Philip Stauffer, PhD.

Translational Research | Bioinformatics | Quantitative Science

Zurich, Zurich, Switzerland

About

I am a postdoctoral scientist advancing translational research in autoimmune rheumatic related progressive interstitial lung disease (ILD), with a focus on identifying molecular drivers, developing clinically feasible diagnostics, and enabling smarter drug development. I bring growing expertise in spatial transcriptomics and proteomics (10x Genomics, Lunaphore COMET) and a strong foundation in high-throughput systems, quantitative science, and bioinformatics. I also develop patient-derived 3D model systems, including Precision Cut Lung Slices, to validate mechanistic insights and support translational drug-screening efforts. Across my work, I aim to accelerate target discovery, improve patient stratification, and strengthen biomarker strategies for complex immune-mediated diseases.

Experience

  • Postdoctoral Fellow at Universitätsspital Zürich
    May 2025 - Present · 1 yr 3 mos

    I am a postdoctoral fellow in the Center of Experimental Rheumatology within USZ's Department of Rheumatology, a EULAR center of excellence. In this role I am leading and developing translational projects to define mechanisms and biomarkers in progressive interstitial lung disease associated with autoimmune rheumatic diseases (ARD-ILD). I lead research projects aimed at closing a major gap in progressive ILD by defining its molecular drivers, heterogeneity, and by developing clinically feasible molecular diagnostics of progression. These efforts support smarter drug development, including target discovery, patient stratification, and biomarker planning. I am developing deep expertise in spatial transcriptomic and proteomic workflows, including 10x Genomics platforms and high-throughput sequential immunofluorescence using the Lunaphore COMET system. Through these approaches, I am expanding my foundation in high-throughput systems, quantitative science, and bioinformatics to extract mechanistic insights from clinical samples at scale. In parallel, I bring extensive experience with developing patient-derived 3D model systems. I am currently leveraging a Precision Cut Lung Slice (PCLS) model of early ARD-ILD to enable experimental validation of molecular findings and translational drug-screening. Together, my work aims to close the gap between preclinical research and meaningful clinical outcomes.

  • Vanderbilt University (6 yrs 5 mos)
    • Ph.D. Researcher
      Sep 2024 - Dec 2024 · 4 mos

    • Ph.D. Candidate
      Aug 2018 - Aug 2024 · 6 yrs 1 mo

      Under the mentorship of Dr. Vito Quaranta, I have utilized high throughput screening instrumentation, bioinformatics, and computational systems biology modeling to study drug tolerant persisters in oncogene driven cancers treated with targeted therapies. I have primarily used BRAF-V600E mutant melanoma to study molecular responses to drug treatment in order to better understand mechanisms of adaptation that lead to relapse in the clinic. My experience includes high throughput assay development and drug screening; development of cross-platform data analysis pipelines using R and Python; bioinformatics analysis of RNAseq and proteomics datasets; Computational modeling; management of diverse and collaborative scientific teams.

  • Proteomics Mass Spec Course Student at Cold Spring Harbor Laboratory
    Aug 2022 - Aug 2022 · 1 mo

    Two week intensive course on Proteomics Mass spec at Cold Spring Harbor, led by Darryl Pappin, Robert Chalkley, and Chad Weisbrod. Topics covered in detail included instrumentation, LC, labeled/label free MS, SRM/PRM, DDA/DIA, PTM enrichment, and various data analysis pipelines. Hands on experience included MS sample prep and data acquisition of everything listed above.

  • Research Assistant at Virginia Tech
    Feb 2016 - May 2018 · 2 yrs 4 mos

    Under the mentorship of Dr. Carla Finklestein, I directed an individual project focused on the interaction between the circadian clock and stress response pathways. In this lab I contributed to several peer-reviewed publications and received various undergraduate research awards. I developed strong skills in molecular biology including: PCR, cloning, site-directed mutagenesis, Immunoprecipitation (IP), western blot, RNA extraction/qrt-PCR

  • Research Assistant at Vanderbilt University
    Jun 2017 - Aug 2017 · 3 mos

    Under the mentorship of Dr. F. Peter Guengerich, I developed enzymatic assays to quantitatively characterize the Michaelis Menten enzyme kinetics of the Zika Virus RNA polymerase used in viral replication.