@article{aghaeepour2012rchyoptimyx,
  title={RchyOptimyx: Cellular hierarchy optimization for flow cytometry},
  author={Aghaeepour, Nima and Jalali, Adrin and O'Neill, Kieran and Chattopadhyay, Pratip K and Roederer, Mario and Hoos, Holger H and Brinkman, Ryan R},
  journal={Cytometry Part A},
  volume={81},
  number={12},
  pages={1022--1030},
  year={2012},
  publisher={Wiley Online Library}
}

@article{aghaeepour2012early,
  title={Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays},
  author={Aghaeepour, Nima and Chattopadhyay, Pratip K and Ganesan, Anuradha and O'Neill, Kieran and Zare, Habil and Jalali, Adrin and Hoos, Holger H and Roederer, Mario and Brinkman, Ryan R},
  journal={Bioinformatics},
  volume={28},
  number={7},
  pages={1009--1016},
  year={2012},
  publisher={Oxford Univ Press}
}

@article{aghaeepour2013critical,
  title={Critical assessment of automated flow cytometry data analysis techniques},
  author={Aghaeepour, Nima and Finak, Greg and Hoos, Holger and Mosmann, Tim R and Brinkman, Ryan and Gottardo, Raphael and Scheuermann, Richard H and others},
  journal={Nature methods},
  volume={10},
  number={3},
  pages={228--238},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{villanova2013integration,
  title={Integration of Lyoplate Based Flow Cytometry and Computational Analysis for Standardized Immunological Biomarker Discovery},
  author={Villanova, Federica and Di Meglio, Paola and Inokuma, Margaret and Aghaeepour, Nima and Perucha, Esperanza and Mollon, Jennifer and Nomura, Laurel and Hernandez-Fuentes, Maria and Cope, Andrew and Prevost, A Toby and others},
  journal={PloS one},
  volume={8},
  number={7},
  pages={e65485},
  year={2013},
  publisher={Public Library of Science}
}

@article{craig2013computational,
  title={Computational analysis optimizes the flow cytometric evaluation for lymphoma},
  author={Craig, Fiona E and Brinkman, Ryan R and Eyck, Stephen Ten and Aghaeepour, Nima},
  journal={Cytometry Part B: Clinical Cytometry},
  year={2013},
  publisher={Wiley Online Library}
}
