About

I work on algorithms and data structures for searching very large collections of sequences. These days the sequences are human genomes.

I am a PhD candidate at the UC Santa Cruz Genomics Institute, advised by Benedict Paten and working closely with Jouni Sirén. My research is on pangenome graphs, which represent hundreds of human genomes in a single structure, and on the compressed indexes that let you search and navigate them. I care about the whole path from an idea to a tool other people use, so a good part of my work is engineering: writing C++ that holds up at the scale of a full pangenome and fits into the pipelines that genomics labs already run.

I did my undergraduate degree in computer engineering at Sharif University of Technology in Tehran. In the summer of 2025 I interned at Roche Diagnostics, working on copy number calling from sequencing data; that work is now a pending patent.

Research & software

Pangenome search and lift-over for the UCSC Genome Browser

2026 · with Jouni Sirén and Benedict Paten

A C++ web service over the full HPRC Release 2 graph. One query searches every haplotype at once, and lift-over between any two haplotypes is computed on demand from the graph rather than from precomputed pairwise chains. Live on the development browser ahead of public release.

464 haplotypes2.6 Tbp23 GiB sampled index~0.1 s per gene

Lossless pangenome indexing with tag arrays

2024 – present · open source, MIT

A run-length-compressed index that extends the r-index to report every graph position of a query with no loss of information. Construction builds chromosomes independently and merges them into a whole-genome index, so it scales to the full HPRC graphs.

Code on GitHubPaper

Personalized pangenomes and pangenome-aware DeepVariant

2023 – present · with the UCSC CGL and Google DeepVariant teams

Evaluation and integration of haplotype-sampled personalized pangenomes in the Giraffe–DeepVariant workflow, and contributions to pangenome-aware DeepVariant, which adds pangenome haplotypes to DeepVariant's pileups.

up to 25.5% fewer errors vs. linear reference

Publications

  • 2026
    Lossless pangenome indexing using tag arrays P. Eskandar, B. Paten, J. Sirén Algorithms for Molecular Biology 21:12 · doi
  • 2026
    HPRC2: A human pangenome reference with near-complete coverage of common genetic variation J. K. Lucas, P. Hebbar, W.-W. Liao, …, P. Eskandar, …, B. Paten (Human Pangenome Reference Consortium) bioRxiv preprint · doi
  • 2025
    Lossless Pangenome Indexing Using Tag Arrays P. Eskandar, B. Paten, J. Sirén WABI 2025, LIPIcs 344, 8:1–8:20 · doi
  • 2025
    Pangenome-aware DeepVariant M. Asri, P.-C. Chang, J. C. Mier, J. Sirén, P. Eskandar, …, A. Carroll, B. Paten, K. Shafin bioRxiv preprint · doi
  • 2024
    Personalized pangenome references J. Sirén, P. Eskandar, M. T. Ungaro, G. Hickey, J. M. Eizenga, A. M. Novak, X. Chang, P.-C. Chang, M. Kolmogorov, A. Carroll, J. Monlong, B. Paten Nature Methods 21, 2017–2023 · doi

Patents

  • Co-inventor, Methods and Systems for Allele-Specific Copy Number Calling. PCT/US2025/044005 (pending), Roche Diagnostics.

News

  • Talk and poster at the HPRC 2026 Annual Meeting on the pangenome search and coordinate translation service for the UCSC Genome Browser.
  • The HPRC Release 2 preprint is out on bioRxiv.
  • Lossless pangenome indexing using tag arrays is published in Algorithms for Molecular Biology.
  • Taught a hands-on Giraffe + DeepVariant pangenome variant-calling workshop at ASHG 2025.
  • Presented the tag array paper at WABI 2025.
  • The Pangenome-aware DeepVariant preprint is out on bioRxiv.