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

Diagnostics of viral infections using high-throughput genome sequencing data. - Ning, Haochen; Boyes, Ian; Numanagic, Ibrahim; Rott, Michael; Xing, Li; Zhang, Xuekui (Briefings Bioinform., 2024)

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

Fast characterization of segmental duplication structure in multiple genome assemblies. - Iseric, Hamza; Alkan, Can; Hach, Faraz; Numanagic, Ibrahim (Algorithms Mol. Biol., 2022)

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

BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. - Iseric, Hamza; Alkan, Can; Hach, Faraz; Numanagic, Ibrahim (2021)

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

Genomic Data Compression. - Zhu, Kaiyuan; Numanagic, Ibrahim; Sahinalp, Süleyman Cenk (2019)

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

Computational identification of micro-structural variations and their proteogenomic consequences in cancer. - Lin, Yen-Yi; Gawronski, Alexander; Hach, Faraz; Li, Sujun; Numanagic, Ibrahim; Sarrafi, Iman; Mishra, Swati; McPherson, Andrew W.; Collins, Colin C.; Radovich, Milan; Tang, Haixu; Sahinalp, Süleyman Cenk (Bioinform., 2018)

Fast characterization of segmental duplications in genome assemblies. - Numanagic, Ibrahim; Gökkaya, Alim S.; Zhang, Lillian; Berger, Bonnie; Alkan, Can; Hach, Faraz (Bioinform., 2018)

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

Fast Characterization of Segmental Duplications in Genome Assemblies. - Numanagic, Ibrahim; Gökkaya, Alim S.; Zhang, Lillian; Berger, Bonnie; Alkan, Can; Hach, Faraz (CoRR, 2018)

Discovery and genotyping of novel sequence insertions in many sequenced individuals. - Kavak, Pinar; Lin, Yen-Yi; Numanagic, Ibrahim; Asghari, Hossein; Güngör, Tunga; Alkan, Can; Hach, Faraz (Bioinform., 2017)

Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data. - Numanagic, Ibrahim; Malikic, Salem; Pratt, Victoria M.; Skaar, Todd C.; Flockhart, David A.; Sahinalp, Süleyman Cenk (Bioinform., 2015)

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. - Dao, Phuong; Numanagic, Ibrahim; Lin, Yen-Yi; Hach, Faraz; Karakoç, Emre; Donmez, Nilgun; Collins, Colin C.; Eichler, Evan E.; Sahinalp, Süleyman Cenk (Bioinform., 2014)

SCALCE: boosting sequence compression algorithms using locally consistent encoding. - Hach, Faraz; Numanagic, Ibrahim; Alkan, Can; Sahinalp, Süleyman Cenk (Bioinform., 2012)