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Chongle Pan

Staff Scientist



Our research is focused on studying environmental microbiology with proteomics, genomics and bioinformatics. A proteogenomic approach is used to characterize complex microbial communities relevant to carbon cycling and environmental remediation. This involves computational/experimental method development and collaborative biological analysis. We are also interested in functional annotation and evolutionary analysis of microbial genomes using novel algorithms and high-performance computing.


  • Ph.D.: Computational Biology-UT/ORNL (2006)


Wang, Y., Kora, G., Bowen, B. P. & Pan, C. “MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics.” Analytical chemistry doi:10.1021/ac5014783 (2014).

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

Haider, B., Ahn, T. H., Bushnell, B., Chai, J., Copeland, A. & Pan, C. “Omega: an Overlap-graph de novo Assembler for Metagenomics.” Bioinformatics, doi:10.1093/bioinformatics/btu395 (2014).

Chai, J., Kora, G., Ahn, T. H., Hyatt, D. & Pan, C. “Functional Phylogenomics Analysis of Bacteria and Archaea using Consistent Genome Annotation with UniFam.” BMC Evolutionary Biology, Accepted (2014).

Ahn, T. H., Chai, J. & Pan, C. “Sigma: Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance.” Bioinformatics, doi:10.1093/bioinformatics/btu641 (2014).

Wang, Y., Ahn, T. H., Li, Z. & Pan, C. “Sipros/ProRata: a versatile informatics system for quantitative community proteomics.” Bioinformatics 29, 2064-2065, doi:10.1093/bioinformatics/btt329 (2013).

Li, Z., Adams, R. M., Chourey, K., Hurst, G. B., Hettich, R. L. & Pan, C. “Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos.” Journal of proteome research 11, 1582-1590, doi:10.1021/pr200748h (2012).

Hyatt, D. & Pan, C. “Exhaustive database searching for amino acid mutations in proteomes.” Bioinformatics 28, 1895-1901, doi:10.1093/bioinformatics/bts274 (2012).

Pan, C., Fischer, C. R., Hyatt, D., Bowen, B. P., Hettich, R. L. & Banfield, J. F. “Quantitative tracking of isotope flows in proteomes of microbial communities.” Molecular & cellular proteomics 10, M110 006049, doi:10.1074/mcp.M110.006049 (2011).

Pan, C. “Measuring dissociation rate constants of protein complexes through subunit exchange: experimental design and theoretical modeling.” PloS one 6, e28827, doi:10.1371/journal.pone.0028827 (2011).

For a complete and up-to-date list of publications, please go to

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