Last Update: 2017/06/15

Albert Lee

Contact Information

Education

  • 2011-2017, Ph.D. in Biomedical Informatics, Columbia University, PI: Raul Rabadan
  • 2011-2013, M.A. in Biomedical Informatics, Columbia University
  • 2006-2010, B.S. in Molecular, Cell, and Developmental Biology, University of California, Los Angeles

Publication

  1. The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3beta inhibition. Nature, to appear 2017.
    G. Varano, S. Raffel, M. Sormani, F. Zanardi, S. Lonardi, C. Zasada, L. Perucho, V. Petrocelli, A. Haake, A. Lee, M. Bugatti, U. Paul, E. Anken, L. Pasqualucci, R. Rabadan, R. Siebert, S. Kempa, M. Ponzoni, F. Facchetti, K. Rajewsky, and S. Casola.

  2. Germ-cell-specific inflammasome component NLRP14 negatively regulates cytosolic nucleic acid sensing to promote fertilization. Immunity, 46 (4) 621–634, 2017.
    T. Abe, A. Lee, R. Sitharam, J. Kesner, R. Rabadan, and S. Shapira.

  3. De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. BMC genomics, 16 (1) 1033, 2015.
    A. Lee, K. Kulcsar, O. Elliott, H. Khiabanian, E. Nagle, M. Jones, B. Amman, M. Sanchez-Lockhart, J. Towner, G. Palacios, and R. Rabadan

  4. High-resolution genomic surveillance of 2014 Ebolavirus using shared subclonal variants. PLoS currents, 7 ,2015.
    K. Emmett, A. Lee, H. Khiabanian, and R. Rabadan.

  5. A targetable GATA2-IGF2 axis confers aggressiveness in lethal prostate cancer. Cancer cell, 27 (2) 223–239, 2015.
    S. Vidal, V. Rodriguez-Bravo, S. Quinn, R. Rodriguez-Barrueco, A. Lujambio, E. Williams, X. Sun, J. de la Iglesia-Vicente, A. Lee, B. Readhead, X. Chen, M. Galsky, B. Esteve, D. Petrylak, J. Dudley, R. Rabadan, J. Silva, Y. Hoshida, S. Lowe, C. Cordon-Cardo, and J. Domingo-Domenech.

  6. Transcriptome reconstruction and annotation of cynomolgus and African green monkey. BMC genomics, 15 (1) 846, 2014.
    A. Lee, H. Khiabanian, J. Kugelman, O. Elliott, E. Nagle, G. Yu, T. Warren, G. Palacios, and R. Rabadan.

  7. Leukaemogenesis induced by an activating [bgr]-catenin mutation in osteoblasts. Nature, 506 (7487) 240–244, 2014. A. Kode, J. Manavalan, I. Mosialou, G. Bhagat, C. Rathinam, N. Luo, H. Khiabanian, A. Lee, V. Murty, R. Friedman, A. Brum, D. Park, N. Galili, S. Mukherjee, J. Teruya-Feldstein, A. Raza, R. Rabadan, E. Berman, and S. Kousteni.

  8. Drivers of morphological diversity and distribution in the Hawaiian fern flora: trait associations with size, growth form, and environment. American Journal of Botany, 98 (6) 956–966, 2011.
    C. Creese, A. Lee, and L. Sack.

Experience

2011–2017, Graduate Research Scientist, Rabadan Lab, Columbia University

  • Multi-institutional Collaboration: Collaborated with researchers from Boston University, U.S. Army Medical Research Institute of Infectious Diseases(USAMRIID), and Centers for Disease Control and Prevention(CDC) on characterizing genome and transcriptome of Egyptian Fruit Bat.
  • Statistical Software Development: Designed and built the statistical framework based on Bayesian multilevel modeling technique to analyze complex(3 tissues/5 time points/14K genes) RNA sequencing(RNA-seq) data by combining tools such as R, Shiny, Stan, and SGE.
  • High Impact Journal Publication: Worked on research questions related to cancer and immunology, the majority of which resulting in high impact scientific journals including Nature, Immunity, and BMC Genomics.

Leadership

Co-chair, Young Generation Professional Forum

Jan-Aug 2014,

  • Led the team of 20+ people, planning for and organizing the international conference designed to provide career development and leadership training for over 200 students and young professionals in science and engineering fields.

President, Consilience and Conscious Discussion Group

2015

  • Organized the bi-weekly informal seminar group consisting of 10+ members giving lectures and discussing topics ranging from sociology to astrophysics to machine learning.

Supervisor, Academic Advancement Program

2009-2010

  • Led the team of 5 tutors. Interviewed and trained newly hired tutors, providing guidance on classroom management and interactions with students.
  • Led a department meeting twice per week with physics tutors to discuss various issues related to tutoring and the program.
  • Designed and developed a database of tutor profiles and student evaluations.

Teaching

Teaching Assistant, Columbia University

Spring 2017, Fall 2015

  • Topological Data Analysis for Genomics and Applications to Cancer: tutored 8 students during office hours with their homework and conceptual understanding. Graded homework, midterms, and final examination. Taught review sessions.
  • Acculturation to Programming & Statistics: tutored 15 students understand the core programming skills and statistics concept during office hours. Graded homework, quiz, and the final examination.

Peer Learning Facilitator, Academic Advancement Program

2008-2010

  • Tutored multiple physics courses covering topics that included mechanics, waves, electricity, and magnetism. Held interactive sessions to provide students with academic support and reinforced their learning through a self-designed curriculum.

Peer Learning Facilitator, Freshman Summer Program

2009

  • Worked as a teaching assistant for a math course that covered the topic of pre- calculus (course title at UCLA: Math1). Led daily recitations / discussions, EXCEL workshops, and evening drop-in tutoring. Developed a system in which teaching assistants could update homework grades online.

Technical Skills

  • Data Collection: Selenium, rvest, BeautifulSoup4, iMacro, curl
  • Data Management: MySQL, sqlite3, AWS systems(EC2, S3, RDS)
  • Data Preprocessing: Unix coreutils(grep, sed, awk, and more), R, python, Perl, Oracle Grid Engine (SGE)
  • Data Analysis: R, Python, Stan
  • Data Visualization: ggplot2, plotly, D3, Shiny
  • Data Communication: HTML, CSS, PowerPoint, R Markdown, Latex
  • Data Techniques: Bayesian statistics, Multilevel modeling, Topological Data Analysis, Feature Engineering
  • Data Tooling: GNU Make, Git, R-Package development, Vim, Tmux, AutoHotKey

I have documented why I used these tools.

Presentations & Tutorials

  • Albert lee, 2017, Introduction to Javaplex, Guest Lecturer at Topological Data Analysis for Genomics and Applications to Cancer. February 20, 2017
  • Albert lee, 2017, Transcriptomic evaluation of the host response to aerosolized Marburg virus Angola exposure in the lymph nodes of Rhesus macaques, Speaker at Department of Biomedical Informatics Student Seminar. March 21, 2017
  • Albert lee, 2017, How to get any data on Internet, Speaker at Department of Biomedical Informatics Student Seminar. January 24, 2017
  • Albert lee, 2016, Introduction to Bayesian Statistics, Guest Lecturer at Introduction to Computer Applications in Health Care & Biomedicine. November 28, 2016
  • Albert lee, 2016, Magic and Mind, Invited Speaker at Young Generation Technical and Leadership Conference. January 22, 2016
  • Albert lee, 2015, Understanding Filovirus Biology via High Throughput Sequencing Technology, Invited Speaker at Department of Biomedical Informatics Student Seminar. February 10, 2015
  • Albert lee, 2015, Design of RNA-seq Experiments, Invited Speaker at Systems Biology Student Seminar. June 29, 2015
  • Albert lee, 2015, Introduction to Topic Modeling, Invited Speaker at Consilience and concurrence meetup. March 3, 2015
  • Albert lee, 2015, Primer on Negative Binomial Distribution in RNA-seq Analysis, Invited Speaker at Young Generation Technical and Leadership Conference. March 3, 2015
  • Albert lee, 2014, Creatures of Habit, Invited Speaker at Young Generation Technical and Leadership Conference. January 13, 2014

Awards

  • 2012, 1st place in Essay Contest, Young Generation Technical and Leadership Conference
  • 2009, Ada Ellis Scholarship
  • 2006-2010, Dean’s List of Distinguished Students

Reviewer for

  • PeerJ

Languages

  • English and Korean

Volunteer

  • Organizer, Young Generation Technical Leadership Conference Jan 2012-Aug 2014,
  • Care Extender, UCLA Ronald Reagan and santa Monica Hospitals, Sep 2008-Sep 2009