My main expertise is in solving computational challenges with an innovative algorithm engineering approach. For more than two decades, I have been studying on such challenges originating from different fields mainly in cryptography and data security, natural language processing, information retrieval, computational biology, data compression and coding, massive data management, and most recently focusing on scalability and security aspects of ML/AI algorithms. I have been devising efficient innovative solutions and/or improving current state-of-art in terms of resource usage, e.g., time, memory, energy, communication costs. I would like to provide a summary of my previous achievements in engineering, research, and administration. Engineering Expertise: After spending around two years on programming point-of-sales devices and regular database programming, I have spent 10+ years in cryptography, where the main focus had been efficient implementation and cryptanalysis of the security&privacy algorithms and protocols both in hardware and software. During those years, despite gaining experience on how to develop programs that run fast and/or with small memory footprint, I had the chance to work with talented mathematicians and hardware engineers, that gave me the opportunity to widen my knowledge on different dimensions, including reverse engineering and FPGA/ASIC design. I also learned a lot on how to develop projects with a team of talent coming from different disciplines. I have observed, and today strongly believe, that theoretical knowledge is vital, but never enough to built efficient systems in practice. The platform that the solution will be executed on and the properties of the input data should always be considered for ground-breaking progress in practical performance. Theory without practice, or vice versa, is akin to trying to fly with one wing. In that sense, the development of the fastest pattern matching solutions and innovating patents that are licensed to companies have been exemplary outcomes of my perspective. Academic Expertise: Following my 15+ years in industry, I joined academia and have been serving as a professor of computer sci- ence. I succeeded to get several research grants and have been also serving in the committees of conferences. Actually, I started publishing in scientific venues when I was with the industry as well. I did my phd on natu- ral language processing, after which I got more engaged with combinatorial algorithms. I mostly published on data compression, combinatorial pattern matching and applications of them on computational biol- ogy/bioinformatics. Most recently, I have been studying scalablity and security aspects in ML/AI systems as well as in information retrieval. I have also experience in massive data management and analysis. I have been teaching courses on algorithms, security/privacy, and related topics. Administrative Expertise: After engineering cryptography for many years, I changed my focus to computational biology, particularly the genomics area. I have served as the deputy director of the National Institute of Genetics and Biotechnology of Turkey for two years, during which I was responsible for the establishment of the first high-throughput DNA sequencing facility of the country. That leadership equipped me with a unique experience of leading an interdisciplinary project with people from computing and life sciences disciplines. The establishment of the lab was supported with more than 2 million dollars grant by the government and was successfully completed in two years. Another leadership experience I had was being the program coordinator of the graduate programs in my university for more than four years. I was responsible by curriculum development and hiring new faculty. I have also served previously as principal investigator in research projects, lead research labs, and delivered project lead positions in industry projects.

Oguzhan Kulekci

Algorithm Engineer, Security/Privacy Researcher, Combinatorial Problem Solver

Research Interests

algorithms

pattern matching

data compression

bioinformatics

security & privacy

Cell Biology

Molecular Biology

Biotechnology

Biochemistry

Applied Mathematics

Genetics

Software

Theoretical Computer Science

Discrete Mathematics and Combinatorics

Computational Theory and Mathematics

Computational Mathematics

Law

Numerical Analysis

Modeling and Simulation

Electrical and Electronic Engineering

Library and Information Sciences

About

Publications

Sketching algorithms for genomic data analysis and querying in a secure enclave

Nature Methods / Mar 01, 2020

Kockan, C., Zhu, K., Dokmai, N., Karpov, N., Kulekci, M. O., Woodruff, D. P., & Sahinalp, S. C. (2020). Sketching algorithms for genomic data analysis and querying in a secure enclave. Nature Methods, 17(3), 295–301. https://doi.org/10.1038/s41592-020-0761-8

Fast Multiple String Matching Using Streaming SIMD Extensions Technology

String Processing and Information Retrieval / Jan 01, 2012

Faro, S., & Külekci, M. O. (2012). Fast Multiple String Matching Using Streaming SIMD Extensions Technology. In Lecture Notes in Computer Science (pp. 217–228). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-34109-0_23

Fast Packed String Matching for Short Patterns

2013 Proceedings of the Fifteenth Workshop on Algorithm Engineering and Experiments (ALENEX) / Jan 07, 2013

Faro, S., & Külekci, M. O. (2013). Fast Packed String Matching for Short Patterns. In 2013 Proceedings of the Fifteenth Workshop on Algorithm Engineering and Experiments (ALENEX) (pp. 113–121). Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611972931.10

Fast Multiple String Matching Using Streaming SIMD Extensions Technology

String Processing and Information Retrieval / Jan 01, 2012

Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree

IEEE/ACM Transactions on Computational Biology and Bioinformatics / Mar 01, 2012

Kulekci, M. O., Vitter, J. S., & Xu, B. (2012). Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(2), 421–429. https://doi.org/10.1109/tcbb.2011.127

Efficient Algorithms for the Order Preserving Pattern Matching Problem

Algorithmic Aspects in Information and Management / Jan 01, 2016

Faro, S., & Külekci, M. O. (2016). Efficient Algorithms for the Order Preserving Pattern Matching Problem. In Lecture Notes in Computer Science (pp. 185–196). Springer International Publishing. https://doi.org/10.1007/978-3-319-41168-2_16

Engineering order‐preserving pattern matching with SIMD parallelism

Software: Practice and Experience / Aug 24, 2016

Chhabra, T., Faro, S., Külekci, M. O., & Tarhio, J. (2016). Engineering order‐preserving pattern matching with SIMD parallelism. Software: Practice and Experience, 47(5), 731–739. Portico. https://doi.org/10.1002/spe.2433

Enhanced Variable-Length Codes: Improved Compression with Efficient Random Access

2014 Data Compression Conference / Mar 01, 2014

Kulekci, M. O. (2014, March). Enhanced Variable-Length Codes: Improved Compression with Efficient Random Access. 2014 Data Compression Conference. https://doi.org/10.1109/dcc.2014.74

Tara: An algorithm for fast searching of multiple patterns on text files

2007 22nd international symposium on computer and information sciences / Nov 01, 2007

Kulekci, M. O. (2007, November). Tara: An algorithm for fast searching of multiple patterns on text files. 2007 22nd International Symposium on Computer and Information Sciences. https://doi.org/10.1109/iscis.2007.4456850

Turkish word segmentation using morphological analyzer

7th European Conference on Speech Communication and Technology (Eurospeech 2001) / Sep 03, 2001

Külekcý, M. O., & Özkan, M. (2001, September 3). Turkish word segmentation using morphological analyzer. 7th European Conference on Speech Communication and Technology (Eurospeech 2001). https://doi.org/10.21437/eurospeech.2001-226

Rule-based prosody prediction for German text-to-speech synthesis

Speech Prosody 2006 / May 02, 2006

Becker, S., Schröder, M., & Barry, W. J. (2006, May 2). Rule-based prosody prediction for German text-to-speech synthesis. Speech Prosody 2006. https://doi.org/10.21437/speechprosody.2006-110

I/O-efficient data structures for non-overlapping indexing

Theoretical Computer Science / Feb 01, 2021

Hooshmand, S., Abedin, P., Oğuzhan Külekci, M., & Thankachan, S. V. (2021). I/O-efficient data structures for non-overlapping indexing. Theoretical Computer Science, 857, 1–7. https://doi.org/10.1016/j.tcs.2020.12.006

Uniquely decodable and directly accessible non-prefix-free codes via wavelet trees

2013 IEEE International Symposium on Information Theory / Jul 01, 2013

Kulekci, M. O. (2013, July). Uniquely decodable and directly accessible non-prefix-free codes via wavelet trees. 2013 IEEE International Symposium on Information Theory. https://doi.org/10.1109/isit.2013.6620570

Nucleotide Sequence Alignment and Compression via Shortest Unique Substring

Bioinformatics and Biomedical Engineering / Jan 01, 2015

Adaş, B., Bayraktar, E., Faro, S., Moustafa, I. E., & Külekci, M. O. (2015). Nucleotide Sequence Alignment and Compression via Shortest Unique Substring. In Lecture Notes in Computer Science (pp. 363–374). Springer International Publishing. https://doi.org/10.1007/978-3-319-16480-9_36

Succinct Non-overlapping Indexing

Combinatorial Pattern Matching / Jan 01, 2015

Ganguly, A., Shah, R., & Thankachan, S. V. (2015). Succinct Non-overlapping Indexing. In Lecture Notes in Computer Science (pp. 185–195). Springer International Publishing. https://doi.org/10.1007/978-3-319-19929-0_16

Time- and space-efficient maximal repeat finding using the burrows-wheeler transform and wavelet trees

2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) / Dec 01, 2010

Kiilekci, M. O., Vitter, J. S., & Xu, B. (2010, December). Time- and space-efficient maximal repeat finding using the burrows-wheeler transform and wavelet trees. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). https://doi.org/10.1109/bibm.2010.5706641

Ranking Assisted Unsupervised Morphological Disambiguation of Turkish

Jan 01, 2023

Agun, H. V. V., & Aslan, Ö. (2023). Ranking Assisted Unsupervised Morphological Disambiguation of Turkish. https://doi.org/10.2139/ssrn.4416225

Dynamic Multi-Server Searchable Encryption Scheme Based on Concept Hierarchy

2018 9th International Symposium on Parallel Architectures, Algorithms and Programming (PAAP) / Dec 01, 2018

Huang, H., Yu, P., & Wu, M. (2018, December). Dynamic Multi-Server Searchable Encryption Scheme Based on Concept Hierarchy. 2018 9th International Symposium on Parallel Architectures, Algorithms and Programming (PAAP). https://doi.org/10.1109/paap.2018.00028

Ψ-RA: a parallel sparse index for genomic read alignment

BMC Genomics / Jan 01, 2011

Oğuzhan Külekci, M., Hon, W.-K., Shah, R., Scott Vitter, J., & Xu, B. (2011). Ψ-RA: a parallel sparse index for genomic read alignment. BMC Genomics, 12(Suppl 2), S7. https://doi.org/10.1186/1471-2164-12-s2-s7

Compressed Context Modeling for Text Compression

2011 Data Compression Conference / Mar 01, 2011

Kulekci, M. O. (2011, March). Compressed Context Modeling for Text Compression. 2011 Data Compression Conference. https://doi.org/10.1109/dcc.2011.44

Pronunciation Disambiguation in Turkish

Computer and Information Sciences - ISCIS 2005 / Jan 01, 2005

Külekci, M. O., & Oflazer, K. (2005). Pronunciation Disambiguation in Turkish. In Lecture Notes in Computer Science (pp. 636–645). Springer Berlin Heidelberg. https://doi.org/10.1007/11569596_66

Range Selection Queries in Data Aware Space and Time

2015 Data Compression Conference / Apr 01, 2015

Kulekci, M. O., & Thankachan, S. V. (2015, April). Range Selection Queries in Data Aware Space and Time. 2015 Data Compression Conference. https://doi.org/10.1109/dcc.2015.53

A Method to Ensure the Confidentiality of the Compressed Data

2011 First International Conference on Data Compression, Communications and Processing / Jun 01, 2011

Kulekci, M. O. (2011, June). A Method to Ensure the Confidentiality of the Compressed Data. 2011 First International Conference on Data Compression, Communications and Processing. https://doi.org/10.1109/ccp.2011.28

An overview of natural language processing techniques in text-to-speech systems

Proceedings of the IEEE 12th Signal Processing and Communications Applications Conference, 2004.

Universitesi, S. (n.d.). An overview of natural language processing techniques in text-to-speech systems. Proceedings of the IEEE 12th Signal Processing and Communications Applications Conference, 2004. https://doi.org/10.1109/siu.2004.1338561

Counting with Prediction: Rank and Select Queries with Adjusted Anchoring

2022 Data Compression Conference (DCC) / Mar 01, 2022

Kulekci, M. O. (2022, March). Counting with Prediction: Rank and Select Queries with Adjusted Anchoring. 2022 Data Compression Conference (DCC). https://doi.org/10.1109/dcc52660.2022.00049

Quality Assessment of High-throughput DNA Sequencing Data via Range analysis

Jan 18, 2017

Külekci, M. O., Fotouhi, A., & Majidi, M. (2017). Quality Assessment of High-throughput DNA Sequencing Data via Range analysis. https://doi.org/10.1101/101469

Preprint repository arXiv achieves milestone million uploads

Physics Today / Jan 01, 2014

Preprint repository arXiv achieves milestone million uploads. (2014). Physics Today. https://doi.org/10.1063/pt.5.028530

A System Architecture for Efficient Transmission of Massive DNA Sequencing Data

Journal of Computational Biology / Nov 01, 2017

Sağiroğlu, M. Ş., & Külekcİ, M. O. (2017). A System Architecture for Efficient Transmission of Massive DNA Sequencing Data. Journal of Computational Biology, 24(11), 1081–1088. https://doi.org/10.1089/cmb.2017.0016

PSI-RA: A parallel sparse index for read alignment on genomes

2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) / Dec 01, 2010

Kulekci, M. O., Hon, W.-K., Shah, R., Vitter, J. S., & Xu, B. (2010, December). PSI-RA: A parallel sparse index for read alignment on genomes. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). https://doi.org/10.1109/bibm.2010.5706648

A framework for assessing a country’s scientific productivity based on published articles by scientists affiliated with that country

Information Discovery and Delivery / Mar 21, 2023

Hamed Golzar, N., Altunok, E., Aghabaiglou, A., & Külekci, M. O. (2023). A framework for assessing a country’s scientific productivity based on published articles by scientists affiliated with that country. Information Discovery and Delivery, 52(1), 23–38. https://doi.org/10.1108/idd-08-2021-0082

Memory–Efficient FM-Index Construction for Reference Genomes

2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) / Dec 06, 2022

Das, A. K., Kulekci, M. O., & Thankachan, S. V. (2022, December 6). Memory–Efficient FM-Index Construction for Reference Genomes. 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). https://doi.org/10.1109/bibm55620.2022.9995057

The future of evaluation of child and adolescent psychiatric treatments

IACAPAP ArXiv / Jan 01, 2021

Falissard, B. (2021). The future of evaluation of child and adolescent psychiatric treatments. IACAPAP ArXiv. https://doi.org/10.14744/iacapaparxiv.2020.20007

GENCROBAT: Efficient transmission and processing of the massive genomic data

NOMS 2016 - 2016 IEEE/IFIP Network Operations and Management Symposium / Apr 01, 2016

Kulekci, M. O., & Sagiroglu, M. G. (2016, April). GENCROBAT: Efficient transmission and processing of the massive genomic data. NOMS 2016 - 2016 IEEE/IFIP Network Operations and Management Symposium. https://doi.org/10.1109/noms.2016.7502942

On stabbing queries for generalized longest repeat

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) / Nov 01, 2015

Xu, B. (2015, November). On stabbing queries for generalized longest repeat. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). https://doi.org/10.1109/bibm.2015.7359738

Turkish Tweet Classification with Transformer Encoder

Proceedings - Natural Language Processing in a Deep Learning World / Oct 22, 2019

Emre Yüksel, A., Alim Türkmen, Y., Özgür, A., & Berna Altınel, A. (2019, October 22). Turkish Tweet Classification with Transformer Encoder. Proceedings - Natural Language Processing in a Deep Learning World. https://doi.org/10.26615/978-954-452-056-4_158

IMPACTS: Results Summary for CY 2010

Mar 01, 2013

(2013). IMPACTS: Results Summary for CY 2010. Office of Scientific and Technical Information (OSTI). https://doi.org/10.2172/1219980

Randomized Data Partitioning with Efficient Search, Retrieval and Privacy-Preservation

Lecture Notes in Computer Science / Dec 09, 2023

Külekci, M. O. (2023). Randomized Data Partitioning with Efficient Search, Retrieval and Privacy-Preservation. In Computing and Combinatorics (pp. 310–323). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-49190-0_22

A Survey on Shortest Unique Substring Queries

Algorithms / Sep 06, 2020

Abedin, P., Külekci, M., & Thankachan, S. (2020). A Survey on Shortest Unique Substring Queries. Algorithms, 13(9), 224. https://doi.org/10.3390/a13090224

The order-preserving pattern matching problem in practice

Discrete Applied Mathematics / Mar 01, 2020

Cantone, D., Faro, S., & Külekci, M. O. (2020). The order-preserving pattern matching problem in practice. Discrete Applied Mathematics, 274, 11–25. https://doi.org/10.1016/j.dam.2018.10.023

Applications of Non-Uniquely Decodable Codes to Privacy-Preserving High-Entropy Data Representation

Algorithms / Apr 17, 2019

Külekci, M. O., & Öztürk, Y. (2019). Applications of Non-Uniquely Decodable Codes to Privacy-Preserving High-Entropy Data Representation. Algorithms, 12(4), 78. https://doi.org/10.3390/a12040078

Optimizing Packed String Matching on AVX2 Platform

High Performance Computing for Computational Science – VECPAR 2018 / Jan 01, 2019

Aydoğmuş, M. A., & Külekci, M. O. (2019). Optimizing Packed String Matching on AVX2 Platform. In Lecture Notes in Computer Science (pp. 45–61). Springer International Publishing. https://doi.org/10.1007/978-3-030-15996-2_4

Privacy–Preserving Text Similarity via Non-Prefix-Free Codes

Similarity Search and Applications / Jan 01, 2019

Külekci, M. O., Habib, I., & Aghabaiglou, A. (2019). Privacy–Preserving Text Similarity via Non-Prefix-Free Codes. In Lecture Notes in Computer Science (pp. 94–102). Springer International Publishing. https://doi.org/10.1007/978-3-030-32047-8_9

A Two-Level Scheme for Quality Score Compression

Journal of Computational Biology / Oct 01, 2018

Voges, J., Fotouhi, A., Ostermann, J., & Külekci, M. O. (2018). A Two-Level Scheme for Quality Score Compression. Journal of Computational Biology, 25(10), 1141–1151. https://doi.org/10.1089/cmb.2018.0065

Quality Assessment of High-Throughput DNA Sequencing Data via Range Analysis

Bioinformatics and Biomedical Engineering / Jan 01, 2018

Fotouhi, A., Majidi, M., & Külekci, M. O. (2018). Quality Assessment of High-Throughput DNA Sequencing Data via Range Analysis. In Lecture Notes in Computer Science (pp. 429–438). Springer International Publishing. https://doi.org/10.1007/978-3-319-78723-7_37

Range selection and predecessor queries in data aware space and time

Journal of Discrete Algorithms / Mar 01, 2017

Külekci, M. O., & Thankachan, S. V. (2017). Range selection and predecessor queries in data aware space and time. Journal of Discrete Algorithms, 43, 18–25. https://doi.org/10.1016/j.jda.2017.01.002

Security analysis on the ADS-B technology

2017 25th Signal Processing and Communications Applications Conference (SIU) / May 01, 2017

Kocaaga, E., & Kulekci, M. O. (2017, May). Security analysis on the ADS-B technology. 2017 25th Signal Processing and Communications Applications Conference (SIU). https://doi.org/10.1109/siu.2017.7960506

Inverse Range Selection Queries

String Processing and Information Retrieval / Jan 01, 2016

Külekci, M. O. (2016). Inverse Range Selection Queries. In Lecture Notes in Computer Science (pp. 166–177). Springer International Publishing. https://doi.org/10.1007/978-3-319-46049-9_17

A simple yet time-optimal and linear-space algorithm for shortest unique substring queries

Theoretical Computer Science / Jan 01, 2015

İleri, A. M., Külekci, M. O., & Xu, B. (2015). A simple yet time-optimal and linear-space algorithm for shortest unique substring queries. Theoretical Computer Science, 562, 621–633. https://doi.org/10.1016/j.tcs.2014.11.004

Huffman Codes versus Augmented Non-Prefix-Free Codes

Experimental Algorithms / Jan 01, 2015

Adaş, B., Bayraktar, E., & Külekci, M. O. (2015). Huffman Codes versus Augmented Non-Prefix-Free Codes. In Lecture Notes in Computer Science (pp. 315–326). Springer International Publishing. https://doi.org/10.1007/978-3-319-20086-6_24

Robustness of Massively Parallel Sequencing Platforms

PLOS ONE / Sep 18, 2015

Kavak, P., Yüksel, B., Aksu, S., Kulekci, M. O., Güngör, T., Hach, F., Şahinalp, S. C., Alkan, C., & Sağıroğlu, M. Ş. (2015). Robustness of Massively Parallel Sequencing Platforms. PLOS ONE, 10(9), e0138259. https://doi.org/10.1371/journal.pone.0138259

Fast and flexible packed string matching

Journal of Discrete Algorithms / Sep 01, 2014

Faro, S., & Külekci, M. O. (2014). Fast and flexible packed string matching. Journal of Discrete Algorithms, 28, 61–72. https://doi.org/10.1016/j.jda.2014.07.003

Shortest Unique Substring Query Revisited

Combinatorial Pattern Matching / Jan 01, 2014

İleri, A. M., Külekci, M. O., & Xu, B. (2014). Shortest Unique Substring Query Revisited. In Lecture Notes in Computer Science (pp. 172–181). Springer International Publishing. https://doi.org/10.1007/978-3-319-07566-2_18

A time--memory trade-off approach for the solution of nonlinear equation systems

Turkish Journal of Electrical Engineering and Computer Sciences / Jan 01, 2013

DEMİRCİ, H., SAĞIROĞLU, M. Ş., & KÜLEKCİ, M. O. (2013). A time--memory trade-off approach for the solution of nonlinear equation systems. Turkish Journal of Electrical Engineering and Computer Sciences. LOCKSS. https://doi.org/10.3906/elk-1103-42

Fast Pattern-Matching via k-bit Filtering Based Text Decomposition

The Computer Journal / Dec 20, 2010

Kulekci, M. O., Vitter, J. S., & Xu, B. (2010). Fast Pattern-Matching via k-bit Filtering Based Text Decomposition. The Computer Journal, 55(1), 62–68. https://doi.org/10.1093/comjnl/bxq090

On enumerating the DNA sequences

Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine / Oct 07, 2012

Külekci, M. O. (2012, October 7). On enumerating the DNA sequences. Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. https://doi.org/10.1145/2382936.2382993

On scrambling the Burrows–Wheeler transform to provide privacy in lossless compression

Computers & Security / Feb 01, 2012

Oğuzhan Külekci, M. (2012). On scrambling the Burrows–Wheeler transform to provide privacy in lossless compression. Computers & Security, 31(1), 26–32. https://doi.org/10.1016/j.cose.2011.11.005

BLIM: A New Bit-Parallel Pattern Matching Algorithm Overcoming Computer Word Size Limitation

Mathematics in Computer Science / Apr 13, 2010

Külekci, M. O. (2010). BLIM: A New Bit-Parallel Pattern Matching Algorithm Overcoming Computer Word Size Limitation. Mathematics in Computer Science, 3(4), 407–420. https://doi.org/10.1007/s11786-010-0035-4

Boosting Pattern Matching Performance via k-bit Filtering

Lecture Notes in Electrical Engineering / Aug 18, 2010

Külekci, M. O., Vitter, J. S., & Xu, B. (2010). Boosting Pattern Matching Performance via k-bit Filtering. In Computer and Information Sciences (pp. 27–32). Springer Netherlands. https://doi.org/10.1007/978-90-481-9794-1_6

A Method to Overcome Computer Word Size Limitation in Bit-Parallel Pattern Matching

Algorithms and Computation / Jan 01, 2008

Külekci, M. O. (2008). A Method to Overcome Computer Word Size Limitation in Bit-Parallel Pattern Matching. In Lecture Notes in Computer Science (pp. 496–506). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-540-92182-0_45

Education

Sabancı University

Ph.D., Computer Science / July, 2006

Istanbul

Experience

Indiana University

Visiting Professor / January, 2022 — Present

Istanbul Teknik Üniversitesi

Professor / November, 2015 — Present

national research institute of electronics and cryptology

Chief Researcher / January, 2007 — March, 2014

Design, analysis, and implementation of cryptographic security and privacy algorithms

Senior Researcher / June, 2004 — May, 2007

Design, analysis, and implementation of cryptographic security and privacy algorithms

Researcher / June, 1999 — June, 2004

Design, analysis, and implementation of cryptographic security and privacy algorithms

Links & Social Media

Research Web Site

Join Oguzhan on NotedSource!

Join Now

At NotedSource, we believe that professors, post-docs, scientists and other researchers have deep, untapped knowledge and expertise that can be leveraged to drive innovation within companies. NotedSource is committed to bridging the gap between academia and industry by providing a platform for collaboration with industry and networking with other researchers.

For industry, NotedSource identifies the right academic experts in 24 hours to help organizations build and grow. With a platform of thousands of knowledgeable PhDs, scientists, and industry experts, NotedSource makes connecting and collaborating easy.

For academic researchers such as professors, post-docs, and Ph.D.s, NotedSource provides tools to discover and connect to your colleagues with messaging and news feeds, in addition to the opportunity to be paid for your collaboration with vetted partners.

Expert Institutions

Proudly trusted by

Connect with researchers and scientists like Oguzhan Kulekci on NotedSource to help your company with innovation, research, R&D, L&D, and more.

Events

Blog

Case Studies

Resources

Events

Blog

Case Studies

Sign Up

Login

Oguzhan Kulekci

Algorithm Engineer, Security/Privacy Researcher, Combinatorial Problem Solver

Research Interests

About

Publications

Sketching algorithms for genomic data analysis and querying in a secure enclave

Fast Multiple String Matching Using Streaming SIMD Extensions Technology

Fast Packed String Matching for Short Patterns

Fast Multiple String Matching Using Streaming SIMD Extensions Technology

Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree

Efficient Algorithms for the Order Preserving Pattern Matching Problem

Engineering order‐preserving pattern matching with SIMD parallelism

Enhanced Variable-Length Codes: Improved Compression with Efficient Random Access

Tara: An algorithm for fast searching of multiple patterns on text files

Turkish word segmentation using morphological analyzer

Rule-based prosody prediction for German text-to-speech synthesis

I/O-efficient data structures for non-overlapping indexing

Uniquely decodable and directly accessible non-prefix-free codes via wavelet trees

Nucleotide Sequence Alignment and Compression via Shortest Unique Substring

Succinct Non-overlapping Indexing

Time- and space-efficient maximal repeat finding using the burrows-wheeler transform and wavelet trees

Ranking Assisted Unsupervised Morphological Disambiguation of Turkish

Dynamic Multi-Server Searchable Encryption Scheme Based on Concept Hierarchy

Ψ-RA: a parallel sparse index for genomic read alignment

Compressed Context Modeling for Text Compression

Pronunciation Disambiguation in Turkish

Range Selection Queries in Data Aware Space and Time

A Method to Ensure the Confidentiality of the Compressed Data

An overview of natural language processing techniques in text-to-speech systems

Counting with Prediction: Rank and Select Queries with Adjusted Anchoring

Quality Assessment of High-throughput DNA Sequencing Data via Range analysis

Preprint repository arXiv achieves milestone million uploads

A System Architecture for Efficient Transmission of Massive DNA Sequencing Data

PSI-RA: A parallel sparse index for read alignment on genomes

A framework for assessing a country’s scientific productivity based on published articles by scientists affiliated with that country

Memory–Efficient FM-Index Construction for Reference Genomes

The future of evaluation of child and adolescent psychiatric treatments

GENCROBAT: Efficient transmission and processing of the massive genomic data

On stabbing queries for generalized longest repeat

Turkish Tweet Classification with Transformer Encoder

IMPACTS: Results Summary for CY 2010

Randomized Data Partitioning with Efficient Search, Retrieval and Privacy-Preservation

A Survey on Shortest Unique Substring Queries

The order-preserving pattern matching problem in practice

Applications of Non-Uniquely Decodable Codes to Privacy-Preserving High-Entropy Data Representation

Optimizing Packed String Matching on AVX2 Platform

Privacy–Preserving Text Similarity via Non-Prefix-Free Codes

A Two-Level Scheme for Quality Score Compression

Quality Assessment of High-Throughput DNA Sequencing Data via Range Analysis

Range selection and predecessor queries in data aware space and time

Security analysis on the ADS-B technology

Inverse Range Selection Queries

A simple yet time-optimal and linear-space algorithm for shortest unique substring queries

Huffman Codes versus Augmented Non-Prefix-Free Codes

Robustness of Massively Parallel Sequencing Platforms

Fast and flexible packed string matching

Shortest Unique Substring Query Revisited

A time--memory trade-off approach for the solution of nonlinear equation systems

Fast Pattern-Matching via k-bit Filtering Based Text Decomposition

On enumerating the DNA sequences

On scrambling the Burrows–Wheeler transform to provide privacy in lossless compression

BLIM: A New Bit-Parallel Pattern Matching Algorithm Overcoming Computer Word Size Limitation

Boosting Pattern Matching Performance via k-bit Filtering

A Method to Overcome Computer Word Size Limitation in Bit-Parallel Pattern Matching

Education

Sabancı University

Experience

Indiana University

Istanbul Teknik Üniversitesi

national research institute of electronics and cryptology

Links & Social Media