About

Xiaoyun Ding is the Bruce S. Anderson Associate Professor in the Paul M. Rady Department of Mechanical Engineering at the University of Colorado Boulder. She is also a faculty member in the Biomedical Engineering Program and the Materials Science & Engineering Program, and serves on the Faculty Council of the BioFrontiers Institute. Her research focuses on biomedical devices and microfluidics aimed at fast diagnosis and therapeutics, with particular interests in intracellular drug delivery, cell mechanics, and micro/nano manipulation. Professor Ding leads the Biomedical Microfluidics Lab, where she mentors research associates, postdoctoral associates, graduate students, and undergraduate students working on various projects related to acoustic microfluidics, protein characterization, blood diagnostics, cell sensing, and biofluidics technologies. Her multidisciplinary approach integrates engineering principles with biomedical applications to advance technologies for rapid and effective medical diagnostics and treatments.

Research topics

• Biology
• Computer Science
• Computational biology
• Bioinformatics
• Cell biology
• Genetics
• Chemistry
• Biophysics
• Materials science
• Cancer research

Selected publications

• Acoustic probing of new biomarkers for rapid sickle cell disease screening

  Lab on a Chip · 2025-12-12

  preprintOpen accessSenior author

  Sickle cell disease (SCD) remains a critical global health issue, with high child mortality in low-resource regions. Early diagnosis is essential for improving health outcomes, but conventional diagnostic methods are unsuitable for widespread use due to the high costs of laboratory equipment. There is an urgent need for portable, cost-effective, and user-friendly point-of-care diagnostic tools that can quickly assess blood health. Here, we explore two new biomarkers enabled by acoustic probing for rapid SCD diagnosis: cell membrane stability from measuring red blood cell (RBC) lysis temperature in whole blood, and plasma protein concentration from measuring relative protein precipitation in blood plasma. Both biomarkers effectively differentiate healthy HbAA samples from pre-/no transfusion HbSS samples with high accuracy. Additionally, the RBC lysis biomarker can distinguish post-transfusion exchange HbSS samples with a lower percentage of sickled cells, indicating the potential to diagnose milder forms of SCD as well as sickle cell trait.

  PublisherOA PDFDOI

• Vector-free DNA transfection by nuclear envelope mechanoporation.

  PubMed · 2025-10-02

  articleOpen accessSenior author

  Genetic engineering of cells has a range of applications in treating incurable diseases. Plasmid DNA is a popular choice of nucleic acid for cell engineering due to its low cost and stability. However, plasmid DNA must survive the protective mechanisms present in the cell's cytoplasm to enter the nucleus for translation. Many of the existing methods for nucleic acid delivery, such as chemical-based and virus-based delivery, suffer from drawbacks induced by the nucleic acid carrier itself. Mechanical methods present an alternative to nucleic acid carriers by physically producing openings in the cell to deliver cargos. However, in most systems, the cell membrane openings are too small to deliver large cargos, or the poration process leads to low cell viability. In this study, we present a microfluidic device with integrated high aspect ratio nanostructures that repeatably rupture the cell membrane and nuclear envelope. These sharp-tipped nanolancets penetrate the cell deep enough to allow direct delivery of cargos into the nucleus, but still allow for cell recovery after treatment. We show the device's ability to deliver cargo to a variety of cell types while maintaining high viability. Then, we demonstrate the rapid onset of plasmid DNA expression that results from direct nuclear delivery of naked DNA, showing expression speeds comparable to microinjection, but with significantly greater throughput. We envision the use of this device as a tool to quickly produce high quantities of genetically engineered cells to treat a myriad of diseases.

  PublisherOA PDF

• Author response for "Acoustic Probing of New Biomarkers for Rapid Sickle Cell Disease Screening"

  2025-07-30

  peer-reviewSenior author
  PublisherDOI

• A Study of Explainable Machine Learning Method to Explore Grassland Resilience in the Arid Ecosystem

  2025-04-18

  preprintOpen access

  Grassland ecosystems in arid regions face mounting stress from intensified climate variability and anthropogenic disturbance. Despite the predictive capabilities of machine learning models, their lack of interpretability challenges the transparency of resilience drivers. This study integrates temporal autocorrelation (TAC) metrics with explainable machine learning (ML) to assess grassland resilience dynamics in an arid ecosystem from 2001 to 2023. Results reveal spatial divergence, with reduced resilience in radiation-dominated arid zones and stronger recovery in hydrothermally stable areas. The model identifies temperature variability and vegetation activity as dominant contributors to resilience trends, exhibiting marked heterogeneity across grassland types. By quantifying both structural and dynamic aspects of resilience, this framework enhances interpretability and diagnostic precision, offering a practical tool for identifying degradation risks and ecological tipping points. Findings support region-specific adaptation strategies and provide a robust foundation for sustainable grassland governance in the face of accelerating global change.

  PublisherOA PDFDOI

• Surface Acoustic Wave Hemolysis Assay for Evaluating Stored Red Blood Cells.

  PubMed · 2025-10-02

  articleOpen accessSenior author

  Blood transfusion remains a cornerstone of modern medicine, saving countless lives daily. Yet the quality of transfused blood varies dramatically among donors-a critical factor often overlooked in clinical practice. Rapid, benchtop, and cost-effective methods for evaluating stored red blood cells (RBCs) at the site of transfusion are lacking, with concerns persisting about the association between metabolic signatures of stored RBC quality and transfusion outcomes. Recent studies utilizing metabolomics approaches to evaluate stored erythrocytes find that donor biology (e.g., genetics, age, lifestyle factors) underlies the heterogeneity associated with blood storage and transfusion. The appreciation of donor-intrinsic factors provides opportunities for precision transfusion medicine approaches for the evaluation of storage quality and prediction of transfusion efficacy. Here we propose a new platform, the Surface Acoustic Wave Hemolysis Assay (SAW-HA), for on-site evaluation of stored RBCs utilizing SAW Hemolysis Temperature (SAWHT) as a marker for RBC quality. We report SAWHT as a mechanism-dependent reproducible methodology for evaluating stored human RBCs up to 42 days. Our results define unique signatures for SAW hemolysis and metabolic profiles in RBCs from two of the six donors in which high body mass index (BMI) and RBC triglycerides associated with increased susceptibility to hemolysis. Metabolic age of the stored RBCs - a recently appreciated predictor of post-transfusion efficacy-reveal that RBCs from the two low SAWHT units were characterized by disrupted redox control, deficient tryptophan metabolism, and high BMI. Together, these findings indicate the potential of the SAW-HA as a point-of-care analysis for transfusion medicine.

  PublisherOA PDF

• High-throughput mechanical nuclear envelope rupture and the intracellular dynamics of massive wound repair

  Research Square · 2025-03-28

  preprintOpen access1st authorCorresponding
  PublisherOA PDFDOI

• Reconfiguring Surface Acoustic Wave Microfluidics via <i>In Situ</i> Control of Elastic Wave Polarization

  Physical Review Letters · 2025-01-23 · 4 citations

  articleSenior author

  We demonstrate in situ control of the elastic wave polarization in a surface acoustic wave (SAW). It allows us to create highly reconfigurable SAW microfluidics that can be switched on demand between the acoustohydrodynamic (AHD) regime and electrohydrodynamic (EHD) regime for manipulating particles and cells. The control of wave polarization comes from our experimental and theoretical identification of an unexpected shear-horizontal (SH) wave mode in a conventional Rayleigh (R) wave design, which is stereotyped to excite only vertically polarized Rayleigh SAWs. The SH wave mode is predominantly horizontally polarized and can be selectively excited to propagate in the same direction as the Rayleigh SAW. Such a selective wave generation between the SH mode and R mode allows for reconfiguration between AHD and EHD regimes that leads to unprecedented colloidal patterns and assembly dynamics. Such a reconfiguration of the particle manipulation mechanism can be explained by the controllable competition or synergism between the coexisting acoustic and electric fields. Remarkably, in the EHD regime, a virtual zero-boundary electric quadrupole is created, and a novel colloidal diamond-shaped assembly is observed in this piezoelectric-quadrupole trap, which was rarely reported in acoustic or electric microfluidics. The presented in situ control of polarization revolutionizes our understanding of SAW and acoustofluidics, expands its potential by assuming the advantages of AHD and EHD on demand, and inspires new strategies in micro- and nanoscale manufacturing and manipulation, with applications beyond fundamental scientific interest.

  PublisherDOI

• Mesenteric panniculitis: A comprehensive description of a rare disease

  Medicina Clínica (English Edition) · 2025-02-01

  articleSenior authorCorresponding
  PublisherDOI

• Evaluation of ecological drought in northwest China by integrating ecological water budget and vegetation status

  Journal of Environmental Management · 2025-07-17 · 8 citations

  articleOpen access

  Global warming is increasing the frequency and intensity of drought events, posing profound threats to ecosystems. Ecological drought is a multifaceted process in terrestrial ecosystems, characterized by the impairment of vegetation eco-physiological functions due to water stress. However, current ecological drought assessments primarily focus on ecological water supply and demand, often overlooking the status of vegetation growth. To address this gap, we developed a standardized composite ecological drought index (SCEDI) that integrates precipitation (Pre), ecological water deficit (EWD), and the vegetation health index (VHI) using a Euclidean distance-based approach. We further analyzed spatiotemporal dynamics of ecological drought and its characteristics, utilizing run theory and empirical orthogonal function (EOF) methods. Results showed that ecological drought intensified in spring (SCEDI change: -0.002) and winter (-0.013), but weakened in summer (0.006) and autumn (0.002). The first EOF mode explained 30.51 % of the total variance, indicating a reversal in wet-dry patterns between mountainous regions and oases around 2002. Over the past 34 years, Xinjiang has experienced more than 19 ecological drought events, each with an average duration of approximately 3.11 months. Regionally, droughts in mountainous areas occurred more frequently but were shorter and less intense, while in oasis areas they were less frequent but more persistent and severe. Furthermore, Shapley Additive Explanations (SHAP) analysis identified EWD (SHAP value: 0.265) and precipitation (0.176) as the most influential drivers of ecological drought. Higher values of both factors were positively associated with ecological drought severity, while lower values had a mitigating effect. This study highlights the potential of SCEDI in accurately capturing ecological drought dynamics and provides a scientific basis for ecological risk assessment and adaptive drought management in arid regions.

  PublisherDOI

• Surface acoustic wave hemolysis assay for evaluating stored red blood cells

  Lab on a Chip · 2025-11-06

  articleOpen accessSenior author

  , genetics, age, lifestyle factors) underlies the heterogeneity associated with blood storage and transfusion. The appreciation of donor-intrinsic factors provides opportunities for precision transfusion medicine approaches for the evaluation of storage quality and prediction of transfusion efficacy. Here we propose a new platform, the surface acoustic wave hemolysis assay (SAW-HA), for on-site evaluation of stored RBCs utilizing SAW hemolysis temperature (SAWHT) as a marker for RBC quality. We report SAWHT as a mechanism-dependent reproducible methodology for evaluating stored human RBCs up to 42 days. Our results define unique signatures for SAW hemolysis and metabolic profiles in RBCs from two of the six donors in which high body mass index (BMI) and RBC triglycerides associated with increased susceptibility to hemolysis. Metabolic age of the stored RBCs - a recently appreciated predictor of post-transfusion efficacy - reveal that RBCs from the two low SAWHT units were characterized by disrupted redox control, deficient tryptophan metabolism, and high BMI. Together, these findings indicate the potential of the SAW-HA as a point-of-care analysis for transfusion medicine.

  PublisherOA PDFDOI

Frequent coauthors

• Tony Jun Huang

  Duke University

  23 shared

• Fei Geng

  22 shared

• Apresio K. Fajrial

  University of Colorado Boulder

  19 shared

• Jinjie Shi

  Guizhou University

  17 shared

• Ruide Yu

  University of Silesia in Katowice

  15 shared

• Le Luo

  Central Academy of Fine Arts

  14 shared

• Zengkun Guo

  Xinjiang Institute of Ecology and Geography

  13 shared

• Yu Gao

  12 shared

Labs

• Biomedical Microfluidics LabPI

  We are from all over the world

Education

• Postdoctral Associate, Chemical Engineering

  Massachusetts Institute of Technology

  2016

• PhD, Engineeing Science and Mechanics

  Pennsylvania State University

  2013

Awards & honors

• The Penn State Graduate School Alumni Society Early Career A…
• NIH MIRA Early Stage Investigator Award (2021)
• Bruce S. Anderson Engineering Faculty Fellow, University of…
• Lab Venture Challenge 2020 winner, Colorado (2020)
• Biomaterials Science Emerging Investigators (2020)