Browsing by Author "Alser, Mohammed"

Now showing items 1-4 of 4

    • Can you really anonymize the donors of genomic data in today’s digital world? 

      Alser, Mohammed; Almadhoun, Nour; Nouri, Azita; Alkan, Can; Ayday, Erman (Springer, 2016-09)
      The rapid progress in genome sequencing technologies leads to availability of high amounts of genomic data. Accelerating the pace of biomedical breakthroughs and discoveries necessitates not only collecting millions of ...

    • GateKeeper-GPU: fast and accurate pre-alignment filtering in short read mapping 

      Bingöl, Zülal; Alser, Mohammed; Mutlu, Onur; Öztürk, Özcan; Alkan, Can (IEEE, 2021-06-24)
      We introduce GateKeeper-GPU, a fast and accurate pre-alignment filter that efficiently reduces the need for expensive sequence alignment. GateKeeper-GPU improves the filtering accuracy of GateKeeper, and by exploiting the ...

    • Shouji: a fast and efficient pre-alignment filter for sequence alignment 

      Alser, Mohammed; Hassan, H.; Kumar, A.; Mutlu, Onur; Alkan, Can (Oxford University Press, 2019)
      The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design ...

    • Technology dictates algorithms: recent developments in read alignment 

      Alser, Mohammed; Rotman, J.; Deshpande, D.; Taraszka, K.; Shi, H.; Baykal, P. I.; Yang, H. T.; Xue, V.; Knyazev, S.; Singer, B. D.; Balliu, B.; Koslicki, D.; Skums, P.; Zelikovsky, A.; Alkan, Can; Mutlu, Onur; Mangul, S. (BioMed Central, 2021-08-26)
      Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to ...