Publications

Preprints

• Arasti, S., Şapcı, A. O. B., Rachtman, E., El-Kebir, M., & Mirarab, S. (2026). Deconvolving Phylogenetic Distance Mixtures (p. 2026.01.18.700179). bioRxiv. https://doi.org/10.64898/2026.01.18.700179

• Melendez, D., Şapcı, A. O. B., Bafna, V., & Mirarab, S. (2025). SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation (p. 2025.11.14.688492). bioRxiv. https://doi.org/10.1101/2025.11.14.688492

Journal Publications

• Şapcı, A. O. B., & Mirarab, S. (2026). krepp: A k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement. Genome Biology. https://doi.org/10.1186/s13059-026-03999-y

• Keleş, M. F., Sapci, A. O. B., Brody, C., Palmer, I., Mehta, A., Ahmadi, S., Le, C., Taştan, Ö., Keleş, S., & Wu, M. N. (2025). FlyVISTA, an integrated machine learning platform for deep phenotyping of sleep in Drosophila. Science Advances, 11(11), eadq8131. https://doi.org/10.1126/sciadv.adq8131

• Şapcı, A. O. B., & Mirarab, S. (2024). Memory-bound k-mer selection for large and evolutionary diverse reference libraries. Genome Research, gr.279339.124. https://doi.org/10.1101/gr.279339.124

• Şapcı, A. O. B., Rachtman, E., & Mirarab, S. (2024). CONSULT-II: Accurate taxonomic identification and profiling using locality-sensitive hashing. Bioinformatics, btae150. https://doi.org/10.1093/bioinformatics/btae150

• Şapcı, A. O. B., Lu, S., Yan, S., Ay, F., Tastan, O., & Keleş, S. (2023). MuDCoD: Multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing. Bioinformatics, 39(10), btad592. https://doi.org/10.1093/bioinformatics/btad592

• Şapcı, A. O. B., Kemik, H., Yeniterzi, R., & Tastan, O. (2023). Focusing on potential named entities during active label acquisition. Natural Language Engineering, 1–23. https://doi.org/10.1017/S1351324923000165

Conference Proceedings

• Şapcı, A. O. B., & Mirarab, S. (2025). Alignment-Free Estimation of Read to Genome Distances and Its Applications. In S. Sankararaman (Ed.), Research in Computational Molecular Biology (pp. 316–320). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-90252-9_30

• Şapcı, A. O. B., & Mirarab, S. (2024). Memory-Bound and Taxonomy-Aware k-Mer Selection for Ultra-Large Reference Libraries. In J. Ma (Ed.), Research in Computational Molecular Biology (pp. 340–343). Springer Nature Switzerland. https://doi.org/10.1007/978-1-0716-3989-4_26

• Şapcı, A. O. B., Rachtman, E., & Mirarab, S. (2023). CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing. In K. Jahn & T. Vinař (Eds.), Comparative Genomics (pp. 196–214). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-36911-7_13

• Şapcı, A. O. B., Taştan, Ö., & Yeniterzi, R. (2020). Active Learning for Turkish Text Classification. 2020 28th Signal Processing and Communications Applications Conference (SIU), 1–4. https://doi.org/10.1109/SIU49456.2020.9302289