Seq • Publications

Publications

Shajii, Ariya, Ibrahim Numanagić, Alexander T. Leighton, Haley Greenyer, Saman Amarasinghe, and Bonnie Berger. “A Python-based programming language for high-performance computational genomics.” Nature Biotechnology (2021). https://doi.org/10.1038/s41587-021-00985-6.

Shajii, Ariya, Ibrahim Numanagić, Alexander T. Leighton, Haley Greenyer, Saman Amarasinghe, and Bonnie Berger. “A Python-based optimization framework for high-performance genomics.” bioRxiv (2020). https://doi.org/10.1101/2020.10.29.361402.
Berger, Emily, Deniz Yorukoglu, Lillian Zhang, Sarah K. Nyquist, Alex K. Shalek, Manolis Kellis, Ibrahim Numanagić, and Bonnie Berger. “Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets.” Nature Communications (2020). https://doi.org/10.1038/s41467-020-18320-z.

Shajii, Ariya, Ibrahim Numanagić, Riyadh Baghdadi, Bonnie Berger, and Saman Amarasinghe. “Seq: a high-performance language for bioinformatics.” OOPSLA (2019). https://doi.org/10.1145/3360551.