2022
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
2021
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.
2020
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.
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.
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.
2019
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. 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
2018
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.Bayrak, H.Oğul, (2017) Microarray missing data imputation using regression, 13th IASTED International Conference on Biomedical Engineering (BIOMED'17), Innsbruck.
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.
E.E.Ozkoc, H.Ogul, (2015), Effect of feature selection on time-series microarray experiment search, Bionengineering Conferece, (BIOENG'15), İstanbul.
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.
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]
2013
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]
2012
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]
2011
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]
2010
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.
2009 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]
2008
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).
2007
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]
2006
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)
2005
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)
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