Liang Lu, Jinliang Zhao and and Chenhong Li, 2020. High-quality genome assembly and annotation of the big-eye mandarin fish (Siniperca knerii). G3: Genes|Genomes|Genetics Early Online, published on January 17, 2020 as doi:10.1534/g3.119.400930

Fangyuan Cheng, Qian Wang, Pierpaolo Maisano Delser, and Chenhong Li, 2019. Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River. Ecology and Evolution, 2019;00:1–14.

Hao Yuan, Calder Atta, Luke Tornabene and Chenhong Li, 2019. Assexon: Assembling Exon Using Gene Capture Data. Evolutionary Bioinformatics, 15:1-13.

Guoxing Yin, Yiling Pan, Anirban Sarker, Mohammad A. Baki, Jin-Koo Kim, Hanlin Wu, Chenhong Li, 2019. Molecular systematics of Pampus (Perciformes: Stromateidae) based on thousands of nuclear loci using target-gene enrichment, Molecular Phylogenetics and Evolution, 140.

Jiamei Jiang, Hao Yuan, Xin Zheng, Qian Wang, Ting Kuang, Jingyan Li, Junning Liu, Shuli Song, Weicai Wang, Fangyuan Cheng, Hongjie Li, Junman Huang, Chenhong Li, 2019. Gene markers for exon capture and phylogenomics in rayfinned Fishes. Ecology and Evolution. 2019;1–11.

Robert S. Sommer, Michael Hofreiter, Frauke Kruger, Björn M. Siemers, Johanna L. A. Paijmans, Chenhong Li and Matthias F. Geiger, 2019. Preliminary results on the molecular study of fish-eating by ‘trawling Myotis’ bat species in Europe. Vertebrate Zoology, 69 (1): 83 – 92.

Yongtao Tang, Chenhong Li, Kunyuan Wanghe, Chenguang Feng, Chao Tong, Fei Tian, Kai Zhao, 2019. Convergent evolution misled taxonomy in schizothoracine fishes (Cypriniformes: Cyprinidae). Molecular Phylogenetics and Evolution, 134:323-337.

Nicolas Straube, Chenhong Li, Matthias Mertzen, Hao Yuan and Timo Moritz, 2018. A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies. BMC Evolutionary Biology, 18:158.

Kuang T, L Tornabene, J Li, J Jiang, P Chakrabartye, J S Spark, G J.P. Naylor, C Li, 2018. Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness. Molecular Phylogenetics and Evolution, 128, 192-202.

Liu S, Wang C, Li C, 2018. Progress in Aquaculture Genetics and Breeding in China. Journal of World Aquaculture Society, 49 (2): 272-276.

Xia J, Wu H, Li C, Wu Y, Liu S, 2018. A new species of Rhinogobius (Pisces: Gobiidae), with analyses of its DNA barcode. Zootaxa 4407 (4): 553-562.

L C. Hughes, G Ortí, Y Huang, Y Sun, C C. Baldwin, A W. Thompson, D Arcila, R Betancur-R, C Li, L Becker, N Bellora, X Zhao, X Li, M W, C Fang, B Xie, Z Zhou, H Huang, S Chen, B Venkatesh, and Q Shi, 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences of the United States of America, 115(24): 6249-6254. doi:10.1073/pnas.1719358115

H Li, Y. He, J. Jiang, Z. Liu, C. Li, 2018. Molecular systematics and phylogenetic analysis of the Asian endemic freshwater sleepers (Gobiiformes: Odontobutidae). Mol. Phylogenet. Evol., 121, 1–11.

Liu J, Jiang J, Song S, Tornabene, L., Chabarria, R., Naylor, G. J. P., Li, C., 2017. Multilocus DNA barcoding - Species Identification with Multilocus Data. Sci. Rep. 7, 16601.

Song, S., Zhao, J., Li, C., 2017. Species delimitation and phylogenetic reconstruction of the sinipercids (Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences. Mol. Phylogenet. Evol. 111, 44-55.

Corrigan, S., Maisano Delser, P., Eddy, C., Duffy, C., Yang, L., Li, C., Bazinet, A.L., Mona, S., Naylor, G.J., 2017. Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks. Mol. Phylogenet. Evol. 110, 122-126.

Wang, Q., Zhang, J., Matsumoto, H., Kim, J., Li, C. 2016. Population structure of elongate ilisha Ilisha elongata along the Northwestern Pacific Coast revealed by mitochondrial control region sequences. Fish Sci, 82 (5): 771 - 785.

PM Delser, Corrigan S., Hale M., Li C., Veuille M., Planes S., Naylor G., Mona S. 2016. Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives. Sci Rep. (6): 33753. doi: 10.1038/srep33753.

Yuan H, Jiang J, Jimenez FA, Hoberg EP,Cook JA, Galbreath KE, Li C. 2016. Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms. Mol Ecol Resour, 16(5):1095-1106. doi: 10.1111/1755-0998.12532.

Chenhong Li, Shannon Corrigan , Lei Yang , Nicolas Straube , Mark Harris , Michael Hofreiter , William T. White , Gavin Naylor, 2015. DNA Capture Reveals Trans Oceanic Gene Flow in Endangered River Sharks. Proceedings of the National Academy of Sciences of the United States of

Nicolas Straube, Chenhong Li, Julien M. Claes, Shannon Corrigan and Gavin J. P. Naylor, 2015. Molecular phylogeny of Squaliformes and first occurrence of bioluminescence in sharks. BMC: Evolutionary Biology, 15:162. DOI 10.1186/s12862-015-0446-6.

Nicolas Straube, William T. White, Hsuan-Ching Ho, Elisabeth Rochel, Shannon Corrigan, Chenhong Li, Gavin J.P. Naylor, 2014. A DNA sequence-based identification checklist for Taiwanese chondrichthyans. Zootaxa, 12/2013; 3752(1): 256-278.

H Ma, C Ma, C Li, J Lu, X Zou, Y Gong, W Wang, W Chen, L Ma, L Xia. 2015. First mitochondrial genome for the red crab (Charybdis feriata) with implication of phylogenomics and population genetics. Scientific Reports, (5), 11524.

Nicolas Straube, Robin W. Leslie, Paul J. Clerkin, David A. Ebert, Elisabeth Rochel, Shannon Corrigan, Chenhong Li, Gavin J.P. Naylor, 2014. On the occurrence of the southern Lanternshark, Etmopterus granulosus, off south Africa, with comments on the validity of E. compagnoi. Deep Sea Research Part II Topical Studies in Oceanography. DOI: 10.1016/j.dsr2.2014.04.004

X. Yao, C. Li, C. W. Dick, 2013. Exon-primed intron-crossing (EPIC) markers for evolutionary studies of Ficus and other taxa in the fig family (Moraceae).Applications in Plant Sciences 1 ( 10 ): 1300037.

P. R. Ströher, C. Li and M. R. Pie, 2013. Exon-primed intron-crossing (EPIC) makers as a tool for ant Phylogeography, Revista Brasileira de Entomologia, AHEAD.

Li, C., M., Hofreiter, N., Straube, S., Corrigan, G. J. P. Naylor, 2013. Capturing protein-coding genes across highly divergent species. BioTechniques 54:321-326.

Betancur-R. R, Broughton RE, Wiley EO, Carpenter K, López JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton II JC, Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, Grande T, Arratia G, Ortí G., 2013. The Tree of Life and a New Classification of Bony Fishes. PLOS Currents Tree of Life. 2013 Apr 18.

Broughton RE, Betancur-R. R, Li C, Arratia G, Ortí G. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLOS Currents Tree of Life. 2013 Apr 16.

Betancur-R., R., C. Li, T. A Munroe, J. A. Ballesteros, G. Ortí. 2013. Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Systematic Biology 62 (5): 763-785.

Li, C., Riethoven, J.-J. M., Naylor, G. 2012. EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies. Molecular Ecology Resources, 12(5):967-71.

Li, C., Matthes, K., Garcia, M., Naylor, G. J. P. 2012. Nuclear markers for phylogenetics of chondrichthyes and the problem in rooting phylogeny with distant outgroup. Molecular Phylogenetics and Evolution, 63:365-373.

Sommer, J. A., Li, C., Brozek, J., Bessert, M. L., Ortí, G., Berra, T. M., 2011. Low genetic diversity in Nurseryfish, Kurtus gulliveri (Perciformes: Kurtidae), and an appraisal of its breeding system using microsatellite loci. The Beagle, Records of the Museums and Art Galleries of the Northern Territory, 2011 27: 179-188.

Li, C., Betancur-R, R., Smith, Wm. L., Ortí, G. 2011. Monophyly and interrelationships of Snook and Barramundi (Centropomidae sensu Greenwood) and five new markers for fish phylogenetics. Molecular Phylogenetics and Evolution, 60: 463-471.

Li, C., Ortí, G., Zhao, J., 2010. The phylogenetic placement of sinipercid fishes (“Perciformes”) revealed by 11 nuclear loci. Molecular Phylogenetics and Evolution, 56: 1096-1104.

Li, C., Riethoven, J.-J. M., Ma, L., 2010. Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes. BMC: Evolutionary Biology, 10: 90.

Li, C., Bessert, M. L., Macrander, J., Ortí, G., 2009. Low variation but strong population structure in mitochondrial control region of the plains topminnow, Fundulus sciadicus. Journal of Fish Biology, 74: 1037-1048.

Li, C., Lu, G., Ortí, G., 2008. Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Systematic Biology, 57(4): 519-539.

Wang, C., Li, C., Li, S., 2008. Mitochondrial DNA-inferred population structure and demographic history of the mitten crab (Eriocheir, sensu stricto) along the coast of mainland China inferred from mitochondrial loci. Molecular Ecology, 17: 3515-3527.

Zhao, J., Li, C., Zhao, L., Wang, W., Cao, Y., 2008. Mitochondrial diversity and phylogeography of the Chinese perch, Siniperca chuatsi (Perciformes: Sinipercidae). Molecular Phylogenetics and Evolution, 49(1): 399-404.

Li, C., Ortí, G., Zhang, G., Lu, G., 2007. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC: Evolutionary Biology, 7: 44.

Li, C., Ortí, G., 2007. Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences, Molecular Phylogenetics and Evolution 44: 386-398.

Li, C., Bessert, M. L., Macrander, J., Ortí, G., 2007. Microsatellite loci for the plains topminnow (Fundulus sciadicus, Fundulidae). Molecular Ecology Notes 7: 691-693.

 Li, C., Li, S., 2003. Genetically improved farmed nile tilapia and its new selected generation in China. In: Proceedings of the Third World Fisheries Congress: Feeding the World with Fish in the Next Millennium--The Balance between Production and Environment. American Fisheries Society Symposium 38.

Li, S., Li, C., Dey, M., Gagalacb, F., Dunham, R., 2002. Cold tolerance of three strains of Nile tilapia, Oreochromis niloticus, in China. Aquaculture 213: 123-129.

Li, C., Li, S., Xing, Y., Hu, B., Zhao, S., Wu, Z., 2001. Evaluation of culture performances of two crab Eriocheir sinensis populations in China. World Aquaculture Magazine, 32(3): 15-16, 68-69.

Li, S., Li, C., Dey, M., Dunham, R., 1999. Seinability of four strains of Nile tilapia, Oreochromis niloticus, in Chinese ponds. Aquaculture, 174: 223-227.