As first author or corresponding author

  1. Dzisoo AM, Kang J, Yao P, Klugah-Brown B, Mengesha BA, Huang J. SSH: A Tool for Predicting Hydrophobic Interaction of Monoclonal Antibodies Using Sequences. Biomed Res Int. 2020;2020:3508107.
  2. Tang Q, Kang J, Yuan J, Tang H, Li X, Lin H, Huang J, Chen W. DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species. Bioinformatics. 2020;36(11):3327-35.
  3. Kang J, Yu S, Lu S, Xu G, Zhu J, Yan N, Luo D, Xu K, Zhang Z, Huang J. Use of a 6-miRNA panel to distinguish lymphoma from reactive lymphoid hyperplasia. Signal Transduct Target Ther. 2020;5:2.
  4. Wang Y, Kang J, Li N, Zhou Y, Tang Z, He B, Huang J. NeuroCS: A Tool to Predict Cleavage Sites of Neuropeptide Precursors. Protein Pept Lett. 2020;27(4):337-45.
  5. Dzisoo AM, He B, Karikari R, Agoalikum E, Huang J. CISI: A Tool for Predicting Cross-interaction or Self-interaction of Monoclonal Antibodies Using Sequences. Interdiscip Sci. 2019;11(4):691-7.
  6. Jiang L, Yu M, Zhou Y, Tang Z, Li N, Kang J, He B, Huang J. AGONOTES: A Robot Annotator for Argonaute Proteins. Interdiscip Sci. 2020;12(1):109-16.
  7. Tang Z, Chen S, Chen A, He B, Zhou Y, Chai G, Guo F, Huang J. CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. Database (Oxford). 2019;2019.
  8. He B, Chen H, Li N, Huang J. SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data. Int J Biol Sci. 2019;15(7):1452-9.
  9. Dong C, Zeng Z, Pu DK, Wen QF, Liu S, Du MZ, Sun Y, Gao YZ, Rao N, Huang J, Guo FB. CasLocusAnno: a web-based server for annotating cas loci and their corresponding (sub)types. FEBS Lett. 2019;593(18):2646-54.
  10. Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J. RIscoper: a tool for RNA-RNA interaction extraction from the literature. Bioinformatics. 2019;35(17):3199-202.
  11. He B, Chen H, Huang J. PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition. PeerJ. 2019;7:e7131.
  12. Ning L, He B, Zhou P, Derda R, Huang J. Molecular Design of Peptide-Fc Fusion Drugs. Current Drug Metabolism. 2018.
  13. Ning L, Li Z, Bai Z, Hou S, He B, Huang J, Zhou P. Computational Design of Antiangiogenic Peptibody by Fusing Human IgG1 Fc Fragment and HRH Peptide: Structural Modeling, Energetic Analysis, and Dynamics Simulation of Its Binding Potency to VEGF Receptor. International Journal of Biological Sciences. 2018;14(8):930-7.
  14. He B, Tjhung KF, Bennett NJ, Chou Y, Rau A, Huang J, Derda R. Compositional Bias in Naive and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing. Scientific Reports. 2018;8(1):1214.
  15. He B, Dzisoo AM, Derda R, Huang J. Development and Application of Computational Methods in Phage Display Technology. Current Medicinal Chemistry. 2018.
  16. He B, Jiang L, Duan Y, Chai G, Fang Y, Kang J, Yu M, Li N, Tang Z, Yao P, Wu P, Derda R, Huang J. Biopanning data bank 2018: hugging next generation phage display. Database : the journal of biological databases and curation. 2018;2018.
  17. Yan M, He B, Liu K, Xu H, Luo D, Wu Z, Xu K, Huang J, Song Y. Pharmacogenetics of genes associated with outcome of conbercept treatment for age-related macular degeneration in a Chinese population. International Journal of Clinical and Experimental Medicine. 2018;11(3).
  18. Kang J, Fang Y, Yao P, Li N, Tang Q, Huang J. NeuroPP: A Tool for the Prediction of Neuropeptide Precursors Based on Optimal Sequence Composition. Interdisciplinary Sciences, Computational Life Sciences. 2018.
  19. Zhang Y, He B, Liu K, Ning L, Luo D, Xu K, Zhu W, Wu Z, Huang J, Xu X. A novel peptide specifically binding to VEGF receptor suppresses angiogenesis in vitro and in vivo. Signal Transduction and Targeted Therapy. 2017;2:17010.
  20. Chai G, Yu M, Jiang L, Duan Y, Huang J. HMMCAS: a web tool for the identification and domain annotations of Cas proteins. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017.
  21. Li N, Kang J, Jiang L, He B, Lin H, Huang J. PSBinder: A Web Service for Predicting Polystyrene Surface-Binding Peptides. BioMed Research International. 2017;2017:5761517.
  22. He B, Kang J, Ru B, Ding H, Zhou P, Huang J. SABinder: A Web Service for Predicting Streptavidin-Binding Peptides. BioMed Besearch International. 2016;2016:9175143.
  23. He B, Chai G, DuanY, YanZ, Qiu L, Zhang H, Liu Z, He Q, Han Ke, Ru B, Guo FB, Ding H, Lin H, Wang X, Rao N, Zhou P, Huang J. BDB: Biopanning Data Bank. Nucleic Acids Research 2016; 44(D1): D1127-D1132.
  24. Tang Q, Nie F, Kang J, Ding H, Zhou P Huang J. NIEluter: Predicting peptides eluted from HLA class I molecules. Journal of Immunological Methods 2015,422:22-27.
  25. Huang J, He B, Zhou P. Mimotope-based prediction of B-cell epitopes. Methods in Molecular Biology. 2014; 1184: 237-243.
  26. Yang C, Wang C, Zhang S, Huang J, Zhou P. Structural and energetic insights into the intermolecular interaction among human leukocyte antigens, clinical hypersensitive drugs and antigenic peptides. Molecular simulation, 2014; 41(9): 741-751.
  27. Ru B, 't Hoen PAC, Nie F, Lin H, Guo FB, Huang J. PhD7Faster: Predicting clones propagating faster from the Ph.D.-7 phage display peptide library. Journal of Bioinformatics and Computational Biology 2014; 12(1): 1450004.
  28. Huang J, Derda R, Huang Y. Phage Display Informatics. Computational and Mathematical Methods in Medicine 2013; 2013: 698395.
  29. He B, Mao C, Ru B, Han H, Zhou P, Huang J. Epitope Mapping of Metuximab on CD147 Using Phage Display and Molecular Docking. Computational and Mathematical Methods in Medicine 2013; 2013: 983829.
  30. Wu Z, Zhou P, Li X, Wang H, Luo D, Qiao H, Ke X, Huang J. Structural Characterization of a Recombinant Fusion Protein by Instrumental Analysis and Molecular Modeling. PLoS ONE 2013; 8(3): e57642.
  31. Zhou P, Wang C, Tian F, Ren Y, Yang C, Huang J. Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity. J Comput Aided Mol Des 2013; 27(1): 67-78
  32. Huang J, Ru B, Zhu P, Nie F, Yang J, Wang X, Dai P, Lin H, Guo FB, Rao N. MimoDB 2.0: a mimotope database and beyond. Nucleic Acids Research 2012; 40(1): D271-D277.
  33. Huang J, Ru B, Dai P. Prediction of protein interaction sites using mimotope analysis. In: Protein-Protein Interactions -- Computational and Experimental Tools. Edited by Cai W and Hong H. InTech; 2012: 189-206.
  34. Huang J, Ru B, Dai P. Bioinformatics resources and tools for phage display. Molecules 2011; 16(1): 694-709.
  35. Ru B, Huang J, Dai P, Li S, Xia Z, Ding H, Lin H, Guo FB, Wang X. MimoDB: a New Repository for Mimotope Data Derived from Phage Display Technology. Molecules 2010; 15(11): 8279-8288.
  36. Huang J, Ru B, Li S, Lin H, Guo F. SAROTUP: Scanner And Reporter Of Target-Unrelated Peptides. Journal of Biomedicine and Biotechnology, 2010; 2010: 101932.
  37. Huang J, Xia M, Lin H, Guo F. Information loss and noise inclusion risk in mimotope based epitope mapping. The 3rd International Conference on Bioinformatics and Biomedical Engineering(iCBBE2009), 2009: 1-3.
  38. Huang J, You Z. Differential performance between structural and functional B-cell epitopic residue prediction. The 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE2008), 2008: 93-96.
  39. Huang J, Honda W, Kanehisa M. Predicting B cell epitope residues with network topology based amino acid indices. Genome Informatics, 2007; 19: 40-49.
  40. Huang J, Kawashima S, Kanehisa M. New amino acid indices based on residue network topology. Genome Informatics, 2007; 18: 152-161.
  41. Huang J, Gutteridge A, Honda W, Kanehisa M. MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics, 2006; 7: 451.
  42. Huang J, Honda W. CED: a conformational epitope database. BMC Immunol, 2006; 7: 7.
  43. Huang J, Cai MY, Wei DP. HLA class I expression in primary hepatocellular carcinoma. World J Gastroenterol, 2002; 8(4): 654-657.

As co-author

  1. Wu D, Huang Y, Kang J, Li K, Bi X, Zhang T, Jin N, Hu Yong, Tan P, Zhang L, Yi Y, Shen W, Huang J, Li XB, Li X, Xu J, Wang Dong. ncRDeathDB: a comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system. Autophagy, 2015.
  2. Yang C, Zhang S, He P, Wang C, Huang J Zhou P. Self-binding peptides: folding or binding? J Chem Inf Model, 2015; 55(2): 329-342.
  3. Ding H, Lin H, Chen W, Li ZQ, Guo FB, Huang J, Rao N. Prediction of protein structural classes based on feature selection technique. Interdiscip Sci, 2014; 6(3): 235-240.
  4. Li Y, Rao N, Yang F, Zhang Y, Yang Y, Liu HM, Guo F, Huang J. Biocomputional construction of a gene network under acid stress in Synechocystis sp. PCC 6803. Res Microbiol, 2014; 165(6): 420-428.
  5. Ning LW, Lin H, Ding H, Huang J, Rao N, Guo FB. Predicting bacterial essential genes using only sequence composition information. Genet Mol Res, 2014; 13(2): 4564-4572.
  6. Wei W, Ning LW, Ye YN, Li SJ, Zhou HQ, Huang J, Guo FB. SMAL: A resource of spontaneous mutation accumulation lines. Mol Biol Evol 2014; 31(5): 1302-1308.
  7. Tang L, Wang X, Ru B, Sun H, Huang J, Gao H. MDC-Analyzer: a novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites. Biotechniques, 2014; 56(6): 301-308.
  8. Ye YN, Hua ZG, Huang J, Rao N, Guo FB. CEG: a database of essential gene clusters. BMC Genomics 2013; 14: 769.
  9. Lin H, Ding C, Yuan LF, Chen W, Ding H, Li ZQ, Guo FB, Huang J, Rao N. Predicting subchloroplast locations of proteins based on the general form of Chou‘s pseudo amino acid composition: approached from optimal tripeptide composition. International Journal of Biomathematics 2013; 13(6): 1350003.
  10. Guo FB, Wei W, Wang XL, Lin H, Ding H, Huang J, Rao N. Co-evolution of genomic islands and their bacterial hosts revealed through phylogenetic analyses of 17 groups of homologous genomic islands. Genet Mol Res, 2012; 11(4): 3735-3743.
  11. Shen X, He Z, Li H, Yao C, Zhang Y, He L, Li S, Huang J, Guo Z. Distinct functional patterns of gene promoter hypomethylation and hypermethylation in cancer genomes. PLoS ONE, 2012; 7(9): e44822.
  12. Zhou P, Huang J, Tian F. Specific Noncovalent Interactions at Protein-Ligand Interface: Implications for Rational Drug Design. Current Medicinal Chemistry, 2012; 19(2): 226-238.
  13. Ding H, Liu L, Guo FB, Huang J, Lin H. Identify Golgi Protein Types with Modified Mahalanobis discriminant Algorithm and Pseudo Amino Acid Composition. Protein Pept Lett, 2011; 18: 58-63.
  14. Guo FB, Ning LW, Huang J, Lin H, Zhang HX. Chromosome translocation and its consequence in the genome of Burkholderia cenocepacia AU-1054. Biochem Biophys Res Commun, 2010; 403(3-4): 375-379.
  15. Lin H, Ding H, Guo FB, Huang J. Prediction of subcellular location of mycobacterial protein using feature selection techniques. Molecular Diversity, 2010; 14(4): 667-671.
  16. You ZL, Xia Q, Liang FR, Tang YJ, Xu CL, Huang J, Zhao L, Zhang WZ, He JJ. Effects on the expression of GABAA receptor subunits by jujuboside A treatment in rat hippocampal neurons. J Ethnopharmacol, 2010; 128(2): 419-423.
  17. Guo FB, Lin H, Huang J. A plot of G + C content against sequence length of 640 bacterial chromosomes shows the points are widely scattered in the upper triangular area. Chromosome Res, 2009; 17(3): 359-364.
  18. Lin H, Ding H, Guo FB, Zhang AY, Huang J. Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition. Protein Pept Lett, 2008; 15(7): 739-744.