references.bib

@article{carbo2023comparison,
  title={A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2},
  author={Carbo, Ellen C and Mourik, Kees and Boers, Stefan A and Munnink, Bas Oude and Nieuwenhuijse, David and Jonges, Marcel and Welkers, Matthijs RA and Matamoros, Sebastien and van Harinxma Thoe Slooten, Joost and Kraakman, Margriet EM and others},
  journal={European Journal of Clinical Microbiology \& Infectious Diseases},
  volume={42},
  number={6},
  pages={701--713},
  year={2023},
  publisher={Springer}
}

@misc{NHGRI2024,
  author       = {{National Human Genome Research Institute}},
  title        = {Base Pair},
  year         = 2024,
  month        = may,
  url          = {https://www.genome.gov/genetics-glossary/Base-Pair},
  publisher    = {National Human Genome Research Institute},
  howpublished = {Web page}
}

@manual{Illumina2016Nextera,
  title = {{Nextera\textsuperscript{\textregistered} DNA Library Prep Reference Guide}},
  organization = {Illumina},
  year = {2016},
  version = {15027987 v01},
  note = {For Research Use Only. Not for use in diagnostic procedures.},
  url = {https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nexteradna/nextera-dna-library-prep-reference-guide-15027987-01.pdf}
}

@article{kandwal2023genetic,
  title={Genetic conservation across SARS-CoV-2 non-structural proteins--Insights into possible targets for treatment of future viral outbreaks},
  author={Kandwal, Shubhangi and Fayne, Darren},
  journal={Virology},
  year={2023},
  publisher={Elsevier}
}

@article{angermueller2016deep,
  title={Deep learning for computational biology},
  author={Angermueller, Christof and P{\"a}rnamaa, Tanel and Parts, Leopold and Stegle, Oliver},
  journal={Molecular systems biology},
  volume={12},
  number={7},
  pages={878},
  year={2016}
}

@article{genslms2023,
  title={GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics},
  author={Zvyagin, Maxim and Brace, Alexander and Hippe, Kyle and Deng, Yuntian and Zhang, Bin and Bohorquez, Cindy Orozco and Clyde, Austin and Kale, Bharat and Perez-Rivera, Danilo and Ma, Heng and others},
  journal={The International Journal of High Performance Computing Applications},
  volume={37},
  number={6},
  pages={683--705},
  year={2023},
  publisher={SAGE Publications Sage UK: London, England}
}

@book{lavravc2021representation,
  title={Representation Learning: Propositionalization and Embeddings},
  author={Lavra{\v{c}}, Nada and Podpe{\v{c}}an, Vid and Robnik-{\v{S}}ikonja, Marko},
  year={2021},
  publisher={Springer}
}