I am a Bioengineering PhD student working with Prof Beth Pruitt at Stanford University. I am interested in studying how cells interpret their physical environment (substrate stiffness, ligand density) to alter their morphology and behavior. To better characterize mechanically-tunable materials used in these experiments, I have focused on microscale indentation testing of polyacrylamide hydrogels using Atomic Force Microscopy. I aim to apply my characterization efforts to evaluate how heart muscle cells adapt their structure and force generation (contractility) in response to substrate stiffness mimicking developing, adult, and diseased heart tissue.

As an undergraduate at UC Berkeley (BS in bioengineering: 2012), I engaged in research to develop sample preparation strategies for analyzing clinical samples on microfluidic immunoassays, specifically tear fluid. Through summer internships in 2010, I investigated the design of hydrodynamic flow biosensors for bacteria detection in raw samples (US Naval Research Lab). In the summers of 2011 and 2012, I upgraded components of and developed imaging assays for novel light sheet microscopy systems to enable continuous imaging of live developing embryos and tissues of zebrafish and fruit flies (Howard Hughes Medical Institute, Janelia).

I am very interested in further pursuing the intersection of microfluidic analysis platforms and light-based microscopy for applications in both basic research and translation to clinical medicine. Before moving to California, I lived in Alexandria, Virginia. Outside the lab, I enjoy performing music (alto sax, piano), sailing, kickboxing, yoga, and science outreach (via interactive demos/presentations).

Honors & Awards

  • NSF Graduate Research Fellow, National Science Foundation (2012 - 2015)

Education & Certifications

  • Master of Science, Stanford University, BIOE-MS (2014)
  • Bachelor of Science, University of California at Berkeley, Bioengineering (2012)

Stanford Advisors

Service, Volunteer and Community Work

  • Bioengineering Bootcamp within the Stanford Institutes of Medicine Summer Research Program, Stanford University, Stanford Institutes of Medicine Summer Research Program (5/1/2013 - Present)

    Bioengineering Bootcamp is a summer program for high school students in biomedical device design which is part of the Stanford Institutes of Medicine Summer Research Program (SIMR). The program exposes students to research topics and enables them to practice critical thinking and problem solving skills in real-world design projects. In the past 3 years, I have worked with a team of students to develop the educational curriculum, secure funding from internal sources to keep the program free-of-charge, mentor the camp participants, and handle daily logistics. I am building a community of graduate students dedicated to this project and transferring my leadership to ensure that Bioengineering Bootcamp continues to help young students to explore engineering paths beyond my graduation.


    Stanford, California

  • Peer mentor for Bioengineering Teaching Assistants, Stanford University (September 2014 - Present)

    I aid graduate students in making the most out of their TA experience. I meet with 3 - 4 mentees a quarter to set goals and serve as a resource for help during their TA-ship. We perform midquarter evaluations to help TAs understand their progress and how to actively improve their interactions with students in the class. We also perform direct observations in the classroom and record students' teaching sessions to support students with constructive feedback to build and improve their teaching skills.


    Stanford, California

All Publications

  • A Biotic Game Design Project for Integrated Life Science and Engineering Education PLOS BIOLOGY Cira, N. J., Chung, A. M., Denisin, A. K., Rensi, S., Sanchez, G. N., Quake, S. R., Riedel-Kruse, I. H. 2015; 13 (3)


    Engaging, hands-on design experiences are key for formal and informal Science, Technology, Engineering, and Mathematics (STEM) education. Robotic and video game design challenges have been particularly effective in stimulating student interest, but equivalent experiences for the life sciences are not as developed. Here we present the concept of a "biotic game design project" to motivate student learning at the interface of life sciences and device engineering (as part of a cornerstone bioengineering devices course). We provide all course material and also present efforts in adapting the project's complexity to serve other time frames, age groups, learning focuses, and budgets. Students self-reported that they found the biotic game project fun and motivating, resulting in increased effort. Hence this type of design project could generate excitement and educational impact similar to robotics and video games.

    View details for DOI 10.1371/journal.pbio.1002110

    View details for Web of Science ID 000352095700019

    View details for PubMedID 25807212

  • Structural and molecular interrogation of intact biological systems. Nature Chung, K., Wallace, J., Kim, S., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., Mirzabekov, J. J., Zalocusky, K. A., Mattis, J., Denisin, A. K., Pak, S., Bernstein, H., Ramakrishnan, C., Grosenick, L., Gradinaru, V., Deisseroth, K. 2013; 497 (7449): 332-337


    Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.

    View details for DOI 10.1038/nature12107

    View details for PubMedID 23575631

  • Hydrodynamic focusing for impedance-based detection of specifically bound microparticles and cells: Implications of fluid dynamics on tunable sensitivity Sensors and Actuators B: Chemical Gusphyl A Justin, Aleksandra K Denisin, Mansoor Nasir, Lisa C Shriver-Lake, Joel P Golden, Frances S Ligler 2012; 166-167: 386–393
  • Post-collection processing of Schirmer strip-collected human tear fluid impacts protein content ANALYST Denisin, A. K., Karns, K., Herr, A. E. 2012; 137 (21): 5088-5096


    We examine the impact of post-collection sample handling on the protein composition of human tear samples. In particular, we characterize diffusion-based protein extraction from Schirmer strips. These strips of filter paper membrane are the de facto standard for tear fluid collection and storage, with diffusion-based protein elution off the strip being the most widely reported protein extraction strategy. Nevertheless, the diffusion-based protein elution strategy remains uncharacterized regarding downstream functional protein assays. Here, the time-dependence, concentration-dependence, and repeatability of the diffusion-based protein recovery protocol are characterized. Levels of protein irrecoverable from the Schirmer strip and lost during sample handling are isolated and compared for several major tear proteins. Further, the impact of the Schirmer strip and sample handling on the downstream concentration of proteins ranging in molecular weight, surface charge, and surface hydropathicity is quantified. Diffusion-based protein extraction from Schirmer strips was observed to be protein-dependent. Schirmer strips retained tear proteins to varying extents: 14.2% of lysozyme, 9.5% of human serum albumin, 27.7% of secretory IgA, and 30.9% of mucin 4. Tear protein loss during sample handling ranged from 2% (lysozyme) to 41.2% (mucin 4). Strip retention of protein was observed to be associated with protein molecular weight and hydrophobic surface area. Greater sample handling loss was associated with increased hydrophobic surface area of model proteins. Surface charge or surface hydrophilicity was not significantly associated with protein loss. We therefore conclude that, although diffusion-based processing of Schirmer strip-collected tear samples is widely used, these protocols may result in total post-collection protein loss which is considerable, consistent, and protein-dependent. This loss alters the relative and absolute protein concentrations in the sample. A priori prediction of strip-losses for individual proteins does not appear to be facile, based on cursory knowledge of protein surface properties. Thus, we emphasize "spike and recover" control experiments to determine expected elution profiles for target proteins when using diffusion-based protein sample preparation for Schirmer strip-collected tear fluid.

    View details for DOI 10.1039/c2an35821b

    View details for Web of Science ID 000309427600030

    View details for PubMedID 22991688