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Liangjiang Wang

Associate Professor
Genetics and Biochemistry Department

Office: Life Science Facility, Room 228B
Phone: 864-656-0733
Fax: 864-656-0393

Email: liangjw@clemson.edu
 

 Educational Background

Ph.D. Botany
University of Georgia 1999

M.S. Computer Science
Mississippi State University 2001

M.S. Biology
Zhejiang University, China 1989

B.S. Biology
Zhejiang University, China 1986

 Courses Taught

GEN/BCHM 4400/4400H/6400 Bioinformatics
GEN 3020/3020H Introduction to Genetics
BCHM 3050 Essential Elements of Biochemistry
GEN/BCHM 4930 Senior Seminar
GEN/BCHM 8100 Principles of Molecular Biology

 Research Interests

The research in my lab has focused on biological knowledge discovery, genomic data integration and mining, and computational systems biology. We have developed machine learning models and web-based tools for biomedical research, including BindN and BindN+ for predicting DNA/RNA-binding residues in protein sequence, MuStab for protein stability prediction, and seeSUMO for protein sumoylation site prediction. We have also integrated and mined the vast amount of publicly available gene expression data for understanding the molecular pathways involved in intellectual disability and other disorders. Recently, we have been conducting RNA-seq data analysis for identification and annotation of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in human and other species. In particular, we have been developing machine learning models and gene co-expression networks to predict and prioritize candidate lncRNAs associated with intellectual disability and autism spectrum disorders.

 Publications

Wang, J. and Wang, L.* (2017) Prediction of back-splicing sites reveals sequence compositional features of human circular RNAs. Proceedings of 2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2017). IEEE.

Gudenas, B.L., Srivastava, A.K. and Wang, L.* (2017) Integrative genomic analyses for identification and prioritization of long non-coding RNAs associated with autism. PLoS ONE, 12(5):e0178532. https://www.ncbi.nlm.nih.gov/pubmed/28562671/

Li, J., Yang, Y., Guevara, J., Wang, L. and Cao, W.* (2017) Identification of a prototypical single-stranded uracil DNA glycosylase from Listeria innocua. DNA Repair (Amst), 57:107-115. https://www.ncbi.nlm.nih.gov/pubmed/28719838

Gudenas, B.L. and Wang, L.* (2017) A genetic algorithm for finding discriminative functional motifs in long non-coding RNAs. In: Cai Z., Daescu O., Li M. (eds) Bioinformatics Research and Applications. ISBRA 2017. Lecture Notes in Computer Science, vol 10330, pp. 408-413. Springer. https://link.springer.com/chapter/10.1007/978-3-319-59575-7_43

Guevara-Coto, J., Schwartz, C.E. and Wang, L.* (2017) Three-state protein stability prediction from sequence-based features. Proceedings of the 2017 International Conference on Bioinformatics and Computational Biology (BIOCOMP’17), pp. 45-49. CSREA Press.

Xia, B., Liu, Y., Guevara, J., Li, J., Jilich, C., Yang, Y., Wang, L., Dominy, B.N. and Cao, W.* (2017) Correlated mutation in the evolution of catalysis in uracil DNA glycosylase superfamily. Scientific Reports, 7:45978. https://www.ncbi.nlm.nih.gov/pubmed/28397787

Cogill, S.B. and Wang, L.* (2016) Support vector machine model of developmental brain gene expression data for prioritization of autism risk gene candidates. Bioinformatics, 32 (23):3611-3618. https://www.ncbi.nlm.nih.gov/pubmed/27506227

Cogill, S.B. and Wang, L.* (2016) PGAR: ASD candidate gene prioritization system using expression patterns. Proceedings of the 2016 International Conference on Bioinformatics and Computational Biology (BIOCOMP’16), pp. 38-43. CSREA Press. http://worldcomp-proceedings.com/proc/p2016/BIC3481.pdf

Zhu, G., Tang, W.*, Wang, L., Wang, C. and Wang, X. (2016) Identification of a uniquely expanded V1R (ORA) gene family in the Japanese grenadier anchovy (Coilia nasus). Marine Biology, 163:126. https://www.ncbi.nlm.nih.gov/pubmed/27340293

Guo, C., Luo, C., Guo, L., Li, M., Guo, X., Zhang, Y., Wang, L. and Chen, L.* (2016) OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice. Journal of Integrative Plant Biology, 58(5):492-502. https://www.ncbi.nlm.nih.gov/pubmed/26172270

Gudenas, B.L. and Wang, L.* (2015) Gene co-expression networks in human brain developmental transcriptomes implicate the association of long non-coding RNAs with intellectual disability. Bioinformatics and Biology Insights, 9(Suppl 1):21-27. https://www.ncbi.nlm.nih.gov/pubmed/26523118

Ma, D.-M., Wang, Z., Wang L., Alejos-Gonzales, F., Sun, M.-A. and Xie, D.-Y.* (2015) A genome-wide scenario of terpene pathways in self-pollinated Artemisia annua. Molecular Plant, 8(11):1580-1598. https://www.ncbi.nlm.nih.gov/pubmed/26192869

Guevara-Coto, J., Schwartz, C.E. and Wang, L.* (2014) Protein sector analysis for the clustering of disease-associated mutations. BMC Genomics, 15(Suppl 11):S4. https://www.ncbi.nlm.nih.gov/pubmed/25559331

Yang, W., Yoshigoe, K., Qin, X., Liu, J.S., Yang, J.Y., Niemierko, A., Deng, Y., Liu, Y., Dunker, A., Chen, Z., Wang, L., Xu, D., Arabnia, H.R., Tong, W. and Yang, M.* (2014) Identification of genes and pathways involved in kidney renal clear cell carcinoma. BMC Bioinformatics, 15(Suppl 17):S2. https://www.ncbi.nlm.nih.gov/pubmed/25559354

Yang, J.Y., Dunker, A., Liu, J.S., Qin, X., Arabnia, H.R.*, Yang, W., Niemierko, A., Chen, Z., Luo, Z., Wang, L., Liu, Y., Xu, D., Deng, Y.*, Tong, W. and Yang, M. (2014) Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms (Editorial). BMC Bioinformatics, 15(Suppl 17):I1. https://www.ncbi.nlm.nih.gov/pubmed/25559210

Cogill, S.B. and Wang, L.* (2014) Co-expression network analysis of human lncRNAs and cancer genes. Cancer Informatics, 13(S5):49-59. https://www.ncbi.nlm.nih.gov/pubmed/25392693

Zhu, G., Wang, L., Tang, W.*, Liu, D. and Yang, J. (2014) De novo transcriptomes of olfactory epithelium reveal the genes and pathways for spawning migration in Japanese grenadier anchovy (Coilia nasus). PLoS ONE, 9(8):e103832. https://www.ncbi.nlm.nih.gov/pubmed/25084282

Luo, C., Guo, C., Wang, W., Wang, L. and Chen, L.* (2014) Overexpression of a new stress-repressive gene OsDSR2 encoding a protein with a DUF966 domain increases salt and simulated drought stress sensitivities and reduces ABA sensitivity in rice. Plant Cell Reports, 33(2):323-336. https://www.ncbi.nlm.nih.gov/pubmed/24247850

Teng, S., Yang, J.Y. and Wang, L.* (2013) Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data. BMC Medical Genomics, 6(Suppl 1):S10. https://www.ncbi.nlm.nih.gov/pubmed/23369200

Li, D., Wang, L., Teng, S., Zhang, G., Guo, L., Mao, Q., Wang, W., Li, M. and Chen, L.* (2012) Proteomic analysis of up-regulated rice proteins in response to bacterial leaf streak disease. Journal of Plant Biology, 55(4):316-324. http://www.springerlink.com/content/ctw13528747k1684/

Teng, S., Luo, H. and Wang, L.* (2012) Predicting protein sumoylation sites from sequence features. Amino Acids, 43(1):447-455. https://www.ncbi.nlm.nih.gov/pubmed/21986959

Yang, J., Zhou, X., Liu, D., Liu, Z., Wang, L. and Tang, W. (2012) Isolation and characterization of polymorphic microsatellite markers from Japanese grenadier anchovy (Coilia nasus). Conservation Genetics Resources, 4(2):519-521. http://link.springer.com/article/10.1007%2Fs12686-011-9532-2

Zhang, K.*, Pirooznia, M., Arabnia, H.R., Yang, J.Y., Wang, L., Luo, Z. and Deng, Y.* (2011) Genomic signatures and gene networking: challenges and promises (Editorial). BMC Genomics, 12(Suppl 5):I1. http://www.biomedcentral.com/1471-2164/12/S5/I1

Zhou, Z., Marepally, S.R., Nune, D.S., Pallakollu, P., Ragan, G., Roth, M.R., Wang, L., Lushington, G., Visvanathan, M.* and Welti, R.* (2011) LipidomeDB data calculation environment: online processing of direct-infusion mass spectral data for lipid profiles. Lipids, 46(9):879-884. https://www.ncbi.nlm.nih.gov/pubmed/21647782

Teng, S., Srivastava, A.K., Schwartz, C.E., Alexov, E. and Wang, L.* (2010) Structural assessment of the effects of amino acid substitutions on protein stability and protein-protein interaction. International Journal of Computational Biology and Drug Design, 3(4):334-349. https://www.ncbi.nlm.nih.gov/pubmed/21297231

Wang, L. *, Huang, C. and Yang, J.Y. (2010) Predicting siRNA potency with random forests and support vector machines. BMC Genomics, 11(Suppl 3):S2. https://www.ncbi.nlm.nih.gov/pubmed/21143784

Wang, L.*, Srivastava, A.K. and Schwartz, C.E. (2010) Microarray data integration for genome-wide analysis of human tissue-selective gene expression. BMC Genomics, 11(Suppl 2):S15. https://www.ncbi.nlm.nih.gov/pubmed/21047382

Teng, S., Srivastava, A.K. and Wang, L.* (2010) Sequence feature-based prediction of protein stability changes upon amino acid substitutions. BMC Genomics, 11(Suppl 2):S5. https://www.ncbi.nlm.nih.gov/pubmed/21047386

Zhang, Z., Teng, S., Wang, L., Schwartz, C.E. and Alexov, E.* (2010) Computational analysis of missense mutations causing Snyder-Robinson Syndrome. Human Mutation, 31(9):1043-1049. https://www.ncbi.nlm.nih.gov/pubmed/20556796

Wang, L.*, Huang, C., Yang, M.Q. and Yang, J.Y. (2010) BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Systems Biology, 4(Suppl 1):S3. https://www.ncbi.nlm.nih.gov/pubmed/20522253

Smith, C.M.*, Liu, X.M., Wang, L., Liu, X., Chen, M.S., Starkey, S. and Bai, G. (2010) Aphid feeding activates expression of a transcriptome of oxylipin-based defense signals in wheat involved in resistance to herbivory. Journal of Chemical Ecology, 36(3):260-276. https://www.ncbi.nlm.nih.gov/pubmed/20229216

Li, D., Wang, L., Yang, X., Zhang, G. and Chen, L.* (2010) Proteomic analysis of blue light-induced twining response in Cuscuta australis. Plant Molecular Biology, 72(1-2):205-213. https://www.ncbi.nlm.nih.gov/pubmed/19876747

Wang, L.*, Yang, M.Q. and Yang, J.Y. (2009) Prediction of DNA-binding residues from protein sequence information using random forests. BMC Genomics, 10(Suppl 1):S1. https://www.ncbi.nlm.nih.gov/pubmed/19594868

Wang, L.*, Irausquin, S.J. and Yang, J.Y. (2008) Prediction of lipid-interacting amino acid residues from sequence features. International Journal of Computational Biology and Drug Design, 1(1):14-25. https://www.ncbi.nlm.nih.gov/pubmed/20054998

Park, Y.*, Aikins, J., Wang, L., Beeman, R.W., Oppert, B., Lord, J.C., Brown, S.J., Lorenzen, M.D., Richards, S., Weinstock, G.M. and Gibbs, R.A. (2008) Analysis of transcriptome data in the red flour beetle, Tribolium castaneum. Insect Biochemistry and Molecular Biology, 38(4):380-386. https://www.ncbi.nlm.nih.gov/pubmed/18342244

Tribolium Genome Sequencing Consortium (Wang, L. as a coauthor) (2008) The genome of the model beetle and pest Tribolium castaneum. Nature, 452(7190):949-955. https://www.ncbi.nlm.nih.gov/pubmed/18362917

 Links

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