proposal.bib

@article{fister2013brief,
title="A brief review of nature-inspired algorithms for optimization",
author="Fister Jr, Iztok and Yang, Xin-She and Fister, Iztok and Brest, Janez and Fister, Dusan",
journal={arXiv preprint arXiv:1307.4186},
year="2013"
}
@article{banks2007review,
  title={A review of particle swarm optimization. Part I: background and development},
  author={Banks, Alec and Vincent, Jonathan and Anyakoha, Chukwudi},
  journal={Natural Computing},
  volume={6},
  number={4},
  pages={467--484},
  year={2007},
  publisher={Springer}
}
@inproceedings{hardin2005dna,
  title={DNA motif detection using particle swarm optimization and expectation-maximization},
  author={Hardin, C Timothy and Rouchka, Eric C},
  booktitle={Proceedings 2005 IEEE Swarm Intelligence Symposium, 2005. SIS 2005.},
  pages={181--184},
  year={2005},
  organization={IEEE}
}
@article{lei2010particle,
  title={A particle swarm optimization-based algorithm for finding gapped motifs},
  author={Lei, Chengwei and Ruan, Jianhua},
  journal={BioData mining},
  volume={3},
  number={1},
  pages={1--12},
  year={2010},
  publisher={BioMed Central}
}
@article{reddy2010planted,
  title={Planted (l, d)-motif finding using particle swarm optimization},
  author={Reddy, U Srinivasulu and Arock, Michael and Reddy, AV},
  journal={IJCA Special Issue ECQT},
  volume={2},
  pages={51--56},
  year={2010},
  publisher={Citeseer}
}
@article{ge2019discovery,
  title={Discovery of DNA motif utilising an integrated strategy based on random projection and particle swarm optimization},
  author={Ge, Hongwei and Yu, Jinghong and Sun, Liang and Wang, Zhen and Yao, Yao},
  journal={Mathematical Problems in Engineering},
  volume={2019},
  year={2019},
  publisher={Hindawi}
}
@article{sebastian2014footprintdb,
  title={footprintDB: a database of transcription factors with annotated cis elements and binding interfaces},
  author={Sebastian, Alvaro and Contreras-Moreira, Bruno},
  journal={Bioinformatics},
  volume={30},
  number={2},
  pages={258--265},
  year={2014},
  publisher={Oxford University Press}
}
@article{ando2021lcm,
  title={LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation},
  author={Ando, Atsumi and Kirkbride, Ryan C and Jones, Don C and Grimwood, Jane and Chen, Z Jeffrey},
  journal={BMC genomics},
  volume={22},
  number={1},
  pages={1--16},
  year={2021},
  publisher={Springer}
}
@article{li2009sequence,
  title={The sequence alignment/map format and SAMtools},
  author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
  journal={Bioinformatics},
  volume={25},
  number={16},
  pages={2078--2079},
  year={2009},
  publisher={Oxford University Press}
}
@article{chen2020genomic,
  title={Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement},
  author={Chen, Z Jeffrey and Sreedasyam, Avinash and Ando, Atsumi and Song, Qingxin and De Santiago, Luis M and Hulse-Kemp, Amanda M and Ding, Mingquan and Ye, Wenxue and Kirkbride, Ryan C and Jenkins, Jerry and others},
  journal={Nature genetics},
  volume={52},
  number={5},
  pages={525--533},
  year={2020},
  publisher={Nature Publishing Group}
}
@article{Julia-2017,
    title={Julia: A fresh approach to numerical computing},
    author={Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B},
    journal={SIAM {R}eview},
    volume={59},
    number={1},
    pages={65--98},
    year={2017},
    publisher={SIAM},
    doi={10.1137/141000671},
    url={https://epubs.siam.org/doi/10.1137/141000671}
}
@conference{Kluyver2016jupyter,
Title = {Jupyter Notebooks -- a publishing format for reproducible computational workflows},
Author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando P{\'e}rez and Brian Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Dami{\'a}n Avila and Safia Abdalla and Carol Willing},
Booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
Editor = {F. Loizides and B. Schmidt},
Organization = {IOS Press},
Pages = {87 - 90},
Year = {2016}
}
@article{betancourt2017conceptual,
  title={A conceptual introduction to Hamiltonian Monte Carlo},
  author={Betancourt, Michael},
  journal={arXiv preprint arXiv:1701.02434},
  year={2017}
}