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Chongle Pan, PhD

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Chongle Pan, Ph.D.

Associate Professor of Microbiolgy and Plant Biology, and Computer Science

110 W. Boyd Street
DEH 231
Norman, OK 73019

Ph.D., 2006, University of Tennessee, Knoxville, TN
B.S., 2001, East China Normal University, Shanghai, China


Research Areas:

Bioinformatics, Computational Biology, Environmental Microbiology, Predictive Genomics, Mass Spectrometry, Proteomics, Artificial Intelligence, and Big -Omics Data

Research interests:

The research in my lab is focused in knowledge discovery from big -omics data and predictive understanding of complex biological systems.  In environment microbiology, we aim to understand the adaptation of natural microbial communities under different environmental conditions using metagenomics, metaproteomics, and stable isotope probing. In predictive genomics, we aim to predict the phenotypic traits of microorganisms, plants, and humans from their genomes and other -omics data. Our computational approaches include artificial intelligence, high-performance computing, network analysis, knowledge graph, and literature mining. Our experimental approaches include mass-spectrometry-based proteomics and metabolomics and sequencing-based genomics and transcriptomics.

Relevant publications:

Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR,Banfield JF (2019)  Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.  DOI:10.1038/s41564-019-0449-y

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 (2018) Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil. Nature Ecology and Evolution2(3):499-509

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

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. (2017) Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system, Environmental Microbiology 19, 1041-1053

S. Bryson, Z. Li, F. Chavez, P. K. Weber, J. Pett-Ridge, R. L. Hettich, C. Pan, X. Mayali, and R. S. Mueller. (2017) Phylogenetically conserved resource partitioning in the coastal microbial loop, The ISME journal.

J. Marlow, C. T. Skennerton, Z. Li, K. Chourey, R. L. Hettich, C. Pan, and V. J. Orphan. (2016) Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities, Frontiers in Microbiology 7.

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

C. Mosier, Z. Li, B. C. Thomas, R. L. Hettich, C. Pan, and J. F. Banfield. (2015) Elevated temperature alters proteomic responses of individual organisms within a biofilm community, ISME Journal 9, 180-194.

Y. Wang, G. Kora, B. P. Bowen, and C. Pan. (2014) MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics, Analytical Chemistry 86, 9496-9503.

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

B. Haider, T.-H. Ahn, B. Bushnell, J. Chai, A. Copeland, and C. Pan. (2014) Omega: an Overlap-graph de novo Assembler for Metagenomics, Bioinformatics 30, 2717-2722.