Skip to Main Content
Muhammad (Oguzhan) Kulekci
Associate Professor
Computer Science and Software Engineering

Oguzhan Kulekci, Ph.D.

Contact Info

513-529-3695
McVey Data Science Building 282
Personal Website

Biographical Information

Dr. Kulekci received his Ph.D. in Computer Science from Sabanci University, Türkiye, following BSc and MSc degrees in Computer Engineering and Biomedical Engineering from Boğaziçi University, Türkiye. He conducted postdoctoral research at Texas A&M University under the supervision of Jeffrey Scott Vitter.

Early in his career, he worked for over a decade as a cryptography engineer at the National Research Institute of Electronics and Cryptology of Türkiye, focusing on the efficient implementation and security analysis of privacy algorithms and protocols in both hardware and software. In 2015, he transitioned to academia as an associate professor at Istanbul Technical University, where he was promoted to full professor of Computer Science in 2019.

Before joining Miami, Dr. Kulekci served as a visiting professor in the Department of Computer Science at Indiana University Bloomington from 2022 to 2025. He has actively contributed to international conferences in algorithm engineering and combinatorial text algorithms, serving on various program committees. Additionally, he holds several patents, some of which have been licensed to industry partners. He has also held administrative roles and actively promoted industry-academia collaborations and technology transfer initiatives.

Education

  • Ph.D. Electrical Engineering and Computer Science, Sabanci University, Turkey (2006)

Research Interests

  • Theoretical Computer Science
  • Algorithms
  • Data Compression and Coding
  • Security/Privacy
  • Bioinformatics

Courses Taught

  • Advanced Algorithms (Spring'25)
  • Systems Programming-I (Spring'25)

Publications

Journal Publications:

  1. Mert Onur Cakiroglu, Hasan Kurban, Parichit Sharma, M Oguzhan Kulekci, Elham Khorasani Buxton, Maryam Raeeszadeh-Sarmazdeh, and Mehmet M Dalkilic. An extended de bruijn graph for feature engineering over biological sequential data. Machine Learning: Science and Technology, 5(3):035020, 2024
  2. Negar Golzar, Amir Aghabaioglou, Elif Altunok, and M. Oguzhan Kulekci. A framework for assessing a country’s scientific productivity based on published articles by scientists affiliated with that country. Information Discovery and Delivery, accepted, 2023
  3. Sahar Hooshmand, Paniz Abedin, M. Oguzhan Külekci, and Sharma V. Thankachan. I/O– efficient data structures for non-overlapping indexing. Theoretical Computer Science, 857:1–7, 2021
  4. Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, M Oguzhan Kulekci, David P Woodruff, and S Cenk Sahinalp. Sketching algorithms for genomic data analysis and querying in a secure enclave. Nature Methods, 17(3):295–301, 2020
  5. Domenico Cantone, Simone Faro, and M. Oguzhan Külekci. The order-preserving pattern matching problem in practice. Discrete Applied Mathematics, 274:11–25, 2020
  6. Paniz Abedin, M. Oguzhan Külekci, and Shama V. Thankachan. A survey on shortest unique substring queries. Algorithms, 13(9):224, 2020
  7. Muhammed Oguzhan Külekci and Yasin Öztürk. Applications of non-uniquely decodable codes to privacy-preserving high-entropy data representation. Algorithms, 12(4):78, 2019
  8. Jan Voges, Ali Fotouhi, Jörn Ostermann, and M. Oğuzhan Külekci. A two-level scheme for quality score compression. Journal of Computational Biology, 25(10):1141–1151, 2018
  9. M. Oğuzhan Külekci and Sharma V. Thankachan. Range selection and predecessor queries in data aware space and time. Journal of Discrete Algorithms, 43:18 – 25, 2017
  10. Mahmut Samil Sağiroğlu and M. Oğuzhan Külekci. A system architecture for efficient trans- mission of massive dna sequencing data. Journal of Computational Biology, 24(11):1081–1088, 2017. PMID: 28414531
  11. Tamanna Chhabra, Simone Faro, M. Oğuzhan Külekci, and Jorma Tarhio. Engineering order- preserving pattern matching with SIMD parallelism. Software: Practice and Experience, 47(5):731– 739, 2017
  12. Pınar Kavak, Bayram Yüksel, Soner Aksu, M. Oguzhan Kulekci, Tunga Güngör, Faraz Hach, S. Cenk Şahinalp, Turkish Human Genome Project, Can Alkan, and Mahmut Şamil Sağıroğlu. Robustness of massively parallel sequencing platforms. PLOS ONE, 10(9):1–11, 09 2015
  13. Atalay Mert Ileri, M. Oguzhan Külekci, and Bojian Xu. A simple yet time-optimal and linear- space algorithm for shortest unique substring queries. Theoretical Computer Science, 562:621– 633, 2015
  14. Simone Faro and M. Oğuzhan Külekci. Fast and flexible packed string matching. Journal of Discrete Algorithms, 28:61–72, 2014
  15. M. Oğuzhan Külekci, Jeffrey Scott Vitter, and Bojian Xu. Efficient maximal repeat finding using the burrows-wheeler transform and wavelet tree. IEEE/ACM Transactions on Compu- tational Biology and Bioinformatics, 9(2):421–429, 2012
  16. M. Oğuzhan Külekci, Jeffrey Scott Vitter, and Bojian Xu. Fast pattern matching via k-bit filtering based text decomposition. The Computer Journal, 55(1):62–68, 2012
  17. M. Oğuzhan Külekci. On scrambling the burrows–wheeler transform to provide privacy in lossless compression. Computers & Security, 31(1):26–32, 2012
  18. M. Oğuzhan Külekci. BLIM: A new bit-parallel pattern matching algorithm overcoming com- puter word size limitation. Mathematics in Computer Science, 3(4):407–420, 2010

Conference Publications:

  1. Sharma Thankachan Arghya Kusum Das, M. Oguzhan Kulekci. Efficient encodings for privacy- preserving data storage and transmission. In Proceedings of the IEEE International Conference on Big Data. IEEE, 2024
  2. M Oguzhan Kulekci. Randomized data partitioning with efficient search, retrieval and privacy- preservation. In The 29th International Computing and Combinatorics Conference (COCOON), 2023
  3. M. Oguzhan Kulekci. Counting with prediction: Rank and select queries with adjusted anchor- ing. In 2022 Data Compression Conference (DCC), pages 409–418, 2022
  4. Arghya Kusum Das, M. Oguzhan Kulekci, and Sharma Thankachan. Memory efficient fm-index construction for reference genomes. In 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022
  5. Burak Cardak, Levent Carkacioglu, and M Oguzhan Kulekci. Tile selection-based H265/HEVC coding. In Proceedings of IEEE 16th International Conference on Signal Image Technology & Internet Based Systems (SITIS), France, 2022. to appear
  6. Arnab Ganguly, Daniel Gibney, Sahar Hooshmand, M. Oguzhan Külekci, and Sharma V. Thankachan. Fm-index reveals the reverse suffix array. In 31st Annual Symposium on Com- binatorial Pattern Matching, CPM 2020, June 17-19, 2020, Copenhagen, Denmark, pages 13:1–13:14, 2020
  7. M. Oguzhan Külekci, Yasin Öztürk, Elif Altunok, and Can Altinigne. Enumerative data com- pression with non-uniquely decodable codes. In Proceedings of Prague Stringology Conference, 2020
  8. SimoneFaro,DomenicoCantone,andM.OguzhanKülekci.Shape-preservingpattern–matching. In 21st Italian Conference on Theoretical Computer Science, ICTCS 2020, September 14-16, 2020, Ischia, Italy, pages 13:1–13:14, 2020
  9. M. Oğuzhan Külekci, Ismail Habib, and Amir Aghabaiglou. Privacy-preserving text similar- ity via non-prefix-free codes. In Giuseppe Amato, Claudio Gennaro, Vincent Oria, and Mi- los Radovanovic, editors, Similarity Search and Applications - 12th International Conference, SISAP 2019, Newark, NJ, USA, October 2-4, 2019, Proceedings, volume 11807 of Lecture Notes in Computer Science, pages 94–102. Springer, 2019
  10. Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, M. Oguzhan Külekci, David P. Woodruff, and Süleyman Cenk Sahinalp. Sketching algorithms for genomic data analysis and querying in a secure enclave. In Lenore J. Cowen, editor, Research in Computational Molecular Biology - 23rd Annual International Conference, RECOMB 2019, Washington, DC, USA, May 5-8, 2019, Proceedings, volume 11467 of Lecture Notes in Computer Science, pages 302–304. Springer, 2019
  11. Sahar Hooshmand, Paniz Abedin, M. Oguzhan Külekci, and Sharma V. Thankachan. Non- Overlapping Indexing - Cache Obliviously. In Gonzalo Navarro, David Sankoff, and Binhai Zhu, editors, Annual Symposium on Combinatorial Pattern Matching (CPM 2018), volume 105 of Leibniz International Proceedings in Informatics (LIPIcs), pages 8:1–8:9, Dagstuhl, Germany, 2018. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik
  12. M. Oguzhan Külekci. An Ambiguous Coding Scheme for Selective Encryption of High Entropy Volumes. In Gianlorenzo D’Angelo, editor, 17th International Symposium on Experimental Al- gorithms (SEA 2018), volume 103 of Leibniz International Proceedings in Informatics (LIPIcs), pages 7:1–7:13, Dagstuhl, Germany, 2018. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik
  13. Mehmet Akif Aydogmus and M. Oguzhan Külekci. Optimizing packed string matching on AVX2 platform. In Hermes Senger, Osni Marques, Rogério Eduardo Garcia, Tatiana Pinheiro de Brito, Rogério Iope, Silvio Luiz Stanzani, and Veronica Gil Costa, editors, High Performance Computing for Computational Science - VECPAR 2018 - 13th International Conference, São Pedro, Brazil, September 17-19, 2018, Revised Selected Papers, volume 11333 of Lecture Notes in Computer Science, pages 45–61. Springer, 2018
  14. Jan Voges, Ali Fotouhi, Jörn Ostermann, and M. Oğuzhan Külekci. A two-level scheme for quality score compression. In Proceedings of the 2018 International Conference on Bioinfor- matics and Computational Biology, pages 161–167. IEEE, 2018
  15. Ali Fotouhi, Mina Majidi, and M. Oguzhan Külekci. Quality assessment of high-throughput DNA sequencing data via range analysis. In Ignacio Rojas and Francisco M. Ortuño Guzman, editors, Bioinformatics and Biomedical Engineering - 6th International Work-Conference, IWB- BIO 2018, Granada, Spain, April 25-27, 2018, Proceedings, Part I, volume 10813 of Lecture Notes in Computer Science, pages 429–438. Springer, 2018
  16. Eren Kocaaga and M. Oguzhan Külekci. Security analysis on the ADS-B technology. In 25th Signal Processing and Communications Applications Conference, SIU 2017, Antalya, Turkey, May 15-18, 2017, pages 1–4, 2017
  17. M. Oguzhan Külekci. Inverse range selection queries. In Shunsuke Inenaga, Kunihiko Sadakane, and Tetsuya Sakai, editors, String Processing and Information Retrieval - 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings, volume 9954 of Lecture Notes in Computer Science, pages 166–177, 2016
  18. Simone Faro and M. Oguzhan Külekci. Efficient algorithms for the order preserving pattern matching problem. In Riccardo Dondi, Guillaume Fertin, and Giancarlo Mauri, editors, Algo- rithmic Aspects in Information and Management - 11th International Conference, AAIM 2016, Bergamo, Italy, July 18-20, 2016, Proceedings, volume 9778 of Lecture Notes in Computer Sci- ence, pages 185–196. Springer, 2016
  19. M. Oguzhan Külekci and M. Samil Sagiroglu. GENCROBAT: efficient transmission and pro- cessing of the massive genomic data. In 2016 IEEE/IFIP Network Operations and Management Symposium, NOMS 2016, Istanbul, Turkey, April 25-29, 2016, pages 999–1000, 2016
  20. M. Oguzhan Külekci and Sharma V. Thankachan. Range selection queries in data aware space and time. In Ali Bilgin, Michael W. Marcellin, Joan Serra-Sagristà, and James A. Storer, editors, 2015 Data Compression Conference, DCC 2015, Snowbird, UT, USA, April 7-9, 2015, pages 73–82. IEEE, 2015
  21. Boran Adas, Ersin Bayraktar, and M. Oguzhan Külekci. Huffman codes versus augmented non- prefix-free codes. In Evripidis Bampis, editor, Experimental Algorithms - 14th International Symposium, SEA 2015, Paris, France, June 29 - July 1, 2015, Proceedings, volume 9125 of Lecture Notes in Computer Science, pages 315–326. Springer, 2015
  22. Domenico Cantone, Simone Faro, and M. Oğuzhan Külekci. An efficient skip-search approach to the order-preserving pattern matching problem. In Jan Holub and Jan Žďárek, editors, Proceedings of the Prague Stringology Conference, pages 22–35, Prague, Czech Republic, 2015
  23. Tamanna Chhabra, M. Oğuzhan Külekci, and Jorma Tarhio. Alternative algorithms for order- preserving matching. In Jan Holub and Jan Žďárek, editors, Proceedings of the Prague Stringol- ogy Conference, pages 36–46, Prague, Czech Republic, 2015
  24. Boran Adas, Ersin Bayraktar, Simone Faro, Ibraheem Elsayed Moustafa, and M. Oguzhan Külekci. Nucleotide sequence alignment and compression via shortest unique substring. In Francisco M. Ortuño Guzman and Ignacio Rojas, editors, Bioinformatics and Biomedical En- gineering - Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17, 2015. Proceedings, Part II, volume 9044 of Lecture Notes in Computer Science, pages 363– 374. Springer, 2015
  25. Muhammed Oğuzhan Külekci. Enhanced variable-length codes: Improved compression with efficient random access. In Proceedings of IEEE Data Compression Conference (DCC), pages 362–371, Snowbird, UT, USA, 2014. IEEE
  26. Atalay Mert İleri, M.Oğuzhan Külekci, and Bojian Xu. Shortest unique substring query revis- ited. In AlexanderS. Kulikov, SergeiO. Kuznetsov, and Pavel Pevzner, editors, Combinatorial Pattern Matching, volume 8486 of Lecture Notes in Computer Science, pages 172–181. Springer International Publishing, 2014
  27. M. Oğuzhan Külekci. Uniquely decodable and directly accessible non-prefix-free codes via wavelet trees. In Proceedings of IEEE International Symposium on Information Theory (ISIT), pages 1969–1973. IEEE, 2013
  28. Simone Faro and M. Oğuzhan Külekci. Fast packed string matching for short patterns. In Proceedings of ACM-SIAM Symposium on Discrete Algorithms – Meeting on Algorithm En- gineering and Experiments (ALENEX), pages 113–121, New Orleans,Louisiana, USA, 2013. SIAM
  29. Simone Faro and M. Oğuzhan Külekci. Towards a very fast multiple string matching algorithm for short patterns. In Jan Holub and Jan Žďárek, editors, Proceedings of the Prague Stringology Conference, pages 78–91, Prague, Czech Republic, 2013
  30. M. Oğuzhan Külekci. On enumerating the dna sequences. In Proceedings of the ACM Con- ference on Bioinformatics, Computational Biology and Biomedicine, pages 442–449, Orlando, FL, USA, 2012. ACM
  31. Simone Faro and M.Oğuzhan Külekci. Fast Multiple String Matching Using Streaming SIMD Extensions Technology. In Liliana Calderón-Benavides, Cristina González-Caro, Edgar Chávez, and Nivio Ziviani, editors, String Processing and Information Retrieval, volume 7608 of Lecture Notes in Computer Science, pages 217–228. Springer Berlin Heidelberg, 2012
  32. M Oğuzhan Külekci. Compressed context modeling for text compression. In Proceedings of IEEE Data Compression Conference (DCC), pages 373–382, Snowbird, UT, USA, 2011. IEEE
  33. M Oguzhan Kulekci. A method to ensure the confidentiality of the compressed data. In 2011 First International Conference on Data Compression, Communications and Processing, pages 203–209. IEEE, 2011
  34. M Oğuzhan Külekci, Jeffrey Scott Vitter, and Bojian Xu. Boosting pattern matching per- formance via k-bit filtering. In Erol Gelenbe, Ricardo Lent, Georgia Sakellari, Ahmet Sacan, Hakki Toroslu, and Adnan Yazici, editors, Computer and Information Sciences, volume 62 of Lecture Notes in Electrical Engineering, pages 27–32. Springer Netherlands, 2010
  35. M. Oğuzhan Külekci, Jeffrey Scott Vitter, and Bojian Xu. Time-and space-efficient maxi- mal repeat finding using the burrows-wheeler transform and wavelet trees. In Proceedings of 2010 IEEE International Conference on Bioinformatics and Biomedicine, pages 622–625, Hong Kong, 2010. IEEE
  36. M Oğuzhan Külekci, Wing-Kai Hon, Rahul Shah, Jeffrey Scott Vitter, and Bojian Xu. Psi- ra: A parallel sparse index for read alignment on genomes. In Proceedings of 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pages 663–668, Hong Kong, 2010. IEEE
  37. M. Oguzhan Külekci. Filter based fast matching of long patterns by using simd instructions. In Proceedings of Prague Stringology Conference, pages 118–128, Prague, Czech Republic, 2009
  38. M. Oguzhan Külekci. A method to overcome computer word size limitation in bit-parallel pattern matching. In Seok-Hee Hong, Hiroshi Nagamochi, and Takuro Fukunaga, editors, Algorithms and Computation, 19th International Symposium, ISAAC 2008, Gold Coast, Aus- tralia, December 15-17, 2008. Proceedings, volume 5369 of Lecture Notes in Computer Science, pages 496–506. Springer, 2008
  39. M. Oğuzhan Külekci. Tara: An algorithm for fast searching of multiple patterns on text files. In Proceedings of 22nd International Symposium on Computer and Information Sciences, pages 1–6, Ankara, Turkey, 2007. IEEE. Best paper award
  40. M. Oğuzhan Külekci. An empirical analysis of pattern scan order in pattern matching. In Proceedings of World Congress on Engineering, International Conference on Data Mining and Knowledge Engineering (ICDMKE), pages 337–341, London, UK, 2007
  41. M Oğuzhan Külekci and Kemal Oflazer. An infrastructure for turkish prosody generation in text-to-speech synthesis. In Proceedings of the Turkish Symposium on Artificial Intelligence and Neural Network (TAINN), Akyaka, Muğla, Turkey, 2006
  42. M. Oğuzhan Külekci and Kemal Oflazer. Pronunciation disambiguation in turkish. In Pınar Yolum, Tunga Güngör, Fikret Gürgen, and Can Özturan, editors, Computer and Information Sciences, volume 3733 of Lecture Notes in Computer Science, pages 636–645. Springer Berlin Heidelberg, 2005
  43. M. Oğuzhan Külekci and Kemal Oflazer. Yazıdan konuşma üretmede kullanılan doğal dil işleme tekniklerine genel bir bakış (an overview of natural language processing techniques in text-to- speech systems). In Proceedings of the IEEE 12th Signal Processing and Communications Applications Conference, pages 454–457. IEEE, 2004
  44. M. Oğuzhan Külekci and Mehmed Özkan. Turkish word segmentation using morphological analyzer. In Proceedings of 7th European Conference on Speech Communication and Tech- nology (2nd INTERSPEECH Event), pages 1053–1056, Aalborg, Denmark, September 2001. International Speech Communication Association