Fast genotyping of known SNPs through approximate k-mer matching. - Ariya Shajii; Deniz Yörükoglu; Yun William Yu; Bonnie Berger (Bioinform., 2016)

Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. - Ariya Shajii; Ibrahim Numanagic; Bonnie Berger (RECOMB, 2018)

Seq: a high-performance language for bioinformatics. - Ariya Shajii; Ibrahim Numanagic; Riyadh Baghdadi; Bonnie Berger; Saman P. Amarasinghe (Proc. ACM Program. Lang., 2019)

Seq (OOPSLA 2019 Artifact). - Ariya Shajii; Ibrahim Numanagic; Riyadh Baghdadi; Bonnie Berger; Saman P. Amarasinghe (Zenodo, 2019)

High-Performance Computational Genomics. - Ariya Shajii (2021)

Sequre: a high-performance framework for rapid development of secure bioinformatics pipelines. - Haris Smajlovic; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (IPDPS Workshops, 2022)

Codon: A Compiler for High-Performance Pythonic Applications and DSLs. - Ariya Shajii; Gabriel Ramirez; Haris Smajlovic; Jessica Ray; Bonnie Berger; Saman P. Amarasinghe; Ibrahim Numanagic (CC, 2023)

Vectron: A Dynamic Programming Auto-vectorization Framework. - Sourena Naser Moghaddasi; Haris Smajlovic; Ariya Shajii; Ibrahim Numanagic (CGO, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)

Shechi: A Secure Distributed Computation Compiler Based on Multiparty Homomorphic Encryption. - Haris Smajlovic; David Froelicher; Ariya Shajii; Bonnie Berger; Hyunghoon Cho; Ibrahim Numanagic (Zenodo, 2025)