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.


  1. Yue, Alice. “Computational methods for cytometry.” Applied Sciences: School of Computing Science; Simon Fraser University, 2022.
  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.
  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.
  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.
  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.
  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.
  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.
  8. Yue, Alice. “Feature-Based Comparison of Flow Cytometry Data.” Applied Sciences: School of Computing Science; Simon Fraser University, 2017.
  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.

Paper review

Reviewed papers for: ACM (2018), ISMB (2019, 2020), Neurips (2020), Oxford Bioinformatics (2016, 2020), and RECOMB (2020)

Committe member for: MLCB (2019)


  • Jan/March 2023-2024 Instructor, Automated analysis of flow cytometry data in R, Physalia / University of Cologne

    Designed and instructed a course on analyzing flow cytometry data with R/Bioconductor via automated gating, clustering, and dimensionality reduction.

  • Summer 2021 Instructor, CMPT 127 (computing laboratory C/C++), SFU

    Delivered assignments, quizzes, and lecture material for the course.

  • Summer 2021 Contractor, faculty of applied science, SFU

    Developed introductory programming material for the START program created to welcome entering undergraduate students.

  • Fall 2018 Guest lecturer, CMPT 884 (data mining seminar), SFU

    Presented research projects.

  • 2018 - 2020 Teaching assistant, faculty of applied science, SFU

    Led tutorials and office hours, marked assignments and quizzes, curated student feedback.

    Courses: CMPT 105 (technical writing; Fall 2019), 120 (introduction to computing science; Spring 2018, Fall 2020), and 225 (data structures; Fall 2018)

  • 2018, 2019 Mentor, AI4All Invent the Future Scholars Program, SFU

    Mentored and created projects for the bioinformatics group during the first and second annual summer enrichment program for high school girls in Canada.

    Github repositories:


  • 2017 - 2022 Treasurer, computing science steward, TSSU (teaching support staff union), SFU

    In charge of bookkeeping (payroll, stipends, remittences, bill payments, etc.), budget creation, financial reporting, and process improvements.

    Acted as liason between students and the TSSU.

  • 2017 - 2021 President (past: VP of Finance, GSS councillor, TSSU steward), Computing science graduate student association, SFU

    Sucessfully re-initiated and created administrative structure to an inactive caucus. Provided oversight, and organized social and academic events for the student body;

    e.g. general meetings, lunch social, facuty candidate seminar lunch, game night, logo contest, amenity cleaning socials, buddy program for new students.

    Acted as the liason between the school, GSS (graduate student society), TSSU, and the student body.

Scholarships and awards

  • 2021 Wilson Clark Graduate Scholarship, SFU
  • 2015 - 2021 Compting Sience Graduate Fellowship, SFU
  • 2017 - 2020 Canada Graduate Scholarships PGS-D, NSERC
  • 2019 DBMiner Award, SFU
  • 2016 Canada Graduate Scholarships MSc Program, NSERC
  • 2015 MADD-Gen MSc fellowship, SFU, NSERC
  • 2014 Audrey May McCormick Scholarship, UVic
  • 2013, 2014 Mrs Annie Greskiw Scholarship, UVic
  • 2012 - 2015 UVic Excellence Scholarship, UVic
  • 2012, 2013 Dr Ken and Barbara Thornton Memorial Award, UVic
  • 2012 Steven A Huesing Memorial Entrance Scholarship, UVic
  • 2012 Governor General Academic Medal, Chancellery of Honours, Canada
  • 2012 Coast Capital Standing Tall Award
  • 2012 Johnson Inc Sky's the Limit Scholarship
  • 2010-2012 Service Award with Distinction, Byrne Creek
  • 2011 National AP Scholar (Canada)