Department Publications

2026

47. PANDA-PLUS-Bench: A Clinical Benchmark for Evaluating the Robustness of AI Foundation Models in Prostate Cancer Diagnosis

    Joshua L. Ebbert^‡ and Dennis Della Corte

    AI Med. 1 (2), 14 (2026).
    
48. Individual glycemic responses scale predictably with the glycemic index: evidence against person-specific food effects

    Karen A. Della Corte, Jennie Brand-Miller, Thomas M.S. Wolever, and Dennis Della Corte

    Am. J. Clin. Nutr., (2026).
49. Conformation-Specific Design: Engineering Extracellular Signal-Regulated Kinase 2 Variants with Bias toward Active or Inactive States

    Joseph P. Talley^‡, Jacob A. Stern^‡, Siba Alharbi, Tyler P. Green^†, Anandsukeerthi Sandholu, Matthew Argyle^‡, William P. Heaps^‡, … and Dennis Della Corte (3 other authors)

    ACS Omega 11 (19), 28717-28724 (2026).
    
50. Glycemic and Cardiometabolic Effects of Rare Sugars Allulose and Tagatose: A Systematic Review and Meta-Analysis of Controlled Human Intervention Trials

    Lauryn Osborn^‡, Kaitlyn DuPuis^‡, Simin Liu, Dennis Della Corte, and Karen A. Della Corte

    Am. J. Clin. Nutr., 101314 (2026).
51. Albumin-Binding Domains in Therapeutic Protein Engineering: A Structural and Computational Perspective on Rational Design

    Matthew J. Argyle^‡, Dallin M. Chipman^‡, Anna Claire Woolley^‡, Bradley C. Bundy, and Dennis Della Corte

    SynBio 4 (1), 5 (2026).
    
52. Advancing NanoLuc Luciferase Stability beyond Directed Evolution and Rational Design through Expert-Guided Deep Learning

    Spencer Gardiner^‡, Joseph Talley^‡, Tyler Green^†, Christopher Haynie^‡, Corbyn Kubalek^‡, Matthew Argyle^‡, William Heaps^‡, Joshua Ebbert^‡, Deon Allen^‡, Dallin Chipman^‡, … and Dennis Della Corte (1 other authors)

    ACS Catal., (2026).
53. CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2

    Oleksandra Herasymenko, Madhushika Silva, Galen J. Correy, Abd Al-Aziz A. Abu-Saleh, Suzanne Ackloo, Cheryl Arrowsmith, … Dennis Della Corte, … Damon Tingey^‡, … (75 other authors)

    J. Chem Inf. Model., (2026).
54. Molecular Survival Strategies Against Kidney Filtration: Implications for Therapeutic Protein Engineering

    William P. Heaps^‡, Anne Elise Packard^‡, Kristina M. McCammon^‡, Tyler P. Green^†, Joseph P. Talley^‡, Bradley C. Bundy, and Dennis Della Corte

    Biophysica 6 (1), 4 (2026).
    

2025

39. PANDA-PLUS: Improved dataset of prostate whole slide images from PANDA Challenge with pixel-level expert annotations

    Spencer Hopson^‡, Carson Mildon^‡, Corbyn Kubalek^‡, Joshua Ebbert^‡, Ryan Vance^‡, Lauren Laverty^‡, Paul Urie, and Dennis Della Corte

    J. Pathol. Inform. 20, 100540 (2025).
    
40. Modeling frameworks in nutritional epidemiology matter: comparing isotemporal and time-lagged Bayesian and frequentist approaches of carbohydrate intake and adiposity

    Sean Titensor^‡, Joshua L. Ebbert^‡, David Camacho^‡, Karen A. Della Corte, Antonio L. Palmeira, R. James Stubbs, … and Dennis Della Corte (2 other authors)

    Front. Nutr. 12, 1700898 (2025).
    
41. ChronoSort: Revealing Hidden Dynamics in AlphaFold3 Structure Predictions

    Matthew J. Argyle^‡, William P. Heaps^‡, Corbyn Kubalek^‡, Spencer S. Gardiner^‡, Bradley C. Bundy, and Dennis Della Corte

    SynBio 3 (4), 18 (2025).
    
42. Resolution of physics and deep learning-based protein engineering filters: A case study with a lipase for industrial substrate hydrolysis

    Spencer Gardiner^‡, Peter Dollinger, Filip Kovacic, Jörg Pietruszka, Daniel H. Ess, Karl-Erich Jaeger, Gunnar F. Schröder, and Dennis Della Corte

    PLoS One 20, 1-21 (2025).
    
43. Estimating area under the curve from graph-derived summary data: a systematic comparison of standard and Monte Carlo approaches

    Sean Titensor^‡, Joshua Ebbert^‡, Karen Della Corte, and Dennis Della Corte

    BMC Med. Educ. 25 (1), 197 (2025).
    
44. Enhancing AI literacy in undergraduate pre-medical education through student associations: an educational intervention

    Spencer Hopson^‡, Carson Mildon^‡, Kyle Hassard^‡, Corbyn Kubalek^‡, Lauren Laverty^‡, Paul Urie, and Dennis Della Corte

    BMC Bioinformatics 25 (1), 999 (2025).
    
45. TrIP2: Expanding the Transformer Interatomic Potential Demonstrates Architectural Scalability for Organic Compounds

    Joshua Ebbert^‡, Bryce Hedelius^†, Jyothish Joy, Daniel H. Ess, and Dennis Della Corte

    J. Phys. Chem. A 129 (21), 4757-4766 (2025).
    
46. Dietary Sugar Intake and Incident Type 2 Diabetes Risk: A Systematic Review and Dose-Response Meta-Analysis of Prospective Cohort Studies

    Karen A. Della Corte, Tyler Bosler^†, Cole McClure^‡, Anette E. Buyken, James D. LeCheminant, Lukas Schwingshackl, and Dennis Della Corte

    Adv. Nutr. 16 (5), 100413 (2025).
    
47. Conformation-specific Design: a New Benchmark and Algorithm with Application to Engineer a Constitutively Active Map Kinase

    Jacob A. Stern^†, Siba Alharbi, Anandsukeerthi Sandholu, Stefan T. Arold, and Dennis Della Corte

    bioRxiv, (2025).
    
48. Association and substitution analyses of dietary sugars, starch and fiber for indices of body fat and cardiometabolic risk– a NoHoW sub-study

    Karen A. Della Corte, Dennis Della Corte, David Camacho^‡, Graham Horgan, Antonio L. Palmeira, James Stubbs, and Berit L. Heitmann

    Eur. J. Nutr. 64 (2), 68 (2025).
    

2024

29. CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein

    Fengling Li, Suzanne Ackloo, Cheryl H. Arrowsmith, Fuqiang Ban, Christopher J. Barden, Hartmut Beck, … Dennis Della Corte, … Spencer S Gardiner^‡, … Austin J Jarrett^‡, … Connor J Morris^‡, … Damon Tingey^‡, … (85 other authors)

    J. Chem Inf. Model. 64 (22), 8521-8536 (2024).
    
30. Equipping Future Physicians with Artificial Intelligence Competencies through Student Associations

    Spencer Hopson^‡, Carson Mildon^‡, Kyle Hassard^‡, Paul M. Urie, and Dennis Della Corte

    Int. Med. Educ. 3 (4), 388-394 (2024).
    
31. Development of a national database for dietary glycemic index and load for nutritional epidemiologic studies in the United States

    Karen A. Della Corte, Dennis Della Corte, Sean Titensor^‡, Bo Yang, and Simin Liu

    Am. J. Clin. Nutr. 120 (2), 380-388 (2024).
    
32. Rise of the Allotrope Simple Model: Update from 2023 Fall Allotrope Connect

    Spencer Gardiner^‡, Christopher Haynie^‡, and Dennis Della Corte

    Drug Discov. Today 29 (4), 103944 (2024).
    

2023

25. TrIP─Transformer Interatomic Potential Predicts Realistic Energy Surface Using Physical Bias

    Bryce E. Hedelius^†, Damon Tingey^‡, and Dennis Della Corte

    J. Chem. Theory Comput. 20 (1), 199-211 (2023).
    
26. A probabilistic view of protein stability, conformational specificity, and design

    Jacob A. Stern^†, Tyler J. Free^†, Kimberlee L. Stern^†, Spencer Gardiner^‡, Nicholas A. Dalley^‡, Bradley C. Bundy, … and Dennis Della Corte (2 other authors)

    Sci. Rep. 13, 15493 (2023).
    
27. Towards a Clinically Useful AI Tool for Prostate Cancer Detection: Recommendations from a PANDA Dataset Analysis

    T. J. Hart^‡, Chloe Engler Hart^‡, Aaryn S. Frewing^‡, Paul M. Urie, and Dennis Della Corte

    JCRMHS, (2023).
    
28. Don't Fear the Artificial Intelligence: A Systematic Review of Machine Learning for Prostate Cancer Detection in Pathology

    Aaryn Frewing^‡, Alexander B. Gibson^‡, Richard Robertson^‡, Paul M. Urie, and Dennis Della Corte

    Arch. Pathol. Lab. Med. 148 (5), 603-612 (2023).
    

2022

21. MILCDock: Machine Learning Enhanced Consensus Docking for Virtual Screening in Drug Discovery

    Connor J. Morris^‡, Jacob A. Stern^†, Brenden Stark^‡, Max Christopherson^‡, and Dennis Della Corte

    J. Chem Inf. Model. 62 (22), 5342-5350 (2022).
    
22. Student-Created Video Content for Assessment and Experiential Learning

    Ben Graul^‡, Matthew L. Rollins^‡, Nathan Powers, and Dennis Della Corte

    Phys. Teach. 60 (6), 491-495 (2022).
    
23. Training undergraduate research assistants with an outcome-oriented and skill-based mentoring strategy

    Dennis Della Corte, Connor J. Morris^‡, Wendy M. Billings^‡, Jacob Stern^‡, Austin J. Jarrett^‡, Bryce Hedelius^†, and Adam Bennion

    Acta Crystallogr. Sect. D-Struct. Biol. 78 (8), (2022).
    
24. Computational methods to simulate molten salt thermophysical properties

    Talmage Porter^‡, Michael M. Vaka^‡, Parker Steenblik^‡, and Dennis Della Corte

    Comm. Chem. 5 (1), 69 (2022).
    
25. Self-reporting data assets and their representation in the pharmaceutical industry

    Dennis Della Corte, Wolfgang Colsman, Heiko Fessenmayr, Alexandre Sawczuk da Silva, and Dana E. Vanderwall

    Drug Discov. Today 27 (1), 207-214 (2022).
    

2021

16. Learning Small Molecule Energies and Interatomic Forces with an Equivariant Transformer on the ANI-1x Dataset

    Bryce Hedelius^‡, Fabian B. Fuchs, and Dennis Della Corte

    ELLIS Machine Learning for Molecule Discovery Workshop (2021).
    
17. Evaluation of Deep Neural Network ProSPr for Accurate Protein Distance Predictions on CASP14 Targets

    Jacob Stern^†, Bryce Hedelius^‡, Olivia Fisher^‡, Wendy M. Billings^‡, and Dennis Della Corte

    Int. J. Mol. Sci. 22, 12835 (2021).
    
18. Delivering Digital Transformation with Self-reporting Data Assets

    Dennis Della Corte, Naomi Young^‡, and Karen A. Della Corte

    Proceedings of the Future Technologies Conference (FTC) 2021, Volume 1. FTC 2021. Lecture Notes in Networks and Systems, vol 358. Springer, Cham.
    
19. Modeling SARS-CoV2 proteins in the CASP-commons experiment

    Andriy Kryshtafovych, John Moult, Wendy M. Billings^‡, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, … (4 other authors)

    Proteins: Struct., Funct., Bioinf., (2021).
    
20. The Data-Centric Lab: A Pharmaceutical Perspective

    Dennis Della Corte and Karen A. Della Corte

    Proceedings of the 2021 Future of Information and Communication Conference (FICC), pp 1-15, (2021).
    
21. The whole is greater than its parts: ensembling improves protein contact prediction

    Wendy M. Billings^‡, Connor J. Morris^‡, and Dennis Della Corte

    Sci. Rep. 11 (1), 8039 (2021).
    
22. Coming of age of allotrope: proceedings from the Fall 2020 Allotrope Connect

    Todd Millecam^‡, Austin J. Jarrett^‡, Naomi Young^‡, Dana E. Vanderwall, and Dennis Della Corte

    Drug Discov. Today 26 (8), 1922-1928 (2021).
    
23. Using molecular docking and molecular dynamics to investigate protein-ligand interactions

    Connor J. Morris^‡ and Dennis Della Corte

    Mod. Phys. Lett. B 35 (8), 2130002 (2021).
    
24. Current computational methods for enzyme design

    Talmage L. Coates^‡, Naomi Young^‡, Austin J. Jarrett^‡, Connor J. Morris^‡, James D. Moody, and Dennis Della Corte

    Mod. Phys. Lett. B 35 (9), 2150155 (2021).
    

2020

7. World trends in sugar-sweetened beverage and dietary sugar intakes in children and adolescents: a systematic review

   Karen Della Corte, Jessica Fife^†, Alexis Gardner, Britta L Murphy^†, Linda Kleis, Dennis Della Corte, … (3 other authors)

   Nutr. Rev. 79 (3), 274-288 (2020).
   
8. Engineering and application of a biosensor with focused ligand specificity

   Dennis Della Corte, Hugo L. van Beek, Falk Syberg, Marcus Schallmey, Felix Tobola, Kai U. Cormann, … Connor J. Morris^‡, … (8 other authors)

   Nat. Commun. 11 (1), 4851 (2020).
   
9. Context-dependent stabilizing interactions among solvent-exposed residues along the surface of a trimeric helix bundle

   Kimberlee L. Stern^†, Mason S. Smith^†, Wendy M. Billings^‡, Taylor J. Loftus^‡, Benjamin M. Conover^‡, Dennis Della Corte, and Joshua L. Price

   Biochemistry 59 (17), 1672-1679 (2020).
   
10. Library eArchiving with ZONTAL Space and the Allotrope Data Format

    Dennis Della Corte, Wolfgang Colsman, Ben Welker, and Brian Rennick

    Digital Library Perspectives 36 (1), (2020).
    

2018

3. Integrated NMR, Fluorescence and MD Benchmark Study of Protein Mechanics and Hydrodynamics

   Christina Möckel, Jakub Kubiak, Oliver Schillinger, Ralf Kuehnemuth, Dennis Della Corte, Gunnar F. Schröder, … (4 other authors)

   J. Phys. Chem. B 123 (7), 1453-1480 (2018).
   

2015

2. Coupling an Ensemble of Homologues Improves Refinement of Protein Homology Models

   André Wildberg, Dennis Della Corte, and Gunnar F. Schröder

   J. Chem. Theory Comput. 11 (12), 5578-5582 (2015).
   
3. Protein structure refinement with adaptively restrained homologous replicas

   Dennis Della Corte, André Wildberg, and Gunnar F. Schröder

   Eleventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (September 2016). Proteins: Struct., Funct., Bioinf. 84 (S1), (2015).
   

^‡Undergraduate Student Author

^†Graduate Student Author