John Aitchison

About

Professor John Aitchison is a member of the UW Biological Physics, Structure and Design faculty, based at the Seattle Children’s Center for Global Infectious Disease Research. His research group seeks to understand biological complexity within the context of the modular organization of the cell. They focus on the three-dimensional structure of the cell, which enables biological systems to sequester, tightly regulate, and increase the efficiency of various cellular processes. The structure of the cell is dynamic, with organelles, specialized domains, and macromolecular machines responding to both internal cellular states and external stimuli. Combining systems biology with cell biology, Professor Aitchison's group studies the origins and dynamics of organelles to understand the networks that underlie cellular function and dysfunction.

Research topics

• Virology
• Biology
• Medicine
• Cell biology
• Genetics
• Computational biology
• Microbiology
• Immunology
• Pathology

Selected publications

• Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape

  eLife · 2021 · 70 citations

  The emergence of SARS-CoV-2 variants threatens current vaccines and therapeutic antibodies and urgently demands powerful new therapeutics that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain, and the S2 subunit, to identify new nanobody binding sites that may reflect novel mechanisms of viral neutralization. Structural…

  DOI

• Early and opposing neutrophil and CD4 T cell responses shape pulmonary tuberculosis pathology

  The Journal of Experimental Medicine · 2025-06-28 · 14 citations

  articleOpen access

  Pulmonary Mycobacterium tuberculosis (Mtb) infection results in a variety of heterogeneous lesion structures, from necrotic granulomas to alveolitis, but the mechanisms regulating their development remain unclear. Using a mouse model of concomitant immunity and subsequent aerosol infection, we demonstrate that counter regulation between neutrophils and CD4 T cells occurs very early during infection and governs these distinct pathologies. In primary Mtb infection, a dysregulated feed-forward circ…

  PublisherDOI

• Preclinical development of a replication-competent vesicular stomatitis virus-based Lassa virus vaccine candidate advanced into human clinical trials

  EBioMedicine · 2025-04-01 · 10 citations

  articleOpen access

  BACKGROUND: Lassa fever (LF) is a zoonotic haemorrhagic disease caused by Lassa virus (LASV), which is endemic in West African countries. The multimammate rat is the main animal reservoir and its geographic range is expected to expand due to influences like climate change and land usage, and this will place larger parts of Africa at risk. We conducted preclinical development on a promising experimental vaccine that allowed its advancement into human trials. METHODS: The LF vaccine is based on a…

  PublisherDOI

• CD4-mediated immunity shapes neutrophil-driven tuberculous pathology

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-04-16 · 9 citations

  preprintOpen access

  (Mtb) infection results in highly heterogeneous lesions ranging from granulomas with central necrosis to those primarily comprised of alveolitis. While alveolitis has been associated with prior immunity in human post-mortem studies, the drivers of these distinct pathologic outcomes are poorly understood. Here, we show that these divergent lesion structures can be modeled in C3HeB/FeJ mice and are regulated by prior immunity. Using quantitative imaging, scRNAseq, and flow cytometry, we demonstrat…

  PublisherOA PDFDOI

• Automated, image-based quantification of peroxisome characteristics with <i>perox-per-cell</i>

  Bioinformatics · 2024-07-01 · 7 citations

  articleOpen accessSenior author

  SUMMARY: perox-per-cell automates cumbersome, image-based data collection tasks often encountered in peroxisome research. The software processes microscopy images to quantify peroxisome features in yeast cells. It uses off-the-shelf image processing tools to automatically segment cells and peroxisomes and then outputs quantitative metrics including peroxisome counts per cell and spatial areas. In validation tests, we found that perox-per-cell output agrees well with manually quantified peroxisom…

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01GM067228

  NIH · $1.7M · 2008

• NIH Grant R21AI124266

  NIH · $520k · 2018

• NIH Grant P50GM076547

  NIH · $57.8M · 2017

Frequent coauthors

• Fred D. Mast

  Infectious Disease Research Institute

  198 shared

• Alexander V. Ratushny

  Bristol-Myers Squibb (United States)

  109 shared

• Samuel A. Danziger

  Institute for Systems Biology

  107 shared

• Jennifer J. Smith

  107 shared

• Ramsey A. Saleem

  Kinnaird College for Women University

  104 shared

• Alexis Kaushansky

  University of Washington

  100 shared

• Michael P. Rout

  93 shared

• Thurston Herricks

  Seattle University

  81 shared

Similar researchers at University of Washington

• Jesse Bloomh-117
• Valerie Daggetth-81
• Frank DiMaioh-76