(1999) University of Georgia
Areas of Expertise
Bioinformatics; plant genomics, proteomics and metabolomics; biological databases and data mining
My bioinformatics lab focuses on three primary research areas: (1) develop bioinformatics software tools, (2) build and maintain biological databases, and (3) conduct data analysis and data mining to address interesting biological questions. Current tool developing is mainly geared toward transcriptome data generated by next-generation sequencing, and we emphasize data cleaning, data integration, data visualization, and data mining.
My general research interest is to use a computational biology approach to understanding gene expression regulation and to elucidate their underlying biological mechanisms. My research is aimed at exploring alternative promoter usages (APU), alternative splicing (AS) and alternative polyadenylation (APA), and advancing our understanding of these alternative processes in mRNA transcription production, using various bioinformatics tools. It is clear that these alternative processes are key mechanisms for the creation and regulation of mRNA variants expressed from a single gene, allowing for variation in mRNA levels and in the functionality of the resultant proteins and non-coding transcripts. Currently, we are using Chlamydomonas and Arabidopsis as the model organisms for APU, AS and APA study. In addition, we are working with many other interesting bioinformatics projects, including eukaryotic gene prediction and genome annotation, cDNA assembly and clustering, genome re-sequencing, and genetic marker databases among others.
Selected Publications(Complete publication list)
Li, P., Ji, G., Dong, M., Schmidt, E., Lenox, D., Chen, L., Liu, Q., Liu, L., Zhang, J. and Liang, C. (2012) CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. Bioinformatics, 28(18): 2382-2384.
Duan, X., Schmidt, E., Li, P., Lenox, D., Liu, L., Shu, C., Zhang, J. and Liang, C. (2012) PeanutDB: An integrated bioinformatics web portal for Arachis hypogaea transcriptomics. BMC Plant Biology, 12:94
Zhou, S., Ji, G., Liu, X., Li, P., Moler, J., Karro, J.E. and Liang, C. (2012) Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data. BMC Biotechnology, 12:16.
Gong, P., Guan, X., Pirooznia, M., Liang, C. and Perkins, E.J. (2012) Gene Expression Analysis of CL-20-Induced Reversible Neurotoxicity Reveals GABA(A) Receptors as Potential Targets in the Earthworm Eisenia fetida. Environ Sci Technol, 46(2):1223-32.
Wu, X., Liu, M., Downie, B., Liang, C., Ji, G., Li, Q.Q. and Hunt, A.G. (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. PNAS, 108(30): 12533-12538.
Specht, M., Stanke, M., Terashima, M., Naumann-Busch, B., Janßen, I., Höhner, R., Hom, E.F.Y., Liang, C. and Hippler, M. (2011) Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome. Proteomics, 11(9):1814–1823.
Echt, C.S., Saha, S., Krutovsky, K.V., Wimalanathan, K., Erpelding, J.E., Liang, C. and Nelson, C.D. (2011) An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genetics, 12:17.
Rao, D.M., Moler, J.C., Ozden, M., Zhang, Y., Liang, C. and Karro, J.E. (2010) PEACE: Parallel Environment for Assembly and Clustering of Gene Expression. Nucleic Acids Research, 38: W737–W742.
Liang, C., Liu, L. and Q.Q. Li (2009) WebGMAP: a web service for mapping and aligning cDNA sequences to genomes. Nucleic Acids Research, doi:10.1093/nar/gkp389.
Liang, C., Liu, Y., Liu, L., Davis, A.C., Shen, Y. and Q.Q. Li (2008) ESTs with cDNA termini - previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics, 179:83-93.
Shen, Y., Y. Liu, L. Liu, Liang, C. and Q. Q. Li (2008) Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii.
Liang, C., Wang, G., Liu, L., Ji, G., Fang, L., Liu, Y., Carter, K., Webb, J.S., Dean,
J.F. ConiferEST: an integrated bioinformatics system for data reprocessing
and mining of conifer expressed sequence tags (ESTs). BMC Genomics 2007,
Conner, J. A., Goel, S., Gunawan, G., Cordonnier-Pratt, M-M, Johnson, V. E., Liang, C., Wang, H., Pratt, L. H., Mullet, J. E., DeBarry, J., Yang, L., Bennetzen, J. L., Klein, P. E., and P. Ozias-Akins (2008) Sequence Analysis of Bacterial Artificial Chromosome Clones from the Apospory-Specific Genomic Region of Pennisetum and Cenchrus. Plant Physiology, 147: 1396-1411.
Liang, C., Wang, G., Liu, L., Ji, G., Liu, Y., Chen, J., Webb, J.S., Reese, G., and Dean, J.F. (2007) WebTraceMiner: a web service for processing and mining EST sequence trace files. Nucleic Acids Research, doi:10.1093/nar/gkm299.
Liang, C., Sun, F., Wang, H., Qu, J., Freeman, R.M., Jr., Pratt, L.H., Cordonnier-Pratt, M.M. 2006. MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. BMC Bioinformatics, 7:115.