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General Information

Full Name Zijian (William) Niu
Email zniu [at] mit.edu

Education

  • 2024 - Present
    Ph.D. in Computational and Systems Biology
    Massachusetts Institute of Technology
  • 2020 - 2024
    B.A., summa cum laude, in Biochemistry, Biophysics, and Physics
    University of Pennsylvania, Roy and Diana Vagelos Scholars Program in the Molecular Life Sciences
    • GPA: 4.00/4.00
    • Relevant Coursework: Molecular Biology and Genetics, Biochemistry, Biophysics, Organic Chemistry, Statistical Mechanics, Analytical Mechanics, Quantum Mechanics, Electrodynamics, Theoretical and Computational Neuroscience, Physical Networks, Machine Learning, Large-Scale Optimization, Probability Theory, Differential Geometry, Differential Equations, Complex Analysis, Real Analysis

Research Experience

  • 2021 - 2024
    Undergraduate Researcher at the Arjun Raj Lab
    Department of Bioengineering and Genetics, University of Pennsylvania
    • Created Piscis, an automatic deep learning algorithm for spot detection in RNA fluorescence in situ hybridization (FISH) images. Significantly outperformed existing computational methods.
    • Mentored a high school researcher on deep learning and writing Python functions for data preprocessing.
    • Contributed to NimbusImage, a web platform for biological image analysis that empowers researchers to visualize their data interactively while leveraging state-of-the-art machine learning algorithms.
    • Deployed NimbusImage via Docker on Linux servers in both the Raj Lab and Shaffer Lab.
  • 2021
    Undergraduate Researcher at the Sydney Shaffer Lab
    Department of Pathology and Bioengineering, University of Pennsylvania
    • Investigated the molecular origins of Barrett's esophagus by analyzing single-cell RNA sequencing data of patient samples in R. Discovered a rare subpopulation of ciliated cells expressing fetal intestinal genes.
    • Created Cellori, a fast and robust algorithm for nuclei segmentation in fluorescence microscopy images.
    • Created DeepTile, a Python library that splits large images into smaller tiles, processes each tile, and stitches together the outputs, allowing functions to scale up to arbitrary input image sizes.

Honors and Awards

  • 2024
    • Hertz Foundation Fellowship
    • PD Soros Fellowship for New Americans
    • DOE Computational Science Graduate Fellowship (CSGF)
    • NSF Graduate Research Fellowship (GRFP) — declined
    • Penn Arts and Sciences Dean's Scholar
    • Penn Physics and Astronomy William E. Stephens Memorial Prize
    • Phi Beta Kappa
  • 2023
    • Barry M. Goldwater Scholarship
  • 2022
    • Roy and Diana Vagelos Science Challenge Award
  • 2020
    • Roy and Diana Vagelos Scholar

Teaching Experience

  • 2023
    Teaching Assistant
    ESE 5300: Elements of Probability Theory
    • Graduate-level electrical engineering (ESE) course at Penn on measure-theoretic probability theory.
    • Hosted two 1.5-hour office hours each week to guide students through assignments and recitations to review and practice important mathematical concepts.
  • 2021 - 2023
    Workshop Leader
    Organic Chemistry Workshops
    • Program coordinated by Penn's Weingarten Learning Resources Center for organic chemistry students.
    • Developed lesson plans and facilitated weekly two-hour workshop sessions to help students reinforce and apply concepts learned from lectures to solve challenging organic chemistry problems.
    • Over 200 students attended my workshops.

Leadership and Community Service

  • 2022 - 2024
    Co-founder, Co-president
    Project Lucid
    • Initiative with the mission of spreading awareness and building confidence among Penn undergraduates for effective science communication.
    • Hosted the Lucid Science Challenge, a research proposal competition based on the National Science Foundation's grant review process, providing a platform for undergraduates to practice adapting their science communication to a new audience.
    • Invited seven Penn professors and an industry scientist and executive from Ginkgo Bioworks to serve on our competition judging panels. Raised over \$1,000 from sponsorships to fund prizes and merch.
    • Hosted a science communication workshop series, covering topics such as audience identification and scientific storytelling.
  • 2020 - 2024
    Operations Committee, Event Supervisor, Urban Initiative Fellow
    Science Olympiad at the University of Pennsylvania (SOUP)
    • One of the most competitive Science Olympiad Invitational Tournaments with over 750 high schoolers participating annually.
    • Organized virtual social and Penn student panel events for the 2021 and 2022 tournaments.
    • Wrote and proctored exams for the Chemistry Lab (2021) and Codebusters (2022, 2023, 2024) events.
    • Mentored high schoolers from underserved Philadelphia high schools on their Science Olympiad events.
  • 2022 - 2023
    Vice President of Community Outreach
    Penn Undergraduate Chemistry Society (PUCS)
    • Organization to promote the appreciation of chemistry within Penn and the Philadelphia community.
    • Hosted a mixer event combining liquid nitrogen ice cream-making with a student research poster session.
    • Launched a community outreach initiative to share the fun of chemistry and its everyday relevance with students from underserved schools. Conducted a successful pilot at Parkway West High School.
  • 2015 - 2020
    Co-Founder, Director, Head Problem Writer
    Winchester Math Competition (WinMaC)
    • Math competition for elementary students in the fourth and fifth grades.
    • Proposed over 300 problems. Managed weekly team meetings. Helped with venue coordination. Fostered relationships with elementary schools. Hosted over 250 participants and 50 teams from 2016 to 2020.

Professional Development

  • 2023
    Summer School Student
    Physics of Life Summer School at Princeton University
    • Summer school offered by Princeton University's Center for the Physics of Biological Function, targeting advanced undergraduates interested in biological physics.
    • One of 24 students chosen by application to attend two weeks of lectures, problem sessions, and hands-on experiments to build an understanding of how physical principles give rise to biological phenomena.