About

Philipp Simon is a Professor affiliated with the USDA and the Department of Plant and Agroecosystem Sciences at the University of Wisconsin-Madison. His research focuses on plant breeding and plant genetics, with specific emphasis on vegetable crops. He is involved in the USDA Vegetable Crops Research Unit and contributes to plant breeding programs, including carrot breeding. His contact information includes a phone number and email address, and his office is located in the Horticulture Building at Madison, WI. His work supports undergraduate and graduate programs in plant science and agroecology, and he is engaged in research, outreach, and educational activities related to plant and agroecosystem sciences.

Research topics

• Biology
• Botany
• Horticulture
• Genetics
• Chemistry
• Food science
• Agronomy
• Biochemistry
• Ecology
• Biotechnology

Selected publications

• Influence of Organic and Conventional Management Systems on Carrot Performance and Implications for Organic Plant Breeding

  Journal of the American Society for Horticultural Science · 2025-03-01 · 2 citations

  articleOpen accessSenior author

  In this study, 36 carrot breeding lines and cultivars widely used for organic production were grown for 4 years in two locations under organic and conventionally managed trials. Highly significant genotypic main effects and genotype × year and, to a lesser extent, genotype × location interactions were observed for all traits, including harvest root and top weight as well as top height and width measured at early season, midseason, and the time of harvest. In contrast, management systems and most management system interactions were not significant. Broad sense heritability (repeatability) for most responses was relatively high (≥0.75), suggesting a high potential for genetic gains through selection, although early-season top height and width heritability were somewhat lower. High rank correlations were found for all traits when comparing genotypes grown under organic and conventional management in both locations when evaluated across all years for each location ( P ≤ 0.001) or with few exceptions when evaluated by individual years ( P ≤ 0.05). An analysis of F1 hybrid cultivars and comparison of the performance of production systems showed no rank correlations for most traits and years. In contrast to the results observed for F1 hybrid cultivars, open-pollinated breeding lines presented more instances of correlation between management systems in given locations and years. The stability analysis provided insights into the relative stability or adaptability of 36 carrot genotypes (cultivars) across environments. Considering all traits evaluated, several open-pollinated and hybrid cultivars demonstrated consistent performance along the environmental index, whereas other cultivars and the more inbred breeding lines did not. An additive main effects and multiplicative interactions analysis did not present any clear patterns for management system or location, but it did reflect the highly significant effect of year in genotype × environment interactions. The first and second principal components explain a range of total variance from 41.8% for early top height to 55.2% for harvest top weight. The results of the current study contribute to the body of knowledge regarding genotype X management system interactions and provide insights into implications for organic crop improvement in carrot. The results further aid in understanding the influence of organic management in horticultural crops, which may differ with the results of grain crops.

  PublisherOA PDFDOI

• Reduced strigolactone exudation as a key resistance mechanism in wild carrots against <i>Phelipanche aegyptiaca</i>

  Plant and Cell Physiology · 2025-09-18

  articleOpen access

  Phelipanche aegyptiaca is a root parasitic plant that causes significant yield losses in many crops, including carrots (Daucus carota). This study investigates the resistance mechanisms of two wild carrot accessions, PI 21793 (Daucus glaber) and PI 341902 (Daucus littoralis), against P. aegyptiaca compared to a cultivated carrot (P0114; D. carota). Wild carrots induced lower germination rates of P. aegyptiaca seeds and fewer successful tubercles, indicating both pre-attachment and partial post-attachment resistance mechanisms. Strigolactone analysis revealed significant quantitative differences between cultivated and wild carrots. While cultivated carrots exuded high levels of two strigolactones, one of which was putatively identified as the non-canonical strigolactone, 4-oxo-methyl-carlalactone, wild carrots released lower amounts of these compounds. Supplementation with the artificial strigolactone analog GR24 increased germination in P. aegyptiaca inoculated on wild carrots, suggesting that strigolactone deficiency and possibly altered composition are key pre-attachment resistance mechanisms. However, higher germination resulted in no significant improvement in tubercle development on wild carrots. Parasite seedlings showed necrosis-like symptoms at their attachment sites on wild carrot roots, indicating an additional post-attachment resistance mechanism. These findings provide new insights into strigolactone-mediated host resistance and highlight the potential of wild carrot accessions to contribute to the development of resistant cultivars against parasitic plants.

  PublisherDOI

• Business Secrets Increase Asset Value

  Management for professionals · 2025-01-01 · 1 citations

  book-chapterSenior author
  PublisherDOI

• A Phase 1b/2, Randomised, Placebo-controlled Study to Evaluate Safety, Tolerability, Efficacy, and Immunogenicity of VTP-200, a Chimpanzee Adenovirus and Modified Vaccinia Ankara-vectored Multigenotype High-risk Human Papillomavirus Vaccine in Women With Low-grade Cervical Lesions

  Clinical Infectious Diseases · 2025-12-09

  article

  BACKGROUND: The clearance of high-risk oncogenic HPV (hrHPV) and related cervical lesions is associated with the development of a robust T cell response. Therapeutic vaccination that induces HPV antigen-specific T cells is a promising approach. METHOD: A two-vector dosing strategy using Chimpanzee Adenovirus Oxford 1 (ChAdOx1-HPV) and Modified Vaccinia virus Ankara (MVA-HPV), both encoding the same multiantigen HPV cassette was given on a 0/28-day schedule to participants with persistent cervical hrHPV and a history of low-grade cervical lesions. An open-label lead-in was followed by a randomized, blinded, placebo-controlled main phase. The primary endpoint was the safety of the different dose regimens; secondary endpoints included immunogenicity, and clearance of hrHPV and associated lesions at 12 months.Nine participants were enrolled in the lead-in and 99 were randomized 67:32 to five active dose arms or placebo, respectively. RESULTS: The regimens were well-tolerated with no Grade 3-related treatment emergent adverse events or serious adverse reactions. All dosing regimens generated antigen-specific CD4+ and CD8+ T cell responses. There was no difference in hrHPV clearance between the pooled active groups and placebo (20/64 (31.3%) vs 10/30 (33.3%), p > 0.99), nor in lesion clearance. A trend toward higher hrHPV clearance (60%) was observed with the highest ChAdOx1-HPV doses. No association between the peripheral immune response and clearance was demonstrated. CONCLUSION: A heterologous, multi-antigenic HPV two-component immunotherapy regimen was well-tolerated and immunogenic but did not result in a statistically significant clearance of either hrHPV or the associated cervical lesions in women with persistent high-risk HPV infections.

  PublisherDOI

• Automated Monitoring of Clinical Practice Guideline Adherence Using FHIR and OMOP: A Multi-Center Study in Intensive Care Units

  medRxiv · 2025-01-03 · 1 citations

  preprintOpen access

  Abstract Background Clinical practice guidelines are important tools for clinical decision support, but monitoring guideline adherence manually is highly resource-intensive. Therefore, we developed an automated system for evaluating guideline adherence based on computer-interpretable representations of guidelines. We implemented the system across multiple university hospitals and assessed its validity and performance by comparing its guideline adherence evaluations to those conducted by medical professionals. Methods We selected six representative clinical guideline recommendations from across 41 intensive care guidelines and translated these text-based recommendations into a computer-interpretable, Fast Healthcare Interoperability Resources (FHIR)-based format using an iterative consensus approach. Clinical data from five university hospitals were transformed into the Observational Medical Outcomes Partnership (OMOP) common data model. A decision support system was developed to interpret FHIR-encoded recommendations and apply them to OMOP-formatted patient data. We evaluated the system retrospectively on intensive care data covering 3.5 years and validated its performance by comparing system-generated decisions with human decisions in three hospitals. We created and iteratively refined a user interface for individual and ward-level adherence visualization. Findings We expert-reviewed more than 18,000 patient days to assess the applicability of and adherence to the recommendations. The system demonstrated 97.0% accuracy in identifying guideline applicability and adherence, with significantly higher accuracy than human reviewers (accuracy 86.6%, p&lt;0.001, McNemar’s Test). The automated system processed more than 2000 patient days per second for a total of 2,200,000 patient days across 82,000 intensive care episodes, compared to humans’ two patient days per minute. Interpretation We demonstrate that an automated adherence monitoring system outperforms human reviewers in both accuracy and time efficiency. Using FHIR-encoded recommendations enables flexibility and scalability across hospitals with different data infrastructures. Future work should focus on integrating unstructured patient data and expanding the range of encoded recommendations. Funding Federal Ministry of Education and Research of Germany.

  PublisherOA PDFDOI

• Exploring functional InDels and genetic diversity: agro-morphometric and molecular insights into the Western and Eastern gene pools of carrot (Daucus carota L.)

  Frontiers in Plant Science · 2025-10-22

  articleOpen accessSenior authorCorresponding

  L.) is a globally cultivated root vegetable with significant genetic diversity. This first study generated and validated carrot InDels to unravel the genetic divergence between Eastern and Western gene pools, integrating agro-morphometric traits with functional InDel markers. Eastern accessions exhibited larger plants, bigger roots with diverse colors, while Western accessions were more uniform orange color and compact in architecture. From RNA-seq data, 271 agarose-resolvable functional InDels (>15bp length difference) were identified, of which 48 validated markers showed high polymorphism (84.21%) across two gene pools supporting secondary domestication changes. Located in coding and UTR regions, these InDels likely regulate gene expression and may have contributed to significant genetic modifications among carrot gene pools. Genetic diversity in the Western gene pool indicated more intense selection and domestication. Population structure and phylogenetic analysis revealed clear gene pool differentiation (Fst = 0.181) with potential gene flow (Nm = 1.716). Functional annotation of linked InDels to key biological processes, highlighted their role in domestication. Key InDels (DcFInDel32, DcFInDel28, and DcFInDel55) were associated with multiple traits, underscoring their utility in marker-assisted selection (MAS). These findings provide insights for developing improved carrot cultivars with high yield and quality adapted to diverse climates.

  PublisherDOI

• Combining genome‐wide association and genomic prediction to unravel the genetic architecture of carotenoid accumulation in carrot

  The Plant Genome · 2025-01-30 · 6 citations

  articleOpen accessSenior authorCorresponding

  Carrots (Daucus carota L.) are a rich source of provitamin A, namely, α- and β-carotene. Breeding programs prioritize increasing β-carotene content for improved color and nutrition. Understanding the genetic basis of carotenoid accumulation is crucial for implementing genomic-assisted selection to develop high-carotenoid lines. While previous studies identified loci (Y2, Y, Or, and REC) associated with carrot color and carotenoid content, this study employed genome-wide association (GWA) in a diverse panel of 738 carrot accessions. We discovered a novel locus with a candidate gene encoding phytoene synthase, a key enzyme in carotenoid biosynthesis. The Y2, Y, Or, and REC loci are mostly fixed in orange varieties, yet considerable variation in carotenoid concentration persists. This suggests a multigenic trait influenced by the environment. GWA of carotenoid concentration identified a quantitative trait locus for total carotenoids and α-carotene. We explored the accuracy of genomic prediction (GP) models to predict carotenoid concentration. We determined the optimal number of plants and plots required for accurate carotenoid phenotyping, finding ≥5 plants per plot and three plots per site as the minimum effective sample per accession. GP models achieved accuracies ranging from 0.06 to 0.40 depending on the carotenoid measured and environment the carrots were assayed. Additional studies in breeding programs will clarify the potential of genomic-assisted selection for high-carotenoid carrots.

  PublisherOA PDFDOI

• Multicenter Evaluation of an Interoperable System for Automated Guideline Adherence Monitoring in ICUs

  Critical Care Medicine · 2025-11-25

  article

  OBJECTIVE: To develop, apply, and validate a system for evaluating critical care guideline adherence, and to identify factors influencing real-world adherence across hospitals. DESIGN: Retrospective, multicenter observational study evaluating guideline adherence over 3.5 years and comparing automated adherence monitoring against expert human review. SETTING: Five university hospitals with different clinical information systems and data infrastructures. PATIENTS: A total of 82,000 intensive care episodes (2.2 million patient days). Six representative recommendations were selected from 41 intensive care guidelines and translated into a standardized digital format. Expert review encompassed more than 18,000 patient days. INTERVENTIONS: An automated system that applies digitally encoded guideline recommendations to standardized patient data extracted from hospital information systems. MEASUREMENTS AND MAIN RESULTS: The system determined, for each patient and recommendation, whether the recommendation applied (applicability) and whether treatment followed it (adherence). The primary outcome was the system's accuracy in identifying guideline applicability and adherence compared with manual clinician reviews. The secondary outcome was an analysis of how adherence to these recommendations varied and which factors influenced their real-world implementation. The system achieved 97.0% accuracy in identifying guideline applicability and adherence, significantly outperforming human reviewers (86.6% accuracy, p < 0.001; McNemar's test). The processing speed of the system exceeded 2000 patient days per second, compared with manual review at 2 patient days per minute. Adherence rates varied substantially across participating sites and over time, reflecting documentation inconsistencies, evolving clinical knowledge, and challenges in maintaining strict compliance. CONCLUSIONS: The guideline adherence monitoring system was successfully applied in multiple hospitals, demonstrating higher accuracy and efficiency compared with human review. Limitations of the system included dependence on consistent and structured documentation, as inconsistencies significantly complicate adherence monitoring. As the system is designed to support any guideline in the digital format used here, it provides a scalable solution for automated quality management in critical care.

  PublisherDOI

• Correction to: Business Secrets Increase Asset Value

  Management for professionals · 2025-01-01

  book-chapterOpen accessSenior author
  PublisherOA PDFDOI

• Screening of carrot wild relatives in warm, dry and saline field conditions with respect to root and seed production

  Acta Horticulturae · 2024-04-01

  article
  PublisherDOI

Frequent coauthors

• Douglas Senalik

  235 shared

• Pablo F. Cavagnaro

  140 shared

• Massimo Iorizzo

  136 shared

• David M. Spooner

  University of Georgia

  98 shared

• Shelby Ellison

  University of Wisconsin–Madison

  68 shared

• C. E. Peterson

  The University of Texas at Austin

  58 shared

• Ahmet İpek

  Karamanoğlu Mehmetbey University

  58 shared

• Meryem İpek

  56 shared

Labs

• Vegetable Crops Research, Madison, WIPI

Education

• Ph.D., Genetics

  University of Wisconsin Madison

  1977