Alice Yue

Research interests

I develop machine learning, data mining, and statistical analysis methods for big and graph-structured single-cell biological data: flow cytometry ❤, mass spectrometry, scRNAseq, bulk RNAseq, and DNA.

Publications

1. Yue, Alice. “Computational methods for cytometry.” Applied Sciences: School of Computing Science; Simon Fraser University, 2022.
   Bibtex

   @article{yue2022computational,
     title={Computational methods for cytometry},
     author={Yue, Alice},
     year={2022},
     publisher={Simon Fraser University}
   }
   

2. Yue, Alice, et al. “Automated Identification of Maximal Differential Cell Populations in Flow Cytometry Data.” Cytometry Part A, 2022, vol. 101, no.2, doi:10.1002/cyto.a.24503.
   Bibtex

   @article{yue2022automated,
     title={Automated identification of maximal differential cell populations in flow cytometry data},
     author={Yue, Alice and Chauve, Cedric and Libbrecht, Maxwell W and Brinkman, Ryan R},
     journal={Cytometry Part A},
     volume={101},
     number={2},
     pages={177--184},
     year={2022},
     publisher={Wiley Online Library}
   }
   

3. Abeler-Dörner, Lucie, et al. “High-Throughput Phenotyping Reveals Expansive Genetic and Structural Underpinnings of Immune Variation.” Nature Immunology, vol. 21, no. 1, Nature Publishing Group, 2020, pp. 86–100, doi:10.1038/s41590-019-0549-0.
   Bibtex

   @article{abeler2020high,
     title = {High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation},
     author = {Abeler-D{\"o}rner, Lucie and Laing, Adam G and Lorenc, Anna and Ushakov, Dmitry S and Clare, Simon and Speak, Anneliese O and Duque-Correa, Maria A and White, Jacqueline K and Ramirez-Solis, Ramiro and Saran, Namita and others},
     journal = {Nature Immunology},
     volume = {21},
     number = {1},
     pages = {86--100},
     year = {2020},
     publisher = {Nature Publishing Group},
     doi = {10.1038/s41590-019-0549-0}
   }
   

4. Yue, Alice, et al. “Identifying Differential Cell Populations in Flow Cytometry Data Accounting for Marker Frequency.” Poster and Spotlight Presentation at the 14th Machine Learning in Computational Biology (MLCB) Conference, Previously a Workshop of NeurIPS, 2019.
   Bibtex

   @conference{yue2019identifying,
     title = {Identifying differential cell populations in flow cytometry data accounting for marker frequency},
     author = {Yue, Alice and Chauve, Cedric and Libbrecht, Maxwell and Brinkman, Ryan},
     booktitle = {poster and spotlight presentation at the 14th Machine Learning in Computational Biology (MLCB) conference, previously a workshop of NeurIPS},
     year = {2019},
     month = dec
   }
   

5. Rajasekaran, Ashwini, et al. “Cholinergic Synapse Pathway Gene Polymorphisms Associated with Allergen-Induced Late Asthmatic Responses.” ERJ Open Research, vol. 5, no. 4, Eur Respiratory Soc, November 2019, doi:10.1183/23120541.00107-2019.
   Bibtex

   @article{rajasekaran2019cholinergic,
     title = {Cholinergic synapse pathway gene polymorphisms associated with allergen-induced late asthmatic responses},
     author = {Rajasekaran, Ashwini and He, Daniel and Yue, Alice and Singh, Amrit and Shannon, Casey P and FitzGerald, J Mark and Boulet, Louis-Philippe and O'Byrne, Paul M and Gauvreau, Gail M and Tebbutt, Scott J},
     journal = {ERJ open research},
     volume = {5},
     number = {4},
     year = {2019},
     month = nov,
     publisher = {Eur Respiratory Soc},
     doi = {10.1183/23120541.00107-2019}
   }
   

6. Cossarizza, Andrea, et al. “Guidelines for the Use of Flow Cytometry and Cell Sorting in Immunological Studies.” European Journal of Immunology, vol. 49, no. 10, Wiley Online Library, 2019, pp. 1457–973, doi:10.1002/eji.201970107.
   Bibtex

   @article{cossarizza2019guidelines,
     title = {Guidelines for the use of flow cytometry and cell sorting in immunological studies},
     author = {Cossarizza, Andrea and Chang, Hyun-Dong and Radbruch, Andreas and Acs, Andreas and Adam, Dieter and Adam-Klages, Sabine and Agace, William W and Aghaeepour, Nima and Akdis, M{\"u}beccel and Allez, Matthieu and others},
     journal = {European journal of immunology},
     volume = {49},
     number = {10},
     pages = {1457--1973},
     year = {2019},
     publisher = {Wiley Online Library},
     doi = {10.1002/eji.201970107}
   }
   

7. Rahim, Albina, et al. “High Throughput Automated Analysis of Big Flow Cytometry Data.” Methods, vol. 134, Elsevier, 2018, pp. 164–76, doi:10.1016/j.ymeth.2017.12.015.
   Bibtex

   @article{rahim2018high,
     title = {High throughput automated analysis of big flow cytometry data},
     author = {Rahim, Albina and Meskas, Justin and Drissler, Sibyl and Yue, Alice and Lorenc, Anna and Laing, Adam and Saran, Namita and White, Jacqui and Abeler-D{\"o}rner, Lucie and Hayday, Adrian and others},
     journal = {Methods},
     volume = {134},
     pages = {164--176},
     year = {2018},
     publisher = {Elsevier},
     doi = {10.1016/j.ymeth.2017.12.015}
   }
   

8. Yue, Alice. “Feature-Based Comparison of Flow Cytometry Data.” Applied Sciences: School of Computing Science; Simon Fraser University, 2017.
   Bibtex

   @mastersthesis{yue2017feature,
     title = {Feature-based Comparison of Flow Cytometry Data},
     author = {Yue, Alice},
     year = {2017},
     school = {Applied Sciences: School of Computing Science},
     pdf = {http://summit.sfu.ca/system/files/iritems1/17604/etd10296_AYue.pdf}
   }
   

9. Cossarizza, Andrea, et al. “Guidelines for the Use of Flow Cytometry and Cell Sorting in Immunological Studies.” European Journal of Immunology, vol. 47, no. 10, Wiley Online Library, 2017, pp. 1584–797.
   Bibtex

   @article{cossarizza2017guidelines,
     title = {Guidelines for the use of flow cytometry and cell sorting in immunological studies},
     author = {Cossarizza, Andrea and Chang, Hyun-Dong and Radbruch, Andreas and Akdis, M{\"u}beccel and Andr{\"a}, Immanuel and Annunziato, Francesco and Bacher, Petra and Barnaba, Vincenzo and Battistini, Luca and Bauer, Wolfgang M and others},
     journal = {European journal of immunology},
     volume = {47},
     number = {10},
     pages = {1584--1797},
     year = {2017},
     publisher = {Wiley Online Library}
   }