Denis Wirtz

About

Denis Wirtz is the vice provost for research at Johns Hopkins University and the Theophilus Halley Smoot Professor in the Department of Chemical and Biomolecular Engineering at the Whiting School. His research spans the interface of physics, biology, and oncology, with seminal contributions to understanding cancer cell migration, cytoskeleton biophysics, and the emerging field of mechanobiology. Wirtz has developed quantitative methods such as particle-tracking microrheology, which are widely used in academia and industry, and has pioneered research in cell migration in 3D settings, bacterial cell division, and high-throughput cell phenotyping. Recently, he developed CODA, an AI-based imaging method for large tissue and tumor volumes in 3D. He co-founded the Johns Hopkins Institute for NanoBioTechnology (INBT) and directs several NCI-funded programs, including a postdoctoral training program in nanotechnology for oncology, the Physical Sciences-Oncology Center (PS-OC), and the Cellular Cancer Biology Imaging Cancer (CCBIR) Center.

Research topics

• Cell biology
• Biology
• Chemistry
• Cancer research
• Biophysics

Selected publications

• Extracellular vesicles in immunomodulation and tumor progression

  Nature Immunology · 2021-03-22 · 589 citations

  reviewOpen accessSenior author
  PublisherOA PDFDOI

• Single-cell morphology encodes metastatic potential

  Science Advances · 2020-01-22 · 208 citations

  articleOpen accessSenior authorCorresponding

  A central goal of precision medicine is to predict disease outcomes and design treatments based on multidimensional information from afflicted cells and tissues. Cell morphology is an emergent readout of the molecular underpinnings of a cell's functions and, thus, can be used as a method to define the functional state of an individual cell. We measured 216 features derived from cell and nucleus morphology for more than 30,000 breast cancer cells. We find that single cell-derived clones (SCCs) es…

  PublisherDOI

• Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories

  Cell · 2025-07-26 · 37 citations

  articleOpen access

  Cells interact as dynamically evolving ecosystems. While recent single-cell and spatial multi-omics technologies quantify individual cell characteristics, predicting their evolution requires mathematical modeling. We propose a conceptual framework-a cell behavior hypothesis grammar-that uses natural language statements (cell rules) to create mathematical models. This enables systematic integration of biological knowledge and multi-omics data to generate in silico models, enabling virtual "though…

  PublisherOA PDFDOI

• InterpolAI: deep learning-based optical flow interpolation and restoration of biomedical images for improved 3D tissue mapping

  Nature Methods · 2025-05-28 · 12 citations

  articleOpen accessSenior author

  Recent advances in imaging and computation have enabled analysis of large three-dimensional (3D) biological datasets, revealing spatial composition, morphology, cellular interactions and rare events. However, the accuracy of these analyses is limited by image quality, which can be compromised by missing data, tissue damage or low resolution due to mechanical, temporal or financial constraints. Here, we introduce InterpolAI, a method for interpolation of synthetic images between pairs of authenti…

  PublisherOA PDFDOI

• Spatial proteomics and transcriptomics reveal early immune cell organization in pancreatic intraepithelial neoplasia

  JCI Insight · 2025-06-26 · 9 citations

  articleOpen access

  Pancreatic ductal adenocarcinoma (PDAC) has a poor survival rate due to late detection. PDAC arises from precursor microscopic lesions, termed pancreatic intraepithelial neoplasia (PanIN), that develop at least a decade before overt disease; this provides an opportunity to intercept PanIN-to-PDAC progression. However, immune interception strategies require full understanding of PanIN and PDAC cellular architecture. Surgical specimens containing PanIN and PDAC lesions from a unique cohort of 5 tr…

  PublisherOA PDFDOI

Recent grants

• NIH Grant R21CA137891

  NIH · $357k · 2012

• NIH Grant R21EB006890

  NIH · $443k · 2009

• NIH Grant R21CA137686

  NIH · $826k · 2012

Frequent coauthors

• Ashley Kiemen

  Johns Hopkins Medicine

  310 shared

• Pei-Hsun Wu

  Johns Hopkins University

  221 shared

• Sashank Reddy

  Johns Hopkins Medicine

  147 shared

• Kyu Sang Han

  Johns Hopkins University

  145 shared

• Pei‐Hsun Wu

  Johns Hopkins University

  141 shared

• Laura D. Wood

  Johns Hopkins Medicine

  141 shared

• Joel C. Sunshine

  Johns Hopkins University

  131 shared

• Ralph H. Hruban

  Cancer Research Center

  124 shared

Labs

• Denis Wirtz LabPI

Education

• PhD, Chemical Engineering

  Stanford University

  1993

Awards & honors

• NSF CAREER award (1995)
• Fellow of the Institute for Medical and Biological Engineeri…
• Fellow of the American Association for the Advancement of Sc…
• Fellow of the American Physical Society (APS) (2010)
• Theophilus H. Smoot Professor of Engineering and Science (20…

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