Curriculum vitae

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Research Interests

Computational biology; metagenomics, phylogenetics and phylogenomics, and sequence analysis. Scalable algorithms, probabilistic data structures, and probabilistic modeling for molecular sequences and genomes.

Education

University of California, San Diego [2022-present]

  • Ph.D. in Bioinformatics and Systems Biology
    • Advisor: Siavash Mirarab

Sabancı University [2020-2022]

  • M.Sc. in Computer Science and Engineering
    • Thesis: “Automated Behavioral Analysis of Sleep in Drosophila melanogaster”
    • Advisors: Öznur Taştan, Sündüz Keleş (co-advisor)

Sabancı University [2015-2020]

  • B.Sc. in Computer Science and Engineering (w/ Minor in Mathematics)
    • Graduation Project: “Active Learning for Turkish Named Entity and Event Recognition”
    • Advisors: Reyyan Yeniterzi, Öznur Taştan

Professional Experience

Research

  • University of California, San Diego [2022-present, Graduate Student Researcher] - Advisor: Siavash Mirarab

  • La Jolla Institute for Immunology - [Fall 2022, Graduate Student Researcher] - Supervisor: Ferhat Ay

  • Sabancı University [2020-2022, Graduate Research Assistant] - Advisors: Öznur Taştan, Sündüz Keleş

  • University of Wisconsin-Madison [Summer 2020, Undergraduate Research Assistant] - Supervisor: Sündüz Keleş

  • Technical University of Munich [Summer 2019, Undergraduate Research Assistant] - Supervisor: Martin Schreiber

  • Sabancı University [Summer & Fall 2018, Undergraduate Research Assistant] - Supervisor: Kamer Kaya

Teaching

UC San Diego - Teaching Assistant

  • ECE 208: Computational Evolutionary Biology [Spring 2026]
  • ECE 30: Introduction to Computer Engineering [Spring 2025]

Sabancı University - Teaching Assistant

  • CS 300: Data Structures [Spring 2022]
  • CS 301: Algorithms [Fall 2021]
  • CS 404: Artificial Intelligence [Spring 2021]
  • CS 302: Formal Languages and Automata Theory [Fall 2020]

Sabancı University - Undergraduate Teaching Assistant

  • CS 301: Algorithms [Spring 2020]
  • CS 201: Introduction to Computing [Fall 2018, Spring 2019]

Fellowships & Awards

Awards

  • ISMB Conference Fellowship ($750) [2026]
  • RECOMB Travel Fellowship ($2,000) [2026]
  • IMSI Workshop Travel Support ($2,200) [2025]
    • “Contemporary Challenges in Large-Scale Sequence Alignments & Phylogenies”
  • RECOMB-CG Best Paper Award [2023]
  • Highest Ranking Student Award - Turkish Council of Higher Education [2015]

Fellowships

  • Powell Fellowship - The Charles Lee Powell Foundation [2022]
    • One-year award for tuition and $40,000 towards stipend.
  • Fulbright Ph.D. Grant - Fulbright Commission (declined in favor of Powell Fellowship) [2022]
  • Full Graduate Scholarship - Sabancı University [2020-2021]
    • Merit-based; tuition, housing, and $\approx$$11,000 stipend annually

(Undergraduate) Scholarships

  • Sakıp Sabancı Fellowship - Sabancı University [2015-2020]
    • Merit-based; tuition, housing, and $\approx$$7,000 stipend annually
  • DEVAK Scholarship - Deloitte Education Foundation [2018-2020]
    • Merit-based stipend; $\approx$$7,000 annually
  • Monthly Financial Aid Scholarship - Hacı Ömer Sabancı Foundation [2016-2018]
    • Need-based stipend; $\approx$$7,000 annually

Publications

Preprints

Journal Publications

  • Şapcı, A. O. B., Arasti, S., Braun, E. L., & Mirarab, S. (2026). Phlag: Scalable detection of genomics regions with unexplained phylogenetic heterogeneity. Bioinformatics, 42 (Supplement 1), btag273. https://doi.org/10.1093/bioinformatics/btag273
  • Melendez, D., Şapcı, A. O. B., Bafna, V., & Mirarab, S. (2026). SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation. Molecular Ecology Resources, 26(3), e70145. https://doi.org/10.1111/1755-0998.70145
  • 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, 27(1), 108. https://doi.org/10.1186/s13059-026-03999-y
  • Keleş, M. F., Şapcı, 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, 34(9), 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, 40(4), btae150. https://doi.org/10.1093/bioinformatics/btae150
  • Şapcı, A. O. B., Lu, S., Yan, S., Ay, F., Taştan, Ö., & 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., & Taştan, Ö. (2023). Focusing on potential named entities during active label acquisition. Natural Language Engineering, 29(6), 1-23. https://doi.org/10.1017/S1351324923000165

Peer-Reviewed Conference Proceedings

  • Şapcı, A. O. B., & Mirarab, S. (2025). Alignment-Free Estimation of Read to Genome Distances and Its Applications. In Research in Computational Molecular Biology (RECOMB) (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 Research in Computational Molecular Biology (RECOMB) (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 Comparative Genomics (RECOMB-CG) (pp. 196-214). Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-36911-7_13 - Best Paper Award
  • Şapcı, A. O. B., Taştan, Ö., & Yeniterzi, R. (2020). Active Learning for Turkish Text Classification. 28th Signal Processing and Communications Applications Conference (SIU), 1-4. https://doi.org/10.1109/SIU49456.2020.9302289 - Selected for oral presentation

Selected Presentations

  • [2026] ISMB - Phlag: Scalable detection of genomics regions w/ unexplained phylogenetic heterogeneity [proceedings talk]
  • [2026] RECOMB - Deconvolving Phylogenetic Distance Mixtures [proceedings talk]
  • [2026] RECOMB-seq - A genome-wide likelihood framework for distance-based pattern matching [short talk]
  • [2026] Sabancı University - Scalable methods for phylogeny-aware sequence analysis [invited lecture]
  • [2025] IMSI, UChicago - Read to genome distance calculation & phylogenetic placement using krepp [tutorial]
  • [2025] RECOMB - Estimating read-genome distances from homologous k-mers [proceedings talk]
  • [2024] RECOMB - Memory-bound and taxonomy-aware k-mer selection [proceedings talk]
  • [2024] BioSys (in conjunction with/ ASPLOS) - Memory-bound and taxonomy-aware k-mer selection [talk]
  • [2023] RECOMB-CG - CONSULT-II: Taxonomic identification using locality sensitive hashing [talk]
  • [2021] MLCB - MuDCoD: Multi-subject community detection in dynamic gene networks [short talk]
  • [2020] SIU - Active Learning for Turkish Text Classification [short talk]

Posters

  • A genome-wide likelihood framework for distance estimation & pattern matching.
    Research in Computational Molecular Biology (RECOMB), Thessaloniki, Greece [May 2026] [poster]
  • A probabilistic framework for sequence distances & genome-wide (phylogenetic) pattern matching.
    Probabilistic Modeling in Genomics (ProbGen), UC Berkeley [March 2026] [poster]
  • Mapping strongly discordant regions on the genome using hidden Markov models.
    Institute for Mathematical and Statistical Innovation, Chicago [August 2025] [poster]
  • MuDCoD: Multi-subject community detection in dynamic gene networks.
    Machine Learning in Computational Biology (MLCB) [November 2021] [poster]

Professional Activities

Organizer

  • ISMB Workshop, Washington D.C. [2026]
    • “Metagenomic sequence analysis using k-mer based methods”
    (a full-day workshop, speakers include Ben Langmead, David Koslicki, Siavash Mirarab, Fengzhu Sun, Yun William Yu)

Reviewer (includes sub/co-reviewing)

  • Journals:

    • Molecular Ecology Resources
    • Genome Research
    • Proceedings of Machine Learning Research
    • Bioinformatics
    • Bioinformatics Advances
    • Machine Learning

  • Conferences:

    • RECOMB (2025, 2026)
    • ISMB (2022)
    • ACML (2021, 2022)

Mentor

  • During my PhD: (undergraduates and MSc students)
    • Isaac Ang [2026 Summer - present]
    • Ali Alabiad [2024 Summer - present]
    • Sankalp Kumaraswamy [2024 Fall - 2025 Fall]