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publications.html
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<!DOCTYPE HTML>
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<a href="index.html" class="logo">the <strong>Seq</strong> programming language</a>
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<h2>Publications</h2>
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<div class="pubs">
<h3>2021</h3>
<ul>
<li>
Shajii, Ariya, Ibrahim Numanagić, Alexander T. Leighton, Haley Greenyer, Saman Amarasinghe, and Bonnie Berger. “<b>A Python-based programming language for high-performance computational genomics</b>.” <i>Nature Biotechnology</i> (2021). <a href="https://doi.org/10.1038/s41587-021-00985-6">https://doi.org/10.1038/s41587-021-00985-6</a>.
</li>
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<h3>2020</h3>
<ul>
<li>
Shajii, Ariya, Ibrahim Numanagić, Alexander T. Leighton, Haley Greenyer, Saman Amarasinghe, and Bonnie Berger. “<b>A Python-based optimization framework for high-performance genomics</b>.” bioRxiv (2020). <a href="https://doi.org/10.1101/2020.10.29.361402">https://doi.org/10.1101/2020.10.29.361402</a>.
</li>
<li>
Berger, Emily, Deniz Yorukoglu, Lillian Zhang, Sarah K. Nyquist, Alex K. Shalek, Manolis Kellis, Ibrahim Numanagić, and Bonnie Berger. “<b>Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets</b>.” <i>Nature Communications</i> (2020). <a href="https://doi.org/10.1038/s41467-020-18320-z">https://doi.org/10.1038/s41467-020-18320-z</a>.
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<h3>2019</h3>
<ul>
<li>
Shajii, Ariya, Ibrahim Numanagić, Riyadh Baghdadi, Bonnie Berger, and Saman Amarasinghe. “<b>Seq: a high-performance language for bioinformatics</b>.” OOPSLA (2019). <a href="https://doi.org/10.1145/3360551">https://doi.org/10.1145/3360551</a>.
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