Amy T. Lam

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Scientist

2022-present

  • Enable Medicine, Menlo Park, CA
  • Technical lead for multimodal human spatial atlas building and curation.
    • Mapped synonyms and ontologies for tissue types, cell phenotypes, diseases, and treatments to facilitate organization and search of the atlas.
    • Set standards for terminology and data quality.
    • Developed tools for automating the curation and data unification process, piloting LLM-based tools on clinical metadata interpretation and organization.
    • Prepared reference datasets including metadata tags and annotations for AI/ML model training and testing.
  • Technical lead for Python image processing toolkit.
    • Led a team of scientists to develop an internal library for multi-channel image processing, directly interfacing with internal databases.
    • Library included functions for basic channel operations, artifact detection, tissue detection, stain-based mask generation, NIQE scoring for image quality, among others.
    • Developed methods for working with and processing large image files.
  • Performed spatial proteomic analysis for pharmaceutical and academic clients on a variety of tissue types and disease indications.
    • Performed cell and tissue segmentation; quality control for biomarker stains, images, and segmentation; phenotyping; and single-cell level spatial analysis for hundreds of CODEX tissue images.
    • Delivered and presented analysis results to clients and collaborators.
  • Wrote paper manuscripts, customer-facing blog posts, and tutorials related to spatial analysis of biological data, establishing best practices for working with mid- to high-plex proteomic images.

Application Scientist

2020-2022

  • ClearLight Biotechnologies, Sunnyvale, CA
  • Designed over 100 lab service projects for customers and potential customers to apply tissue clearing and 3D immunohistochemistry to answer biological questions.
    • Developed biomarker panels and selected antibodies for staining.
  • Analyzed customer data and created 3D renderings and videos using Bitplane Imaris software.
  • Processed and analyzed terabyte 3D image data files.
  • Co-authored a methods chapter on 3D immunofluorescence imaging.

Postdoctoral Scholar

2015-2020

  • Stanford University, Stanford, CA
  • University of Arizona, Tucson, AZ
  • Biophysics of Multi-Cellular Patterns Laboratory
  • Adviser: Prof. Ingmar Riedel-Kruse

Projects

  • Designed a setup for investigating principles of active matter and controllable swarming using Euglena gracilis as a model agent.
    • Developed a programming paradigm for controlling biological/microrobotic swarm agents
  • Designed and built prototype exhibits for interactive biology education for the San Francisco Exploratorium to determine how modes of interactivity affect learning outcomes.
    • One prototype has become a permanent exhibit at the Exploratorium.
  • Investigated active self-assembly with genetically modified E. coli as a model system.
  • Ran user studies on an ultra-low-cost liquid handling robot for STEM education.

Graduate Research Assistant

2010-2015

  • Columbia University, New York City, NY
  • Laboratory for Nanobiotechnology and Synthetic Biology
  • Adviser: Prof. Henry Hess

Projects

  • Studied the physical principles of dynamically self-assembling systems using molecular motors and cytoskeletal filaments as a model system.
    • Investigated molecular mechanisms of and limitations on force-production, adaptation, and self-healing by designing and implementing proof-of-concept systems.
    • Developed a non-fouling surface coating functionalized with kinesin motor binding sites.
      • Binding strength was tailored to support continual adsorption and desorption (i.e., weak binding) of the motors while also supporting microtubule motility.
    • Controlled the size of structures formed through active self-assembly through motor protein gradient surfaces.
  • Determined the entropic cost to adsorption kinetics.
  • Compared structures arising from diffusion-driven and actively-driven (i.e., propelled) self-assembly.

Summer Undergraduate Research Fellow

2008 and 2009

  • California Institute of Technology, Pasadena, CA
  • Cellular Morphodynamics and Imaging Lab
  • Adviser: Prof. Chin-Lin Guo
  • Designed and created controllable PDMS microenvironments for the study of cellular differentiation and morphogenesis.
  • Optimized procedures for photolithography and production of microfluidic devices.
  • Performed basic biology lab protocols for gel electrophoresis, cell culture, PCR, gene amplification, and protein purification.

Summer Undergraduate Research Fellow

2007

  • California Institute of Technology, Pasadena, CA
  • Caltech Nanofabrication Group
  • Adviser: Prof. Axel Scherer
  • Wrote and debugged C software for concurrent operation of lab equipment.

Publications

  1. "Spatial proteomics of human diabetic kidney disease, from health to class III." A. Kondo, M. McGrady, D. Nallapothula, H. Ali, A. E. Trevino, A. T. Lam, R. Preska, H. B. D'Angio, Z. Wu, L. N. Lopez, H. K. Badhesha, C. R. Vargas, A. Ramesh, N. Wiegley, S. S. Han, M. Dall'Era, K.-Y. Jen, A. T. Mayer, M. Afkarian, Diabetologia, (2024). [doi]
  2. "emObject: domain specific data abstraction for spatial omics." E. A. G. Baker, M. Y. Huang, A. T. Lam, M. K. Rahim, M. H. Bieniosek, B. Wang, N. R. Zhang, A. T. Mayer, A. E. Trevino, bioRxiv, (2023). [doi]
  3. "3D Imaging for Cleared Tissues and Thicker Samples on Confocal and Light-Sheet Microscopes." S. L. White, A. T. Lam, H. D. Buck, in Methods in Molecular Biology, 143-161 (2022). [doi]
  4. DIY liquid handling robots for integrated STEM education and life science research. E. Li*, A. T. Lam*, T. Fuhrmann, L. Erikson, M. Wirth, M. L. Miller, P. Blikstein, I. H. Riedel-Kruse, PLoS One, 17(11), e0275688 (2022). [doi]
  5. Scientific Inquiry in Middle Schools by combining Computational Thinking, Wet Lab Experiments, and Liquid Handling Robots. T. Fuhrmann, D. I. Ahmed, L.Arikson, M. Wirth, M. L. Miller, E. Li, A. T. Lam, P. Blikstein, I. H. Riedel-Kruse, Interaction Design and Children, 444-449 (2021). [doi]
  6. Pac-Euglena: A Living Cellular Pac-Man Meets Virtual Ghosts. A. T. Lam, J. Griffin, M. Loeun, N. Cira, S. A. Lee, I. H. Riedel-Kruse, Proceedings of the 2020 CHI Conference on Human Factors in Computing Systems, 1-13 (2020). [doi]
  7. First-hand, immersive full-body experiences with living cells through interactive museum exhibits. A. T. Lam, J. Ma, C. Barr, S. A. Lee, A. K. White, K. Yu, I. H. Riedel-Kruse, Nature Biotechnology 37(10), 1238-1241 (2019). [doi]
  8. Polygonal motion and adaptable phototaxis via flagellar beat switching in the microswimmer Euglena gracilis. A. Tsang, A. T. Lam, I. H. Riedel-Kruse, Nature Physics 14(12), 1216-1222 (2018). [doi]
  9. Adaptive non-equilibrium molecular-scale systems with reversibly-bound molecular building blocks. A. T. Lam, S. Tsitkov, Y. Zhang, H. Hess, Nano Letters 18(2), 1530-1534 (2018). [doi]
  10. Device and programming abstractions for spatiotemporal control of active micro-particle swarms. A. T. Lam, K. G. Samuel-Gama, J. Griffin, M. Loeun, L. C. Gerber, Z. Hossain, N. J. Cira, S. A. Lee, I. H. Riedel-Kruse, Lab on a Chip 17(8), 1442-1451 (2017). [doi]
    • Listed as a "HOT" article (top 10% score during peer-review)
  11. Cytoskeletal motor-driven active self-assembly in in vitro systems. A. T. Lam, V. VanDelinder, A. M. R. Kabir, H. Hess, G. D. Bachand, A. Kakugo, Soft Matter 12(4), 988-997 (2016). [doi]
  12. Controlling self-assembly of microtubule spools via kinesin motor density. A. T. Lam, C. Curschellas, D. Krovvidi, H. Hess, Soft Matter 10(43), 8731-8736 (2014). [doi]
  13. Modeling negative cooperativity in streptavidin adsorption onto biotinylated microtubules. S. He‡, A. T. Lam‡, Y. Jeune-Smith‡, H. Hess, ‡ indicates equal contribution, Langmuir 28(29), 10635-10639 (2012). [doi]
  14. Nanoscale transport enables active self-assembly of millimeter-scale structures. O. Idan, A. T. Lam, J. Kamcev, J. Gonzales, A. Agarwal, H. Hess, Nano Letters 12(1), 240-245 (2012). [doi]

Presentations

  1. Single-cell spatial proteomic analysis of the tumor microenvironment in treatment-naive NSCLC samples with immunotherapy treatment and response data. M. Cumberbatch, G. Ivison, A. T. Lam, M. Rahim, A. Mayer, M. Bhagat (poster) AACR Annual Meeting, Orlando, FL (2023).
  2. Directed by light: microswimmer biophysics, swarm programming, and interactive exhibits. A. T. Lam, A. C. H. Tsang, I. H. Riedel-Kruse, (talk) Molecules, Materials, Devices and Systems in Medicine, New York City, NY (2018).
  3. Compression and release dynamics of an active matter system of Euglena gracilis. A. T. Lam, A. C. H. Tsang, N. Ouellette, I. H. Riedel-Kruse, (talk) American Physical Society March Meeting, New Orleans, LA (2017).
  4. Modeling cooperative self-assembly. S. He, A. T. Lam, Y. Jeune-Smith, H. Hess, (poster) Biomedical Engineering Society Annual Meeting, Hartford, CT (2011).
  5. Near millimeter length microtubule wires: Bridging the gap between nanoscale and macroscale. O. Idan, J. Kamcev, J. Gonzales, A. T. Lam, A. Agarwal, Y. Jeune-Smith, H. Hess, (poster) 17th International Conference on DNA Computing and Molecular Programming, Pasadena, CA (2011).
  6. Modeling cooperative self-assembly. S. He, A. T. Lam, Y. Jeune-Smith, H. Hess, (poster) 8th Annual Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices, Snowbird, UT (2011).

Part-time faculty, Axiom Learning Center

2019-2022

  • Work one-on-one with K-12 students to improve their learning efficiency and executive functioning

Co-mentor for Motorocracy BIOMOD team, Columbia University

2014

Tutor for Star Learning Center, Goddard Riverside Community Center

2013

  • Tutored an elementary school student from a low-income household in math and reading

Teaching Assistant, Columbia University

2011-2012

Thermodynamics of Biological Systems (BMEN4200)

  • Ran weekly recitations, held office hours, generated answer keys, and graded all assignments and exams
  • Earned scores of 4.6/5 (2011) and 4.9/5 (2012) for overall quality in student teaching evaluations

Consultant, Hixon Writing Center

2007-2010

  • Provided one-on-one consultations for any piece of writing for the Caltech community, including grants, humanities essays, and applications
  • Presented at the Southern California Writing Center Conference (March 2009)

Treasurer and Board Member, Art of Practicing and Performing Institute

2016-2019

  • Duties include fundraising, grant writing, and accounting for the 501(c) non-profit institute

Staff Writer, Intern, Engineering and Science Magazine

2009

  • Wrote article “Staying Firm Under Pressure” (Engineering and Science Magazine, Fall 2009, 5-6), aimed towards a lay audience

Editor, little t publication

2008-2009

The Caltech undergraduate guidebook

  • Duties included recruiting advertisers, book layout, generating content
  • Was the first little t in several years to be published on time and within budget

Columbia University, New York City, NY

2010-2016

  • PhD, Biomedical Engineering : February 2016
  • MS, Biomedical Engineering : February 2012

California Institute of Technology, Pasadena, CA

2006-2010

  • BS, Applied Physics : June 2010 (with Honors)
  • Finalist for the Katharine McCormick Advanced Postdoctoral Scholar Fellowship — awarded to support women in academic medicine (2018).
  • Morton B. Friedman Memorial Prize — awarded periodically to an undergraduate or graduate student in the School of Engineering and Applied Sciences at Columbia University who best exhibits Dean Friedman's characteristics of academic excellence, visionary leadership, and outstanding promise for the future (2016).
  • The Yuen-huo Hung and Chao-chin Huang Award in Biomedical Engineering — given to a graduating doctoral student in the Department of Biomedical Engineering at Columbia University who demonstrated great potential for making significant contributions to the fields of biomedical engineering and public health, and for serving as an ambassador of biomedical engineering (2016).
  • Honorable Mention for the National Science Foundation Graduate Research Fellowship (2011).
  • Semi-finalist for the Doris S. Perpall Speaking Competition — an undergraduate science presentation competition (2009).
  • Alexander P. and Adelaide F. Hixon Prize for Writing — awarded to an undergraduate student for the best composition in a freshman humanities course. The prize recipient is chosen by a humanities committee (2007).
  • Nanofabrication: Photolithography, mask design, process development, soft lithography
  • Biology: Cell culturing, gel electrophoresis, gene amplification, protein purification, PCR
  • Modeling: Rate modeling, Monte Carlo simulations
  • Microscopy: Total internal reflection fluorescence (TIRF), epifluorescence, brightfield, custom microscope construction
  • Programming: Basic Python, MATLAB, Mathematica, web development
  • Human-Computer-Interactions: User interface design, user study design