Publications

All Publications:

• On Google Scholar
• On NIH PubMed

Selected Publications:

Computer Science:

• Luedeking-Piret Regression for Multi-Step-Ahead Forecasting and Clone Selection in mAb Biomanufacturing
  P. Wang, D. Verma, Y. Chiu, J. Klier, C. Pan
  Communication Engineering (Accepted)

• Unified modeling language code generation from diagram images using multimodal large language models (2025)
  A. Bates, R. Vavricka, S. Carleton, R. Shao, C. Pan
  Machine Learning with Applications, 20:100660. doi: 10.1016/j.mlwa.2025.100660

• Integration of Nested Cross-Validation, Automated Hyperparameter Optimization, and High-Performance Computing to Reduce and Quantify the Variance of Test Performance Estimation of Deep Learning Models (2025)
  P. Calle, A. Bates, J.C. Reynolds, Y. Liu, H. Cui, S. Ly, C. Wang, Q. Zhang, A.J. de Armendi, S.S. Shettar, K.M. Fung, Q. Tang, C. Pan
  Computer Methods and Programs in Biomedicine, 10;272:109063. doi: 10.1016/j.cmpb.2025.109063

• Towards AI-Driven Healthcare: Systematic Optimization, Linguistic Analysis, and Clinicians’ Evaluation of Large Language Models for Smoking Cessation Interventions (2024)
  P. Calle, R. Shao, Y. Liu, E. Hebert, D. Kendzor, J. Neil, M. Businelle, C. Pan
  Proceedings of the 2024 ACM CHI Conference on Human Factors in Computing Systems (CHI), Hawaii, USA

• Explainable Multi-Task Learning Improves the Parallel Estimation of Polygenic Risk Scores for Many Diseases Through Shared Genetic Basis (2023)
  A. Badré, C. Pan
  PLoS Computational Biology, 19(7):e1011211. doi: 10.1371/journal.pcbi.1011211

• LINA: A Linearizing Neural Network Architecture for Accurate First-Order and Second-Order Interpretations (2022)
  A. Badré and C. Pan
  IEEE Access 10:36166-36176. doi: 10.1109/access.2022.3163257

• Deep Neural Network Improves the Estimation of Polygenic Risk Scores for Breast Cancer (2021)
  A. Badré, L. Zhang, W. Muchero, J.C. Reynolds, C. Pan
  Journal of Human Genetics, 66(4):359-369. doi: 10.1038/s10038-020-00832-7

• Deep-learning-aided forward optical coherence tomography endoscope for percutaneous nephrostomy guidance (2021)
  C. Wang, P. Calle, N. Ton, Z. Zhang, F. Yan, A.M. Donaldson, N.A. Bradley, Z. Yu, C. Pan, Q. Tang
  Biomedical Optics Express, 12(4):2404-2418. doi: 10.1364/BOE.421299

• Sipros Ensemble Improves Database Searching and Filtering for Complex Metaproteomics (2018)
  X. Guo, Z. Li, Q. Yao, R.S. Mueller, J. K. Eng, D. L. Tabb, W. J. Hervey, and C. Pan
  Bioinformatics 34(5):795-802

• Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance (2015)
  T.-H. Ahn, J. Chai, and C. Pan
  Bioinformatics 31, 170-177

Biological Sciences:

• Proteomic Stable Isotope Probing with an Upgraded Sipros Algorithm for Improved Identification and Quantification of Isotopically Labeled Proteins (2024)
  Y. Xiong, R.S. Mueller, S. Feng, X. Guo, C. Pan
  Microbiome, 12(1):148. doi: 10.1186/s40168-024-01866-1

• Metaproteomics-Informed Stoichiometric Modeling Reveals the Responses of Wetland Microbial Communities to Oxygen and Sulfate Exposure (2024)
  D. Wang, P. Candry, K.A. Hunt, Z. Flinkstrom, Z. Shi, Y. Liu, N.Q. Wofford, M.J. McInerney, R.S. Tanner, K.B. De León, J. Zhou, M.H. Winkler, D.A. Stahl, C. Pan
  NPJ Biofilms and Microbiomes, 10(1):55. doi: 10.1038/s41522-024-00525-5

• Cross-Feedings, Competition, and Positive and Negative Synergies in a Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to Methane (2023)
  D. Wang, K.A. Hunt, P. Candry, X. Tao, N.Q. Wofford, J. Zhou, M.J. McInerney, D.A. Stahl, R.S. Tanner, A. Zhou, M. Winkler, C. Pan
  mBio, 14(2):e0318922. doi: 10.1128/mbio.03189-22

• Islet Autoantibody Seroconversion in Type-1 Diabetes is Associated with Metagenome-Assembled Genomes in Infant Gut Microbiomes (2022)
  L. Zhang, K.R. Jonscher, Z. Zhang, Y. Xiong, R.S. Mueller, J.E. Friedman, C. Pan
  Nature Communications, 13(1). doi: 10.1038/s41467-022-31227-1

• Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil (2018)
  Q. Yao, Z. Li, Y. Song, S.J. Wright, X. Guo, S.G. Tringe, M.M. Tfaily, L. Paša-Tolić, T.C. Hazen, B.L. Turner, M.A. Mayes, C. Pan
  Nature Ecology and Evolution, 2(3):499–509

• Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes (2022)
  L. Zhang, K.R. Jonscher, Z. Zhang, Y. Xiong, R.S. Mueller, J.E. Friedman, C. Pan
  Nature Communications 13(1):3551. doi: 10.1038/s41467-022-31227-1

• Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol (2019)
  Z. Li, Q. Yao, X. Guo, A. Crits-Christoph, M.A. Mayes, W.J. Hervey, S.L. Lebeis, J.F. Banfield, G.B. Hurst, R.L. Hettich, C. Pan
  Frontier in Microbiology 10:2706. doi: 10.3389/fmicb.2019.02706

• Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system (2017)
  Z. Li, Q. Yao, S.P. Dearth, M.R. Entler, H.F. Castro Gonzalez, J.K. Uehling, R.J. Vilgalys, G.B. Hurst, S.R. Campagna, J.L. Labbe, and C. Pan
  Environmental Microbiology 19(3):1041-1053. doi: 10.1111/1462-2920.13605

• Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil. (2018)
  Q. Yao, Z. Li, Y. Song, S. J. Wright, X. Guo, S. G. Tringe, M.M. Tfaily, L. Paša-Tolic, T. C. Hazen, B. L. Turner, M. A. Mayes, C. Pan
  Nature Ecology and Evolution 2(3):499-509

• Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community (2014)
  Z. Li, Y. Wang, Q. Yao, N. B. Justice, T.-H. Ahn, D. Xu, R. L. Hettich, J. F. Banfield, and C. Pan
  Nature Communications 5:4405. doi: 10.1038/ncomms5405