% BibTeX Template File
% Examples of properly formatted entries for all common types

% =============================================================================
% JOURNAL ARTICLES
% =============================================================================

@article{Jumper2021,
  author  = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {\v{Z}}{\'\i}dek, Augustin and Potapenko, Anna and others},
  title   = {Highly Accurate Protein Structure Prediction with {AlphaFold}},
  journal = {Nature},
  year    = {2021},
  volume  = {596},
  number  = {7873},
  pages   = {583--589},
  doi     = {10.1038/s41586-021-03819-2}
}

@article{Watson1953,
  author  = {Watson, James D. and Crick, Francis H. C.},
  title   = {Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid},
  journal = {Nature},
  year    = {1953},
  volume  = {171},
  number  = {4356},
  pages   = {737--738},
  doi     = {10.1038/171737a0}
}

@article{Doudna2014,
  author  = {Doudna, Jennifer A. and Charpentier, Emmanuelle},
  title   = {The New Frontier of Genome Engineering with {CRISPR-Cas9}},
  journal = {Science},
  year    = {2014},
  volume  = {346},
  number  = {6213},
  pages   = {1258096},
  doi     = {10.1126/science.1258096}
}

% =============================================================================
% BOOKS
% =============================================================================

@book{Kumar2021,
  author    = {Kumar, Vinay and Abbas, Abul K. and Aster, Jon C.},
  title     = {Robbins and Cotran Pathologic Basis of Disease},
  publisher = {Elsevier},
  year      = {2021},
  edition   = {10},
  address   = {Philadelphia, PA},
  isbn      = {978-0-323-53113-9}
}

@book{Alberts2014,
  author    = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Morgan, David and Raff, Martin and Roberts, Keith and Walter, Peter},
  title     = {Molecular Biology of the Cell},
  publisher = {Garland Science},
  year      = {2014},
  edition   = {6},
  address   = {New York, NY},
  isbn      = {978-0-815-34432-2}
}

% Book with editor instead of author
@book{Sambrook2001,
  editor    = {Sambrook, Joseph and Russell, David W.},
  title     = {Molecular Cloning: A Laboratory Manual},
  publisher = {Cold Spring Harbor Laboratory Press},
  year      = {2001},
  edition   = {3},
  address   = {Cold Spring Harbor, NY},
  isbn      = {978-0-879-69576-7}
}

% =============================================================================
% CONFERENCE PAPERS (PROCEEDINGS)
% =============================================================================

@inproceedings{Vaswani2017,
  author    = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N. and Kaiser, {\L}ukasz and Polosukhin, Illia},
  title     = {Attention is All You Need},
  booktitle = {Advances in Neural Information Processing Systems 30 (NeurIPS 2017)},
  year      = {2017},
  pages     = {5998--6008},
  address   = {Long Beach, CA},
  url       = {https://proceedings.neurips.cc/paper/2017/hash/3f5ee243547dee91fbd053c1c4a845aa-Abstract.html}
}

@inproceedings{He2016,
  author    = {He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
  title     = {Deep Residual Learning for Image Recognition},
  booktitle = {Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR)},
  year      = {2016},
  pages     = {770--778},
  address   = {Las Vegas, NV},
  doi       = {10.1109/CVPR.2016.90}
}

% =============================================================================
% BOOK CHAPTERS
% =============================================================================

@incollection{Brown2020,
  author    = {Brown, Peter O. and Botstein, David},
  title     = {Exploring the New World of the Genome with {DNA} Microarrays},
  booktitle = {DNA Microarrays: A Molecular Cloning Manual},
  editor    = {Eisen, Michael B. and Brown, Patrick O.},
  publisher = {Cold Spring Harbor Laboratory Press},
  year      = {2020},
  pages     = {1--45},
  address   = {Cold Spring Harbor, NY}
}

% =============================================================================
% PHD THESES / DISSERTATIONS
% =============================================================================

@phdthesis{Johnson2023,
  author  = {Johnson, Mary L.},
  title   = {Novel Approaches to Cancer Immunotherapy Using {CRISPR} Technology},
  school  = {Stanford University},
  year    = {2023},
  type    = {{PhD} dissertation},
  address = {Stanford, CA}
}

% =============================================================================
% MASTER'S THESES
% =============================================================================

@mastersthesis{Smith2022,
  author  = {Smith, Robert J.},
  title   = {Machine Learning Methods for Protein Structure Prediction},
  school  = {Massachusetts Institute of Technology},
  year    = {2022},
  type    = {{Master's} thesis},
  address = {Cambridge, MA}
}

% =============================================================================
% TECHNICAL REPORTS
% =============================================================================

@techreport{WHO2020,
  author      = {{World Health Organization}},
  title       = {Clinical Management of {COVID-19}: Interim Guidance},
  institution = {World Health Organization},
  year        = {2020},
  type        = {Technical Report},
  number      = {WHO/2019-nCoV/clinical/2020.5},
  address     = {Geneva, Switzerland}
}

% =============================================================================
% PREPRINTS
% =============================================================================

% bioRxiv preprint
@misc{Zhang2024preprint,
  author       = {Zhang, Yi and Chen, Li and Wang, Hui and Liu, Xin},
  title        = {Novel Therapeutic Targets in {Alzheimer}'s Disease},
  year         = {2024},
  howpublished = {bioRxiv},
  doi          = {10.1101/2024.01.15.575432},
  note         = {Preprint}
}

% arXiv preprint
@misc{Brown2024arxiv,
  author       = {Brown, Alice and Green, Bob},
  title        = {Advances in Quantum Computing},
  year         = {2024},
  howpublished = {arXiv},
  note         = {arXiv:2401.12345}
}

% =============================================================================
% DATASETS
% =============================================================================

@misc{AlphaFoldDB2021,
  author       = {{DeepMind} and {EMBL-EBI}},
  title        = {{AlphaFold} Protein Structure Database},
  year         = {2021},
  howpublished = {Database},
  url          = {https://alphafold.ebi.ac.uk/},
  doi          = {10.1093/nar/gkab1061},
  note         = {Version 4}
}

% =============================================================================
% SOFTWARE / CODE
% =============================================================================

@misc{McKinney2010pandas,
  author       = {McKinney, Wes},
  title        = {pandas: A Foundational {Python} Library for Data Analysis and Statistics},
  year         = {2010},
  howpublished = {Software},
  url          = {https://pandas.pydata.org/},
  note         = {Python Data Analysis Library}
}

% =============================================================================
% WEBSITES / ONLINE RESOURCES
% =============================================================================

@misc{NCBI2024,
  author       = {{National Center for Biotechnology Information}},
  title        = {{PubMed}: Database of Biomedical Literature},
  year         = {2024},
  howpublished = {Website},
  url          = {https://pubmed.ncbi.nlm.nih.gov/},
  note         = {Accessed: 2024-01-15}
}

% =============================================================================
% SPECIAL CASES
% =============================================================================

% Article with organization as author
@article{NatureEditorial2023,
  author  = {{Nature Editorial Board}},
  title   = {The Future of {AI} in Scientific Research},
  journal = {Nature},
  year    = {2023},
  volume  = {615},
  pages   = {1--2},
  doi     = {10.1038/d41586-023-00001-1}
}

% Article with no volume number (some journals)
@article{OpenAccess2024,
  author  = {Williams, Sarah and Thomas, Michael},
  title   = {Open Access Publishing in the 21st Century},
  journal = {Journal of Scholarly Communication},
  year    = {2024},
  pages   = {e123456},
  doi     = {10.1234/jsc.2024.123456}
}

% Conference paper with DOI
@inproceedings{Garcia2023,
  author    = {Garc{\'i}a-Mart{\'i}nez, Jos{\'e} and M{\"u}ller, Hans},
  title     = {International Collaboration in Science},
  booktitle = {Proceedings of the International Conference on Academic Publishing},
  year      = {2023},
  pages     = {45--52},
  doi       = {10.1109/ICAP.2023.123456}
}

% Article with PMID but no DOI (older papers)
@article{OldPaper1995,
  author  = {Anderson, Philip W.},
  title   = {Through the Glass Lightly},
  journal = {Science},
  year    = {1995},
  volume  = {267},
  number  = {5204},
  pages   = {1615--1616},
  note    = {PMID: 17808148}
}

