Barış Ekim (ˌbɑːrʌʃ ˌɛkɪm)

Publications

You can also find my work on my Google Scholar profile.

Articles and Manuscripts

  1. Karami, M., Mohammadi, A. S., Martin, M., Ekim, B., Shen, W., Guo, L., Xu, M., Pibiri, G. E., Patro, R., Sahlin, K., Evaluating randstrobe construction techniques for sequence similarity analyses. Bioinformatics, 40(4) 2024.
  2. Ekim, B., Sahlin, K., Medvedev, P., Berger, B., Chikhi, R., Efficient mapping of accurate long reads in minimizer space with mapquik. Genome Research, 33 (7): 1188-1197 (2023).
  3. Pellow, D., Pu, L., Ekim, B., Kotlar, L., Berger, B., Shamir, R., Orenstein, Y., Efficient minimizer orders for large values of k using minimum decycling sets. Proceedings of the 27th International Conference in Computational Molecular Biology (RECOMB 2023); Genome Research, 33 (7): 1154-1161 (2023)
  4. Ekim, B., Sahlin, K., Medvedev, P., Berger, B., Chikhi, R., mapquik: Efficient low-divergence mapping of long reads in minimizer space. Proceedings of the 27th International Conference in Computational Molecular Biology (RECOMB 2023). (2023)
  5. Ekim, B., Berger, B., Chikhi, R., Memory-efficient whole genome assembly of long reads. US Patent App., 17/903, 654 (2023).
  6. Ekim, B. C., Scalable sketching and indexing algorithms for large biological datasets. Master's Degree Thesis, (2022).
  7. Ekim, B., Berger, B., Chikhi, R., Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. Cell Systems, 12: 1-11 (2021).
  8. Ekim, B., Berger, B., Orenstein, Y., A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets. Proceedings of the 24th International Conference in Computational Molecular Biology (RECOMB 2020), 37-53 (2020).
  9. Kuzu, A.T., Berenji, K.R., Ekim, B.C., Bakkal, M., The thermal modeling of deep-hole drilling process under MQL condition. Journal of Manufacturing Processes, 29: 194-203 (2017).
  10. Ekim, B., A novel entropy-based hierarchical clustering framework for ultrafast protein structure search and alignment, arXiv preprint, 1701.01975 (2017).
  11. Bakkal, M., Bodur, M.S., Sonmez, H.E., Ekim, B.C., The effect of chemical treatment methods on the outdoor performance of waste textile fiber-reinforced polymer composites. Journal of Composite Materials, 51: 2009-2021 (2016).

Conferences, Workshops, and Seminars

  1. mapquik: Efficient low-divergence mapping of long reads in minimizer space. 27th International Conference in Computational Molecular Biology (RECOMB 2023), Istanbul, Turkey, April 2023.
  2. Approximate pattern counting in de Bruijn graphs is #W[1]-hard. Data Structures in Bioinformatics (DSB) 2022, Dusseldorf, Germany, June 2022.
  3. Minimizer-space de Bruijn graphs. 25th International Conference in Computational Molecular Biology (RECOMB 2021), Padova, Italy, May 2021.
  4. A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets. 24th International Conference in Computational Molecular Biology (RECOMB 2020), Padova, Italy, May 2020.
  5. Computing universal hitting sets for sequence analysis: Methods and applications. Sabanci University Program for Undergraduate Research (PURE) Seminar Series, Istanbul, Turkey, July 2019.
  6. Applications of universal hitting sets (UHS) in sequence analysis. Webinar for International Society for Computational Biology (ISCB) Regional Student Group (RSG) Turkey, November 2019.
  7. A novel entropy-based hierarchical clustering framework for ultrafast protein structure search and alignment. 2nd International Symposium on Multidisciplinary Studies and Innovative Technologies (ISMSIT), Ankara, Turkey, October 2018.
  8. Haplotype-aware de novo genome assembly: Novel approaches and applications. Istanbul University Bioinformatics Seminar Series, Istanbul, Turkey, October 2018.

Contributed Posters

  1. Fast detection of maximal exact matches with universal k-mer sampling. International Symposium on Health Informatics and Bioinformatics (HIBIT), Izmir, Turkey, October 2019.
  2. Memory-efficient parallel algorithms for approximating compact universal hitting sets. Workshop on Algorithms in Bioinformatics (WABI), Niagara Falls, NY, September 2019.
  3. Parallelizing algorithms for universal hitting sets. 7th Annual Broad-ISF Symposium, Jerusalem, Israel, July 2019.
  4. Parallel algorithms for approximating compact universal hitting sets. MIT Biology Undergraduate Student Association (BUSA) Life Sciences Undergraduate Poster Symposium, May 2019.

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