2013), Integrating microRNA and mRNA expression data for cancer classification, 2nd International Conference on Pattern Recognition Applications and Methods (ICPRAM'13), Barcelona, Spain. [pdf]




H.Oğul, E.Ekmekçiler, (2012), Two-way colloborative filtering on semantically enhanced movie ratings, 34th Int Conference on Information Technology Interfaces (ITI'2012), Cavtat, Croatia. [pdf]


B.B.Oğul, Y.Y.Tuncel, S.U.Umu, M.S.Akkaya, H.Oğul, (2012), mmDB: a repository of paired microRNA-messengerRNA expression profiles, 7th International Sympoisum on Health Informatics and Bioinformatics (HIBIT'2012), Ürgüp, Turkey. [pdf]




H.Oğul, M.S.Akkaya, (2011), Data integration in functional analysis of microRNAs, Current Bioinformatics 6, 462-472. [link] [pdf-early version]


H.Oğul, S.U.Umu, Y.Y.Tuncel, M.S.Akkaya, (2011), A probabilistic approach to microRNA-target binding, Biochemical and Biophysical Research Communications 413, 111-115. [link]


H.Oğul, S.U.Umu, Y.Y.Tuncel, M.S.Akkaya, (2011), A probabilistic method for prediction of microRNA-target interactions, 3rd Int.Conf. on Neural Computation Theory and Applications, NCTA 2011, Paris, France. [pdf]




H.Oğul, (2010), MicroRNA informatics: challenges and opportunities, 1st International IFIP Conference on Bioinformatics (IFIP-BIO’10), Surat, India.


H.Oğul, Ç.Beyan, Ö.Eren, K.Yıdız, T.Erçelebi, B.Sönmez, (2010), MicroRNA target recognition from compositional features of aligned microRNA-mRNA dublexes, Int. Sym on Innovations in Intelligent Systems and Applications, Kayseri, Turkey. [pdf]


M.Gök, A.T.Özcerit, H.Oğul, (2010), Predicting hiv protease cleavage site using support vector machines with physicochemical properties, Int. Sym on Innovations in Intelligent Systems and Applications, Kayseri, Turkey.



H.Oğul, J.Salojarvi, P.Jaspers, A.Ajanki, M.Brosche, J.Kangasjarvi, S.Kaski, (2009), Exploring transcription factor target gene relationships by condition dependent module networks,, 17th International Conference on Intelligent Systems for Molecular Biology (ISMB’09), Stockholm, Sweden.


J.Salojarvi, H.Oğul, P.Jaspers, A.Ajanki, M.Brosche, J.Kangasjarvi, S.Kaski, (2009), Inferring target genes of transcription factors by probabilistic modeling,, Plant ROS Meeting (ROS’09), Helsinki, Finland.


H.Oğul (2009), Variable context Markov chains for HIV protease cleavage site prediction, Biosystems 96, 3, 246-250. [link]




Ç.Beyan, H.Oğul, (2008), A fuzzy kNN aprroach for cancer diagnosis with microarray gene expression data, Proceedings of 3rd International Sympoisum on Health Informatics and Bioinformatics (HIBIT'2008). [pdf]


H.Oğul, (2008), Prediction of disulfide connectivity patterns from protein sequence, Proceedings of International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC'08). [pdf]


A.C.Polatkan, H.Oğul, H.Sever, (2008), A data fusion approach in remote homology detection, Proceedings of International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies (BIOTECHNO'08). [pdf]


Ö.Eren, H.Oğul, (2008) Automated classification of allergen proteins, Proceedings of 14th Annual Biomedical Engineering Conference (BIYOMUT'08).




H.Oğul, E.Mumcuoğlu, (2007), Subcellular localization prediction with new protein encoding schemes, IEEE/ACM Transactions on Computational Biology and Bioinformatics 4, 227-232. [link]


H.Oğul, E.Mumcuoğlu, (2007), A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets, Biosystems 87, 75-81. [link]




H.Oğul, E.Mumcuoğlu, (2006), SVM-based detection of distant protein structural relationships using pairwise probabilistic suffix trees, Computational Biology and Chemistry 30, 292-299. [link]


H.Oğul, E.Mumcuoğlu, (2006), Protein solvent accessibility prediction using support vector machines and sequence conservations, Artificial Intelligence and Neural Networks, LNAI 3949, 141-148. [link]


H.Oğul, PhD Thesis, (2006) Computational Representation of Protein Sequences for Homology Detection and Classification, METU Informatics Institute, Department of Information Systems, Ankara, Turkey.(Advisor: Assoc.Prof.Dr.Erkan Mumcuoğlu)




H.Oğul, E.Mumcuoğlu, (2005), Discriminative remote homology detection using maximal unique sequence matches, Advances in Intelligent Data Analysis, LNCS 3546, 283-292. [link]


H.Oğul, E.Mumcuoğlu, (2005), Prediction of protein subcellular localization using support vector machines and probabilistic suffix trees, Proceedings of 1st International Symposium on Health Informatics and Bioinformatics (HIBIT'05 56-62).


before 2005


H.Oğul, E.Mumcuoğlu, (2004), Finding maximal unique secondary structure matches in protein families (in Turkish), Proceedings of 10th Annual Biomedical Engineering Conference (BIYOMUT'04 107-113).


H.Oğul, K. Erciyes, (2001), Identifying all local and global alignments between two DNA sequences, Proceedings of 16th International Symposium on Computer and Information Sciences (ISCIS'01 468-475).


H.Oğul, K. Erciyes, (2001), Parallel Sequence Alignment Using a Cluster of Workstations, Ege Univ., International Computing Institute.


H.Oğul, MS Thesis, (2001) Algorithms for DNA Sequence Comparison and Alignment, Ege Univ., International Computing Institute, Department of Information Technologies, İzmir, Turkey.(Advisor: Prof.Dr.Kayhan Erciyes)