Publications in BSB Lab:

2017

Li W X, He K, Tang L, Dai S X, Li G H, Lv W W, Guo Y C, An S Q, Wu G Y, Liu D, Huang J F.
Comprehensive tissue-specific gene set enrichment analysis and transcription factor analysis of breast cancer by integrating 14 gene expression datasets.
Oncotarget. 2017, 8(4): 6775-86.

Wang, Q., W.X. Li, S.X. Dai, Y.C. Guo, F.F. Han, J.J. Zheng, G.H. Li, and J.F. Huang.
Meta-Analysis of Parkinson's Disease and Alzheimer's Disease Revealed Commonly Impaired Pathways and Dysregulation of NRF2-Dependent Genes.
Journal of Alzheimer's Disease. 2017. 56(4): p. 1525-1539.

Liu, J.Q., S.X. Dai, J.J. Zheng, Y.C. Guo, W.X. Li, G.H. Li, and J.F. Huang.
The identification and molecular mechanism of anti-stroke traditional Chinese medicinal compounds.
Scientific reports. 2017. 7: p. 41406.

2016

Li W X, Dai S X, Wang Q, Guo Y C, Hong Y, Zheng J J, Liu J Q, Liu D, Li G H, Huang J F.
Integrated analysis of ischemic stroke datasets revealed sex and age difference in anti-stroke targets.
PeerJ. 2016, 4(e2470)

Wen-Xing, L., L. Wei, C. Jia-Qian, Y. Haiyue, S. Yuanyuan, H. Zhang, Q. Zhang, T. Ling, W. Manman, and J.-F. Huang.
Folate Deficiency Was Associated with Increased Alanine Aminotransferase and Glutamyl Transpeptidase Concentrations in a Chinese Hypertensive Population: A Cross-Sectional Study.
Journal of Nutritional Science and Vitaminology. 2016. 62(4): p. 265-271.

Li, W., K. He, L. Tang, S. Dai, G. Li, W. Lv, Y. Guo, S. An, G. Wu, and D. Liu.
Comprehensive tissue-specific gene set enrichment analysis and transcription factor analysis of breast cancer by integrating 14 gene expression datasets.
Oncotarget. 2016

Dai, S. X., Li, W. X., Han, F. F., Guo, Y. C., Zheng, J. J., Liu, J. Q., ... & Huang, J. F.
In silico identification of anti-cancer compounds and plants from traditional Chinese medicine database.
Scientific reports. 2016; 6: 25462.

Guo, Y. C., Zhang, L., Dai, S. X., Li, W. X., Zheng, J. J., Li, G. H., & Huang, J. F.
Independent Evolution of Winner Traits without Whole Genome Duplication in Dekkera Yeasts.
PloS one 2016, 11(5), e0155140.

Dai, S. X., Li, W. X., Li, G. H., & Huang, J. F.
Proteome-wide prediction of targets for aspirin: new insight into the molecular mechanism of aspirin.
PeerJ. 2016, 4: e1791.

Li, W. X., Dai, S. X., Liu, J. Q., Wang, Q., Li, G. H., & Huang, J. F.
Integrated Analysis of Alzheimer’s Disease and Schizophrenia Dataset Revealed Different Expression Pattern in Learningand Memory.
Journal of Alzheimer's Disease. 2016 (Preprint): 1-9.

Wang, H., Jiang, X., Zhang, L., Huang, J., Zhang, Y., Zhou, X., & Liang, B.
Iron Overload Coordinately Promotes Ferritin Expression and Fat Accumulation in Caenorhabditis elegans.
Genetics. 2016: genetics. 116.186742.

Han, F., Li, G., Dai, S., & Huang, J.
Genome-wide metabolic model to improve understanding of CD4+ T cell metabolism, immunometabolism and application in drug design.
Molecular BioSystems. 2016.

2015

Dai, S. X., Li, G. H., Gao, Y. D., & Huang, J. F.
Pharmacophore‐Map‐Pick: A Method to Generate Pharmacophore Models for All Human GPCRs.
Molecular Informatics. 2015.

Zhao, H., Du, Y., Chen, S., Qing, L., Wang, X., Huang, J., ... & Zhang, Y.
The prion protein gene polymorphisms associated with bovine spongiform encephalopathy susceptibility differ significantly between cattle and buffalo.
Genetics and Evolution.2015, 36: 531-538.

Shan, L. L., Guo, H., Song, N. N., Jia, Z. P., Hu, X. T., Huang, J. F., ... & Xu, L.
Light exposure before learning improves memory consolidation at night
Scientific reports. 2015, 5.

Li, W. X., Dai, S. X., Zheng, J. J., Liu, J. Q., & Huang, J. F.
Homocysteine Metabolism Gene Polymorphisms (MTHFR C677T, MTHFR A1298C, MTR A2756G and MTRR A66G) Jointly Elevate the Risk of Folate Deficiency .
Nutrients.2015, 7(8): 6670-6687.

Li, W. X., Lv, W. W., Dai, S. X., Pan, M. L., & Huang, J. F.
Joint associations of folate, homocysteine and MTHFR, MTR and MTRR gene polymorphisms with dyslipidemia in a Chinese hypertensive population: a cross-sectional study[J]. Lipids in health and disease
Lipids in health and disease. 2015, 14(1): 1.

Zhao, Y., Wang, Y., Gao, Y., Li, G., & Huang, J.
Integrated analysis of residue coevolution and protein structures capture key protein sectors in HIV-1 proteins.
PloS one. 2015, 10(2): e0117506.

2014

Jiang, H. Y., Li, G. D., Dai, S. X., Bi, R., Zhang, D. F., Li, Z. F., ... & Yao, Y. G.
Identification of PSEN1 mutations p. M233L and p. R352C in Han Chinese families with early-onset familial Alzheimer’s disease.
Neurobiology of Aging. 2014.

Gao, Yue-Dong, Yuqi Zhao, and Jingfei Huang.
Metabolic Modeling of Common Escherichia coli Strains in Human Gut Microbiome.
BioMed research international. 2014.

Zhao, Y., Ji, S., Wang, J., Huang, J., & Zheng, P.
mRNA-Seq and microRNA-Seq whole-transcriptome analyses of rhesus monkey embryonic stem cell neural differentiation revealed the potential regulators of rosette neural stem cells.
DNA Research. 2014, dsu019.

Wang, R. R., Yang, Q. H., Luo, R. H., Peng, Y. M., Dai, S. X., Zhang, X. J., ... & Zheng, Y. T.
Azvudine, A Novel Nucleoside Reverse Transcriptase Inhibitor Showed Good Drug Combination Features and Better Inhibition on Drug-Resistant Strains than Lamivudine In Vitro.
PloS one. 2014, 9(8): e105617.

Cheng D Q, Li Y, Huang J F.
Molecular Evolution of the Primate Alpha/Theta Defensin Multigene Family.
PloS one. 2014, 9(5): e974252.

Chen S, Gao S, Cheng D, Huang JF.
The characterization and comparison of amyloidogenic segments and non-amyloidogenic segments shed light on amyloid formation.
Biochemical and biophysical research communications. 2014, 447(2): 255-262.

Li GH, Huang JF.
Inferring therapeutic targets from heterogeneous data: HKDC1 is a novel potential therapeutic target for cancer.
Bioinformatics. 2014 Mar 15;30(6):748-52.

2013

Li, Z., Li, T., Dai, S., Xie, X., Ma, X., Zhao, W., ... & Wang, P. G.
New Insights into the Pharmacological Chaperone Activity of C2‐Substituted Glucoimidazoles for the Treatment of Gaucher Disease.
ChemBioChem. 2013, 14(10): 1239-1247.

Zhang AD, Dai SX, and Huang JF
Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data.
BioMed Research International 2013, Volume 2013.doi:10.1155/2013/187509.

Yu Q, Huang JF.
The DEER database: A bridge connecting drugs, environmental effects, and regulations.
Gene. 2013 May 15;520(2):98-105.

Wang J, Zhao YQ, Wang Y, Huang JF.
Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex.
FEBS Lett. 2013 Jan 16;587(2):136-141

Wu M, Yu Q, Li X, Zheng J, Huang JF, Kwoh CK.
Benchmarking human protein complexes to investigate drug-related systems and evaluate predicted protein complexes.
PLoS One. 2013;8(2):e53197.

Xin YN, Zhao YQ, Lin ZH, Jiang X, Xuan SY, Huang JF
Molecular dynamics simulation of PNPLA3 I148M polymorphism reveals reduced substrate access to the catalytic cavity.
Proteins. 2013 Mar;81(3):406-414.

2012

Li GH and Huang JF.
CDRUG: a web server for predicting anticancer activity of chemical compounds
Bioinformatics . 2012 Dec; 28(24):3334-3335.

Zhao YQ, Wang JW, Wang YJ, Huang JF.
A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse
J Clin Bioinforma . 2012 May 1;2(1):10.

Zhang YR, Zhao YQ, Huang JF.
Retinoid-Binding Proteins: Similar Protein Architectures Bind Similar Ligands via Completely Different Ways
PLoS ONE . 2012;7(5):e36772

Yu Q, Huang JF.
The analysis of the druggable families based on topological features in the protein-protein interaction network
Letters in Drug Design & Discovery . 2012, Vol 9, 426-430

Dai SX, Zhang AD, Huang JF.
Evolution, expansion and expression of the Kunitz/BPTI gene family associated with long-term blood feeding in Ixodes Scapularis
BMC Evol Biol . 2012. Jan 14;12:4

Yu Q, Li GH, Huang JF
MOfinder: a novel algorithm for detecting overlapping modules from protein-protein interaction network. Journal of biomedicine and biotechnology
Journal of biomedicine and biotechnology 2012.Volume 2012, Article ID 103702,10 pages doi:10.1155/2012/103702

Zhao YQ, Sheng ZZ, Huang JF.
A systematic analysis of heart transcriptome highlights divergent cardiovascular disease pathways between animal models and humans.
Mol. BioSyst. 2012. Feb;8(2):504-10.

Fen Wang1,min Liu,Baoxing Song,Dengyun Li,Huimin Pei,Yang Guo,Jingfei Huang* and Deli Zhang.
Prediction and characterization of protein-protein interaction networks in swine.
Proteome Sci. 2012, 10(2).

2011

Zhao YQ, Huang JF
Reconstruction and analysis of human heart-specific metabolic network based on transcriptome and proteome data.
Biochemical and biophysical research communications. 2011 Nov;415(3):450-4.

Sheng Zi-Zhang, zhao Yu-Qi , Huang Jing-Fei
Functional Evolution of BRCT Domains from Binding DNA to Protein.
Evolutionary Bioinformatics.2011,7: 87–97

Zhang WQ, Wu WW, Dai L, Zhou PF, Lin WC, Zhang Y, Huang JF, Zhang DL.
Deciphering Heterogeneity in Pig Genome Assembly Sscrofa9 by Isochore and Isochore-like Region Analysis.
PLoS ONE, 2010, 5 (10): e13303.doi:10.1371/journal.pone.0013303.

Li, G-H, Huang, J-F.
CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation.
BMC Bioinformatics. 2010, 11: 439-451.

Li Y, Huang JF.
Identification and molecular evolution of cow CENP-A gene family.
Mamm. Genome. 2008, 19(2):139-143.

Tang SN, Huang JF.
Evolution of different oligomeric glycyl-tRNA synthetases.
FEBS Lett. 2005, 579: 1441-1445.

Lin J, Huang JF.
Evolution of phenylalanyl-tRNA synthetase by domain losing.
Acta Biochim. Biophy. Sin. 2003, 35(12): 1601-1605.

Huang JF
Different protein tyrosine phosphatase superfamilies resulting from different gene reading frames.
Mol. Biol. Evol. 2003, 20: 815-820.

Shi XF, Liu SX, Xiangyu JG, Zhang YP, Huang JF, Liu SQ, Liu CQ.
Strcuture analysis of human CCR2b and Primate CCR2b by molecular modeling and molecular dynamics simulation.
J. Mol. Model. 2002,8: 217-222.

Huang JF, Liu CQ.
Identification of protein superfamily from structure-based sequence motif.
Chinese Sci. Bull. 2002, 47: 1377- 1381.

Sowdhamini R, Burke DF, Deane CM, Huang J-F. Mizuguchi K, Nagaaraajaram HA, Srinivasan N, Steward, RE and Blundell TL.
Protein 3D Structural Databases: Domains, Structurally Aligned Homologues and Superfamilies.
Acta Crystall. D 1998.54:1168-1177.

Sowdhamini R, Burke DF, Huang J-F, Mizuguchi K, Nagaaraajaram HA, Srinivasan N, Steward RE. and Blundell TL.
CAMPASS: A Database of Structural aligned Protein Superfamilies.
Structure 1998. 6: 1087-1094.