The Consortium of Molecular Design at BYU provides cutting edge interdisciplinary research opportunities for students to push the envelope for protein engineering and drug discovery.
We use close collaboration between laboratories at BYU in Physics, Chemistry, Computer Science, LifeSciences, and Engineering to tackle these challenging topics from all angles.
We actively seek industrial collaboration and support for our efforts and are excited to explore mutually beneficial application of all state-of-the-art technologies to revolutionize molecular design.
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Selected Publications
The glomerular filtration barrier poses a significant challenge for circulating proteins, with molecules below ~60–70 kDa facing rapid renal clearance. Endogenous proteins have evolved sophisticated evasion mechanisms including oligomerization, carrier binding, electrostatic repulsion, and FcRn-mediated recycling. Understanding these natural strategies provides blueprints for engineering therapeutic proteins with improved pharmacokinetics. This review examines how endogenous proteins resist filtration, evaluates their application in protein engineering, and discusses clinical translation including established technologies (PEGylation, Fc-fusion) and emerging strategies (albumin-binding domains, glycoengineering). We address critical challenges of balancing half-life extension with tissue penetration, biological activity, and immunogenicity—essential considerations for the rational design of next-generation therapeutics with optimized dosing and enhanced efficacy.
Artificial intelligence (AI)-based prostate cancer detection through whole slide images (WSIs) offers promising potential to address the global pathologist shortage while improving clinical consistency. Digital slides and improving image analysis methods encourage the creation of tools to aid in WSI classification. Despite promising advances, these tools are still limited by available training data. Current publicly available datasets, such as Kaggle's PANDA Challenge, while large in scale, rely on slide-level labels that may introduce noise and limit model reliability. Others contain detailed annotations, but are smaller in size due to manual processing efforts. In this work, we introduce PANDA-PLUS, a 546-image dataset derived from PANDA images with improved pixel-level annotations, as well as an accompanying annotation pipeline that reduces pathologists' time commitment. We present a detailed comparative analysis between PANDA-PLUS and PANDA using Gleason score and ISUP grade, supported by agreement values, κ, and PABAK under multiple weighting schemes. The results demonstrate consistently lower grading in PANDA-PLUS, with disagreement patterns especially pronounced at higher grades. We also demonstrate through single rater grading of various annotation granularities how slide- and patch-level labels may distort grading proportions and alter image scores. PANDA-PLUS not only improves annotation granularity and reduces label noise but also exposes potential grading errors in the original PANDA dataset. We present PANDA-PLUS's annotations as an improved alternative to the PANDA labels and conclude that it represents a step forward in the development of higher-quality public datasets for clinical AI applications in prostate cancer pathology.
Background: Understanding how different modeling strategies affect associations in nutritional epidemiology is critical, especially given the temporal complexity of dietary and health data.
Objective: To compare how different modeling frameworks—including isotemporal versus time-lagged designs and frequentist versus Bayesian inference—affect estimated associations between carbohydrate subtypes and adiposity.
Methods: Longitudinal data of 415 adults from the NoHoW Study were used to investigate associations between four carbohydrate predictors (free sugars, intrinsic sugars, starch, and dietary fiber) and three indices of adiposity (body fat percentage, BMI, and waist circumference) as outcomes. Four statistical approaches were used contrasting frequentist and Bayesian methods across both isotemporal (concurrent measurement) and time-lagged (6-month temporal shift) frameworks. To specifically evaluate change in adiposity outcomes over time, we implemented additional baseline-adjusted longitudinal models.
Results: Isotemporal and time-lagged models showed directional agreement for nearly all associations; in all but one case, the models either aligned in the direction of the association or differed only in relation to the null. However, time-lagged models identified statistically significant associations and produced larger effect sizes for body fat outcomes and for starch and fiber predictors. Other associations, including intrinsic and free sugars, were weaker and varied with model specification, losing statistical support under time-lagged models. Frequentist models exhibited greater variation across temporal frameworks, including one directional shift among significant associations. Effect estimates were substantially attenuated after adjustment for baseline adiposity.
Discussion: Time-lagged modeling shifted associations between carbohydrate intake and anthropometric outcomes, with increased effect sizes and additional significant associations for starch and fiber, and fewer statistically significant associations for intrinsic and extrinsic sugars. In contrast to frequentist models, Bayesian models yielded more stable and consistent estimates across time-lagged and isotemporal frameworks, showing no differences in the directions of associations across temporal frameworks. Models unadjusted for baseline adiposity overstate dietary impacts; including baseline adiposity is essential to isolate true diet-change effects from initial weight.
Conclusion: Our findings suggest that incorporating temporal structure, especially through Bayesian models, can uncover relevant relationships that concurrent models may overlook. This study demonstrates that model specification, both in temporal framework and statistical approach, meaningfully influences both the detection and interpretations of associations in nutritional epidemiology.