Publications

All Publications:

• On Google Scholar
• On NIH PubMed

Selected Publications:

Computer Science:

• 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:

• 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