The project entitled “Non-prefix free codes with applications” received a grant of amount 130K TL from the TUBITAK-1001 program for 18 months. Two graduate and two undergraduate students will be supported. Candidates with “excellent” knowledge of C/C++ and a strong interest in algorithms & data structures are encouraged to contact me by sharing their CVs.
Our paper entitled “Quality Assessment of High-Throughput DNA Sequencing Data via Range Analysis” with my student Ali Fotouhi and Mina Majidi is accepted to the International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO) 2018 conference.
I have served as the opponent at the Ph.D. defense of Sukhpal Ghuman at Department of Computer Science, Aalto University, Helsinki, Finland on 15th of January, 2018.
Our paper entitled “A Two-level Scheme for Quality Score Compression”, has been accepted by the 2018 International Conference on Bioinformatics and Computational Biology (BICoB 2018).
I have visited Lab for Bioinformatics and Computational Genomics at School of Informatics, Computing, and Engineering, Indiana University Bloomington, IN, USA led by Prof. Cenk Sahinalp in August, 2017. I gave a talk entitled An Ambiguous Coding Scheme To Achieve Data Security with Less Encryption in Department of Computer Science colloquia seminers. Thanks a lot for the hospitality and the sincere atmosphere.
Our recent study entitled “A System Architecture for Efficient Transmission of Massive DNA Sequencing Data” with Mahmut Şamil Sagiroglu from Erlab Technology has appeared in Fast Track of Journal of Computational Biology.
In this study we focus on the problem “How to transmit massive DNA sequencing data from where they are produced to where they will be processed ?”. The DNA sequencing data analysis pipelines require significant computational resources. In that sense, cloud computing infrastructures appear as a natural choice for this processing. However, the first practical difficulty in reaching the cloud computing services is the transmission of the massive DNA sequencing data from where they are produced to where they will be processed. We proposed a new system architecture that incorporates the computational resources available on the client side while dynamically adapting itself to the available bandwidth. We analyse several real-life scenarios, which provide useful insights for the sequencing data producers, especially on deciding when to use a cloud service and in what conditions. This work has been partially supported by TÜBİTAK grants TEYDEB-7150616 and ARDEB-114E293.
with Sharma V. Thankacha,has appeared online at Journal of Discrete Algorithms.
We have made a patent application based on a recent technique that we have developed. This method aims to lessen the energy consumption while encrypting large volumes of data, and may help to increase the battery life in resource-limited environments such as the sensor networks, unmanned aerial vehicles, satellite communications, and etc.
Do not hesitate to contact in case you have a project that you believe this makes sense. We will be happy to discuss any further opportunities.
Our recent work Engineering order-preserving pattern matching with SIMD parallelism ,which was prepared in collaboration with colleagues T. Chhabra, S. Faro, and J. Tarhio, has appeared in Software:Practice & Experience journal.