John-Liu-2011-pictureJohn Liu

Associate Provost & Associate Vice President for Research; Professor

School of Fisheries, Aquaculture and Aquatic Sciences

education

1989 Ph.D.Molecular and Cellular Biology, University of Minnesota, St. Paul, MN
1986 M.S.Plant Pathology, University of Minnesota, St. Paul, MN
1981 B.S., Plant Pathology and Entomology, with highest honor, Northwestern Agricultural University, China

Professional Experience

—Associate Provost and Associate Vice President for Research 2013-present
—Associate Dean for Research and Professor, College of Agriculture, and Assistant Director, Alabama Agricultural Experiment Station (AAES), Auburn University 2007-2013
—Alumni Professor, Department of Fisheries and Allied Aquacultures and the Program of Cell and Molecular Biosciences 2003-2007
—Professor and China Programs Coordinator, College of Agriculture, Auburn University 2003-2007
—Associate Professor, Department of Fisheries and Allied Aquacultures and the Program of Cell and Molecular Biosciences, Auburn University 1999-2003
—Assistant Professor, Department of Fisheries and Allied Aquacultures, Auburn University 1995-2002
—Director, R&D, National Biosciences, Inc., Plymouth, Minnesota 1994-1995
—Research Professor, Institute of Human Genetics, University of Minnesota 1991-1994
—Postdoctoral Fellow, USDA-ARS Cereal Disease Laboratory, St. Paul, MN 1990-1991
—Graduate Research Assistant and Teaching Assistant, Department of Genetics and Cell Biology, University of Minnesota 1986-1989
—Graduate Research Assistant, Department of Plant Pathology, University of Minnesota 1983-1986

Honors and Awards

—Selected as the 2017 NRSP-8 Distinguished Speaker 2016
—Dean’s Grantsmanship Award, College of Agriculture 2010, 2014, 2015
—Fulbright Specialist Grant Award, US Department of State 2015
—Hou Ji Scholar, Northwest A&F University, Yanglin, China 2011-present
—Honorary Dean, College of Marine Science and Engineering, Qingdao Agricultural University, China 2012-present
—USDA Recognition for significant contribution to “National Animal Genome Program”, USDA CSREES. 2009
—Honorary Director, Applied Genomics Institute, the Chinese Academy of Fisheries Sciences 2009-2015
—Fellow, American Association for the Advancement of Science (AAAS). Since 2007
—Creative Research & Scholarship Award, the highest research award at Auburn University. 2007
—Alumni Professorship, Auburn University, in recognition of “outstanding contributions in research and teaching”. 2002-2007
—Academic Master for Aquaculture under “111” Project of China. 2007-present
—Director’s Outstanding Senior Research Award, Alabama Agricultural Experiment Station.
—Governor’s Golden Summit Award, Sichuan Province, China
—“Catfish Genome Research” exhibited on Capitol Hill, sponsored by NASULGC. 2000
—Distinguished Research Award by Alabama Catfish Producers in recognition of outstanding research contributions and dedication to Alabama’s catfish industry. 1999
—Research featured on the cover of Nature Biotechnology. 1990

professional affiliations

—Member, World Aquaculture Society
—Fellow, AAS

Research activities

My research programs focus on genomics and informatics of aquaculture species. Specifically, we have sequenced and assembled the whole genome reference sequence for channel catfish and blue catfish, and used the genome information to determine genes involved in production and performance traits important for aquaculture. Some examples of our work are QTL mapping of disease resistance, heat tolerance, low oxygen tolerance, growth rates, and body conformation. We are also working on comparative genomics and functional genomics, and informatics to deal with big data out of transcriptome and genome studies.

Select Publications

Publications of the last three years (out of 300 total):

  1.  Jin Y, Zhou T, Liu S, Geng X, Chen A, Yao J, Jiang C, Wang X, Su B, Liu ZJ. 2016. A genome-wide association study (GWAS) of heat stress-associated SNPs in catfish. Animal Genetics, in press.
  2.  Yuan Z, Liu S, Yao J, Zeng Q, Liu ZJ. 2016. Expression of Bcl-2 genes in channel catfish after bacterial infection and hypoxia stress. Developmental and Comparative Immunology 65: 79-90.
  3.  Liu S, Yao J, Zhang J, and Liu ZJ. 2016. Next generation sequencing yields the complete mitochondrial genome of the striped raphael catfish, Platydoras armatulus (Siluriformes: Doradidae). Mitochondria DNA 27:1963-1964.
  4.  Zeng Q, Liu S, Yao J, Zhang Y, Yuan Z, Chen A, Jiang C, Fu Q, Su B, Dunham R, and Liu ZJ. Transcriptome display during testicular differentiation of channel catfish as revealed by RNA-Seq analysis. Biology of Reproduction, in press DOI:10.1095/biolreprod.116.138818.
  5.  Zhou X, Cui J, Liu S, Kong D, Sun H, Gu C, Wang H, Qiu X, Chang Y, Liu ZJ, Wang X. 2016. Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicas. PeerJ 4:e1779.
  6.  Li Z, Yao J, Xie Y, Geng X, Liu ZJ. 2016. Phosphoinositide 3-kinase family in channel catfish and their regulated expression after bacterial infection. Fish Shellfish Immunology 49:364-373.
  7.  Fu Q, Li Y, Yang Y, Li C, Yao J, Zeng Q, Qin Z, Li Dao, Liu ZJ. 2016. Septin genes in channel catfish (Ictalurus punctatus) and their involvement in disease defense responses. Fish and Shellfish Immunology 49:110-121.
  8.  Liu ZJ, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Wang R, Koren S, Jiang Y, Zimin A, Xu P, Phillippy AM, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann RG, Schroeder S, Scheffler B, Duke MV, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby ML, Tian Y, Flanagan ME, Mu W, Waldbieser GC. 2016. The channel catfish genome sequence provides insights into evolution of scale formation in teleosts. Nature Communications 7:11757, DOI: 10.1038/ncomms11757.
  9.  Chen A, Wang, R, Liu S, Peatman E, Sun L, Bao L, Jiang, C, Li C, Li Y, Zeng Q, Liu ZJ. 2016. Ribosomal protein genes are highly enriched among genes with allele-specific expression in the interspecific F1 hybrid catfish. Molecular Genetics and Genomics 291:1083-1093. DOI: 10.1007/s00438-015-1162-z
  10.  Song L, Li C, Xie Y, Liu S, Zhang J, Yao J, Jiang C, Li Y, Liu ZJ. 2016. Genome-wide identification of Hsp70 genes in channel catfish and their regulated expression after bacterial infection. Fish and Shellfish Immunology 49:154-162.
  11.  Su B, Shang M, Grewe P, Patil JG, Peatman E, Perera D, Cheng Q, Li C, Weng C, Li P, Liu ZJ and Dunham R. 2015. Suppression and restoration of primordial germ cell marker gene expression in channel catfish, Ictalurus punctatus, using knock-down constructs regulated by copper transport protein gene promoters: potential for reversible transgenic sterilization. Theriogenology 84:1499-1512.
  12.  Jiang C, Zhang J, Yao J, Liu S, Li Y, Song L, Li C, Wang X, Liu ZJ. 2015. Complement regulatory protein genes in channel catfish and their involvement in disease defense response. Developmental and Comparative Immunology 53:33-41.
  13.  Wang H, Liu S, Cui J, Li C, Hu Y, Zhou W, Chang Y, Qiu X, Liu ZJ, Wang X. 2015. Identification and characterization of microRNAs from longitudinal muscle and respiratory tree in sea cucumber (Apostichopus japonicus) using high-throughput sequencing. PLoS One 10(8):e0134899. doi:10.1371/journal.pone.0134899.
  14.  Xie, Y, Song L, Weng Z, Liu S, Liu ZJ. 2015. Hsp90, Hsp60 and sHsp families of heat shock protein genes in channel catfish and their expression after bacterial infections. Fish and Shellfish Immunology 44:642-651.
  15.  Tian Y, Yao J, Liu S, Jiang C, Zhang J, Li Y, Liu ZJ. 2015. Identification and expression analysis of 26 oncogenes of the receptor tyrosine kinase family in channel catfish after bacterial infection and hypoxic stress. Comparative Biochemistry and Physiology Part D, Genomics and Proteomics 14:16-25.
  16.  Liu S, Li Y, Qin Z, Geng X, Bao L, Kaltenboeck L, Kucuktas H, Dunham R, Liu ZJ. 2015. High-density SNP-based genetic mapping of interspecific hybrid catfish reveals intrinsic genomic incompatibility between Channel catfish and Blue catfish. Animal Genetics 47:81-90. doi:10.1111/age.12372.
  17.  Geng X, Sha J, Liu S, Bao L, Zhang J, Wang R, Yao J, Li C, Feng J, Sun F, Sun L, Jiang C, Dunham R, Zhi D, Liu ZJ. 2015. A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance. BMC Genomics 16:196. DOI 10.1186/s12864-015-1409-4.
  18.  Sun L, Liu S, Bao L, Li Y, Feng J, Liu ZJ. 2015. Claudin multigene family in channel catfish and their expression profiles in response to bacterial infection and hypoxia as revealed by meta-analysis of RNA-Seq datasets. Comparative Biochemistry and Physiology, Part D, Genomics and Proteomics 13:60-69.
  19.  Li Y, Liu S, Qin Z, Yao J, Jiang C, Song L, Dunham R, Liu ZJ. 2015. The serpin superfamily in channel catfish: Identification, phylogenetic analysis and expression profiling in mucosal tissues after bacterial infections. Developmental and Comparative Immunology 49:267-277.
  20.  Li Y, Liu S, Qin Z, Waldbieser G, Wang R, Sun L, Bao L, Danzmann R, Dunham R, Liu ZJ. 2015. Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish. DNA Research 22:39-52. doi:10.1093/dnares/dsu038
  21.  Feng J, Liu S, Wang R, Zhang J, Wang X, Kaltenboeck L, Li J, Liu ZJ. 2015. Molecular characterization, phylogenetic analysis and expression profiling of myoglobin and cytoglobin genes in response to heat stress in channel catfish. Journal of Fish Biology 86:592-604.
  22.  Song L, Zhang J, Li C, Yao J, Jiang C, Li Y, Liu S, Liu ZJ. 2015. Genome-wide identification of Hsp40 genes in channel catfish and their regulated expression after bacterial infection. PLoS One 9(12):e115752. doi:10.1371/journal.pone.
  23.  Mu W, Yao J, Zhang J, Liu S, Wen H, Feng J, Liu ZJ. 2015. Expression of tumor suppressor genes in channel catfish after bacterial infections. Developmental and Comparative Immunology 48:171-177.
  24.  Yao J, Mu W, Liu S, Zhang J, Wen H, Liu ZJ. 2015. Identification, phylogeny and expression analysis of suppressors of cytokine signaling in channel catfish. Molecular Immunology 64:276-284.
  25.  Liu ZJ. 2014. Editorial, GIA 2013: Genomics in Aquaculture 2013 symposium. Marine Genomics, 18:1-2. doi:10.1016/j.margen.2014.10.005
  26.  Wang H, Liu S, Cui J, Li C, Qiu X, Chang Y, Liu ZJ, Wang X. 2014. Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicas. PLoS One 9(11):e111820.
  27.  Liu S, Zhang J, Yao J, and Liu ZJ. 2014. The complete mitochondrial genome of the armored catfish, Hypostomus plecostomus (Siluriformes: Loricariidae). Mitochondria DNA 20:1-2.
  28.  Sun L, Liu S, Wang R, Jiang Y, Zhang Y, Zhang J, Bao L, Kaltenboeck L, Dunham R, Waldbieser G, Liu ZJ. 2014. Identification and analysis of genome-wide SNPs provide insight into signatures of selection and domestication in catfish. PLoS One 9(10):e109666.
  29.  Argue B, Kuhlers D, Liu ZJ, Dunham RA. 2014. Growth of channel catfish (Ictalurus punctatus), blue catfish (I. furcatus), and their F1, F2, F3, and F1 reciprocal backcross hybrids in earthen ponds. Journal of Animal Science 92(10):4297-305.
  30.  Xu P, Zhang X, Wang X, Li J, Liu G, Kuang Y, Xu J, Zheng X, Ren L, Wang G, Zhang Y, Huo L, Zhao Z, Cao D, Lu C, Li C, Zhou Y, Liu ZJ, Fan Z, Shan G, Li X, Wu S, Song L, Hou G, Jiang Y, Jeney Z, Yu D, Wang L, Shao C, Song L, Sun J, Ji P, Wang J, Li Q, Xu L, Sun F, Feng J, Wang C, Wang S, Wang B, Li Y, Zhu Y, Xue W, Zhao L, Wang J, Gu Y, Lv W, Wu K, Xiao J, Wu J, Zhang Z, Yu J, Sun X. 2014. Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics 6(11):1212-1219. doi: 10.1038/ng.3098.
  31.  Sun L, Liu S, Wang R, Li C, Zhang J, Liu ZJ. 2014. Pathogen recognition receptors in channel catfish: IV. Identification, phylogeny and expression analysis of peptidoglycan recognition proteins. Developmental and Comparative Immunology 46:291-299.
  32.  Jiang Y, Xu P, Liu ZJ. 2014. Generation of physical map contig-specific sequences. Frontiers in Genetics 5:243.
  33.  Dunham R, Taylor JF, Rise M, Liu ZJ, 2014. Development of strategies for integrated breeding, genetics and applied genomics for genetic improvement of aquatic organisms. Aquaculture 420-421:S121-S123.
  34.  Zhang J, Yao J, Wang R, Zhang Y, Liu S, Sun L, Jiang Y, Feng J, Liu N, Nelson D, Waldbieser G, Liu ZJ. 2014. The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq datasets. Biochimica et Biophysica Acta-General Subjects 1840:2813-2828.
  35.  Yao J, Li C, Zhang J, Liu S, Feng J, Wang R, Li Y, Jiang C, Song L, Chen A, Liu ZJ. 2014. Expression of nitric oxide synthase (NOS) genes in channel catfish is highly regulated and time dependent after bacterial challenges. Developmental and Comparative Immunology 45:74-86.
  36.  Hutson AM, Liu ZJ., Kucuktas H, Umali-Maceina G, Su B, and Dunham RA. 2014. QTL map for growth and morphometric traits using a channel catfish x blue catfish interspecific hybrid system. Journal of Animal Science 92:1850-1865.
  37.  Wang R, Zhang Y, Liu S, Li C, Sun L, Bao L, Feng J, Liu ZJ. 2014. Analysis of 52 Rab GTPases from channel catfish and their involvement in immune responses after bacterial infections. Developmental and Comparative Immunology 45:21-34.
  38.  Liu S, Sun L, Li Y, Sun F, Jiang Y, Zhang Y, Zhang J, Feng J, Kaltenboeck L, Kucuktas H, and Liu ZJ. 2014. Development of the catfish 250K SNP array for genome-wide association studies. BMC Research Notes 7:135. DOI: 10.1186/1756-0500-7-135.
  39.  Geng X, Feng J, Liu S, Wang Y, 2, Arias C, Liu ZJ. 2014. Transcriptional regulation of hypoxia inducible factors alpha (HIF-alpha) and their inhibiting factor (FIH-1) of channel catfish (Ictalurus punctatus) under hypoxia. Comparative Biochemistry and Physiology, Part B, Biochemistry and Molecular Biology 169:38-50.
  40.  Cui J, Liu S, Zhang B, Wang H, Sun H, Song S, Qiu X, Liu Y, Wang X, Jiang Z, Liu ZJ. 2014. Transciptome analysis of the gill and swimbladder of Takifugu rubripes by RNA-Seq. PLoS ONE 9:e85505. doi:10.1371/journal.pone.0085505
  41.  Cui J, Wang H, Liu S, Zhu L, Qiu X, Jiang Z, Wang X, Liu ZJ. 2014. SNPs discovery from transcriptome of the swimbladder of Takifugu rubripes. PLoS ONE 9: e92502. doi:10.1371/journal.pone.0092502
  42.  Feng J, Liu S, Wang X, Kaltenboeck L, Kucuktas H, Li J, Liu ZJ 2014. Hemoglobin genes are differentially regulated under heat stress conditions between sensitive and tolerant catfish in different tissues. Comparative Biochemistry and Physiology, Part D, Genomics and Proteomics 9:11-22.
  43.  Wong LL, peatman E, Kelly L, Kucuktas H, Na-Nakorn U, and Liu ZJ. 2014. Catfish species identification using Lab-on-Chip PCR-RFLP. Journal of Aquatic Food Product Technology 23:2-13.