Integrative System Biology Laboratory

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Publications »  All

• Control of matrix stiffness promotes endodermal lineage specification by regulating SMAD2/3 via lncRNA LINC00458.

  Y.F. Chen, Y.J. Li, C.H. Chou, M.Y. Chiew, H.D. Huang, J.H. Ho*, S. Chien* and O.K. Lee*
  Sci Adv. 2020 Feb 5;6(6):eaay0264.  

• Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis.

  W.Y. Li, S.W. Huang, S.F. Wang, H.F. Liu, C.H. Chou, S.J. Wu, H.D. Huang, P.L. Lu, C.S. Fann, M. Chen, Y.H. Chen and Y.A. Chen*
  J Microbiol Immunol Infect. 2020 Jan 27. pii: S1684-1182(20)30002-5.  

• Pilot Study to Establish a Novel Five-Gene Biomarker Panel for Predicting Lymph Node Metastasis in Patients With Early Stage Endometrial Cancer.

  C.Y. Huang, K.W. Liao, C.H. Chou, S. Shrestha, C.D. Yang, M.Y. Chiew, H.T. Huang, H.C. Hong, S.H. Huang, T.H. Chang* and H.D. Huang*
  Front Oncol. 2020 Jan 21;9:1508.  

• miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.

  H.Y. Huang, Y.C. Lin, J. Li, K.Y. Huang, S. Shrestha, H.C. Hong, Y. Tang, Y.G. Chen, C.N. Jin, Y. Yu, J.T. Xu, Y.M. Li, X.X. Cai, Z.Y. Zhou, X.H. Chen, Y.Y. Pei, L. Hu, J.H. Su, S.D. Cui, F. Wang, Y.Y. Xie, S.Y. Ding, M.F. Luo, C.H. Chou, N.W. Chang, K.W. Chen, Y.H. Cheng, X.H. Wan, W.L. Hsu, T.Y. Lee*, F.X. Wei* and H.D. Huang*
  Nucleic Acids Res. 2020 Jan 8;48(D1):D148-D154.  

• Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.

  C. Liu, Y.C. Liu, H.D. Huang and W. Wang*.
  Bioinformatics. 2019 Dec 1;35(23):4867-4870.  

• Bone marrow concentrate-induced mesenchymal stem cell conditioned medium facilitates wound healing and prevents hypertrophic scar formation in a rabbit ear model.

  C.H. Hu, Y.W. Tseng, C.Y. Chiou, K.C. Lan, C.H. Chou, C.S. Tai, H.D. Huang, C.W. Hu, K.H. Liao, S.S. Chuang, J.Y. Yang and O.K. Lee*
  Stem Cell Res Ther. 2019 Aug 28;10(1):275.  

• Enterotype-based Analysis of Gut Microbiota along the Conventional Adenoma-Carcinoma Colorectal Cancer Pathway.

  T.W. Yang, W.H. Lee, S.J. Tu, W.C. Huang, H.M. Chen, T.H. Sun, M.C. Tsai, C.C. Wang, H.Y. Chen, C.C. Huang, B.H. Shiu, T.L. Yang, H.T. Huang, Y.P. Chou, C.H. Chou, Y.R. Huang, Y.R. Sun, C. Liang, F.M. Lin, S.Y. Ho, W.L. Chen, S.F. Yang, K.C. Ueng, H.D. Huang*, C.N. Huang, Y.J. Jong* and C.C. Lin*
  Sci Rep. 2019 Jul 29;9(1):10923.  

• Mechanical stretch induces hair regeneration through the alternative activation of macrophages.

  S.Y. Chu, C.H. Chou, H.D. Huang, M.H. Yen, H.C. Hong, P.H. Chao, Y.H. Wang, P.Y. Chen, S.X. Nian,Y.R. Chen, L.Y. Liou, Y.C. Liu, H.M. Chen, F.M. Lin, Y.T. Chang, C.C. Chen* and O.K. Lee*
  Nat Commun. 2019 Apr 3;10(1):1524.  

• Atheroprotective Flow Upregulates ITPR3 (Inositol 1,4,5-Trisphosphate Receptor 3) in Vascular Endothelium via KLF4 (Krüppel-Like Factor 4)-Mediated Histone Modifications.

  M. He, T.S. Huang, S. Li, H.C. Hong, Z. Chen, M. Martin, X. Zhou, H.Y. Huang, S.H. Su, J. Zhang, W.T. Wang, J. Kang, H.D. Huang, J. Zhang, S. Chien* and J.Y. Shyy*
  Arterioscler Thromb Vasc Biol. 2019 May;39(5):902-914.  

• Resistin Enhances Monocyte Chemoattractant Protein-1 Production in Human Synovial Fibroblasts and Facilitates Monocyte Migration.

  W.C. Chen, S.W. Wang, C.Y. Lin, C.H. Tsai, Y.C. Fong, T.Y. Lin, S.L. Weng, H.D. Huang, K.W. Liao* and C.H. Tang*
  Cell Physiol Biochem. 2019;52(3):408-420.  

• Liver X Receptor/Retinoid X Receptor Pathway Plays a Regulatory Role in Pacing-Induced Cardiomyopathy.

  Y.S. Lin, T.H. Chang, C.S. Shi, Y.Z. Wang, W.C. Ho, H.D. Huang, S.T. Chang, K.L. Pan and M.C. Chen*
  J Am Heart Assoc. 2019 Jan 8;8(1):e009146.  

• dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.

  K.Y. Huang, T.Y. Lee*, H.J. Kao, C.T. Ma, C.C. Lee, T.H. Lin, W.C. Chang, H.D. Huang*
  Nucleic Acids Res. 2019 Jan 8;47(D1):D298-D308.  

• MicroRNA-224 down-regulates Glycine N-methyltransferase gene expression in Hepatocellular Carcinoma.

  J.H. Hung, C.H. Li, C.H. Yeh, P.C. Huang, C.C. Fang, Y.F. Chen, K.J. Lee, C.H. Chou, H.Y. Cheng,H.D. Huang, M. Chen, T.F. Tsai, A.M. Lin, C.H. Yen, A.P. Tsou, Y.C. Tyan, Y.A. Chen
  Sci Rep. 2018 Aug 16;8(1):12284. doi: 10.1038/s41598-018-30682-5.  

• Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops

  C.D. Yang, H.Y. Huang, S. Shrestha, Y.H. Chen, H.D. Huang, C.P. Tseng
  Int J Mol Sci. 2018 Aug 9;19(8). pii: E2335. doi: 10.3390/ijms19082335.  

• Mitral valve repair versus replacement in patients with ischemic mitral regurgitation.

  M.L. Lee, T.H. Chen, H.D. Huang, S.M. Hou
  J Thorac Dis. 2018 May;10(5):2820-2828. doi: 10.21037/jtd.2018.04.93.  

• Extension of C. elegans lifespan using the ·NO-delivery dinitrosyl iron complexes.

  W.H. Huang, Y.H. Lin, M.H. Lin, Y.R. Huang, C.H. Chou, H.C. Hong, M.R. Wang, Y.T. Tseng, P.C. Liao, M.C. Chung, Y.J. Ma, S.C. Wu, Y.J. Chuang, H.D. Wang, Y.M. Wang, H.D. Huang, T.T. Lu, W.F. Liaw
  J Biol Inorg Chem 2018 Jun 1. doi: 10.1007/s00775-018-1569-1.  

• The aquatic animals‘ transcriptome resource for comparative functional analysis.

  C.H. Chou, H.Y. Huang, W.C. Huang, S.D. Hsu, C.D. Hsiao, C.Y. Liu, Y.H. Chen, Y.C. Liu, W.Y. Huang, M.L. Lee, Y.C. Chen, H.D. Huang,
  BMC Genomics. 2018 May 9;19(Suppl 2):103. doi: 10.1186/s12864-018-4463-x.  

• Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis.

  Y.C. Liu, H.C. Hong, C.D. Yang, W.H. Lee, H.T. Huang, H.D. Huang,
  BMC Genomics. 2018 May 9;19(Suppl 2):171. doi: 10.1186/s12864-018-4456-9.  

• Integrated microRNA and mRNA expression profile analysis of tumor-associated macrophages after exposure to single-dose irradiation.

  W.H. Kung, C.L. Lee, C.D. Yang, C.F. Yu, M.Y. Chiew, F.H. Chen, H.D. Huang,
  Comput Biol Chem. 2018 Jun;74:368-378. doi: 10.1016/j.compbiolchem.2018.03.016. Epub 2018 Mar 13.  

• AMPK Phosphorylation of ACE2 in Endothelium Mitigates Pulmonary Hypertension.

  J. Zhang, J. Dong, M. Martin, M. He, B. Gongol, T.L. Marin, L. Chen, X. Shi, Y. Yin, F. Shang, Y. Wu, H.Y. Huang, J. Zhang, Y. Zhang, J. Kang, E.A. Moya, H.D. Huang, F.L. Powell, Z. Chen, P.A. Thistlethwaite, Z.Y. Yuan, J.Y. Shyy,
  Am J Respir Crit Care Med. 2018 Mar 23. doi: 10.1164/rccm.201712-2570OC. [Epub ahead of print]  

• A Three-MicroRNA Signature as a Potential Biomarker for the Early Detection of Oral Cancer.

  Y.A. Chang, S.L. Weng, S.F. Yang*, C.H. Chou, W.C. Huang, S.J. Tu, T.H. Chang, C.N. Huang, Y.J. Jong, H.D. Huang*
  INT J MOL SCI. 2018 Mar 7;19(3). pii: E758. doi: 10.3390/ijms19030758.  

• Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs

  Y.C. Liu, Y.J. Chiu, C.H. Sun, C.C. Liu, H.D. Huang*
  BMC Genomics. 2018 Jan 19;19(Suppl 1)  

• Compositional and functional variations of oral microbiota associated with the mutational changes in oral cancer

  S.F. Yang, H.D. Huang, W.L. Fan, Y.J. Jong, M.K. Chen, C.N. Huang, C.Y. Chuang, Y.L. Kuo, W.H. Chung, S.C. Su*
  Oral Oncology. 2018 Feb;77:1-8  

• PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli

  M.J. Tsai, J.R. Wang, C.D. Yang, K.C. Kao, W.L. Huang, C.P. Tseng, H.D. Huang, S.Y. Ho*
  Scientific Reports. 2018 Jan 17;8(1):951  

• miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.

  C.H. Chou, S Shrestha, C.D. Yang, N.W. Chang, Y.L. Lin, K.W. Liao, W.C. Huang, T.H. Sun, S.J. Tu, W.H. Lee, M.Y. Chiew, C.S. Tai, T.Y. Wei, T.R. Tsai,H.T. Huang, C.Y. Wang, H.Y. Wu, S.Y. Ho, P.R. Chen, C.H. Chuang, P.J. Hsieh, Y.S. Wu, W.L. Chen, M.J.Li, Y.C. Wu, X.Y. Huang, F.L. Ng,H.D. Huang*
  Nucleic Acids Research. 2018 Jan 4;46(D1):D296-D302.  

• Integrated MicroRNA-mRNA Analysis Reveals miR-204 Inhibits Cell Proliferation in Gastric Cancer by Targeting CKS1B, CXCL1 and GPRC5A.

  Shrestha S, C.D. Yang, H.C. Hong, C.H. Chou, C.S. Tai, M.Y. Chiew, W.L. Chen, S.L. Weng, C.C. Chen, Y.A. Chang, M.L. Lee, W.Y. Huang, S.D. Hsu, Y.C. Chen, H.D. Huang*
  Int J Oncol. 2017 Dec 28;19(1)  

• Bacterial alterations in salivary microbiota and their association in oral cancer.

  W.H. Lee, H.M. Chen, S.F. Yang, C. Liang, C.Y. Peng, F.M. Lin, L.L., Tsai, B.C. Wu,C.H. Hsin, C.Y. Chuang, T. Yang, T.L. Yang, S.Y. Ho, W.L. Chen, K.C. Ueng, H.D. Huang*, C.N. Huang*, Y.J. Jong*
  Scientific Reports.2017 Nov 28;7(1):16540. doi: 10.1038/s41598-017-16418-x.  

• Krüppel-Like Factor 4 Regulation of Cholesterol-25-Hydroxylase and Liver X Receptor Mitigates Atherosclerosis Susceptibility.

  Li Z, Martin M, Zhang J, Huang HY, Bai L, Zhang J, Kang J, He M, Li J, Maurya MR, Gupta S, Zhou G, Sangwung P, Xu YJ, Lei T, Huang HD, Jain M, Jain MK, Subramaniam S, Shyy JY.
  Circulation.2017 Oct 3;136(14):1315-1330  

• α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming.

  P.S. Llu, H. Wang, X. Li, T. Chao, T. Teav, S. Christen, G. Di Conza, W.C. Cheng, C.H. Chou, M. Vavakova, C. Muret, K. Debackere, M. Mazzone, H.D. Huang, S.M. Fendt, J. Ivanisevic, P.C. Ho*
  Nat Immunol. 2017 Sep;18(9):985-994  

• MicroRNA-92a Mediates Endothelial Dysfunction in CKD.

  F. Shang, S.C. Wang, C.Y. Hsu, Y. Miao, M. Martin, M. Y. Yin, C.C. Wu, Y.T. Wang, G. Wu, S. Chien, H.D. Huang, D.C. Tarng, Y.T. Shiu, A.K. Cheung, P.H. Huang, Z. Chen, J.Y. Shyy*
  J Am Soc Nephrol. 2017 Jul 10. pii: ASN.2016111215  

• Evaluation of whole exome sequencing by targeted gene sequencing and Sanger sequencing

  Y.S. Chang, H.D. Huang, K.T. Yeh, J.G. Chang*
  Clin Chim Acta. 2017 Aug;471:222-232  

• DNA Methyltransferases Modulate Hepatogenic Lineage Plasticity of Mesenchymal Stromal Cells

  C.W. Lee, W.C. Huang, H.D. Huang, Y.H. Huang, J.H. Ho, M.H. Yang, V.W. Yang, O.K. Lee*
  Stem Cell Reports. 2017 Jul 11;9(1):247-263  

• Gene expression profiling of tumor-associated macrophages after exposure to single-dose irradiation

  W.H. Kung, C.F. Yu, A.C. Lee, C.D. Yang, Y.C. Liu, F.H. Chen*, H.D. Huang*
  Comput Biol Chem. 2017 Aug;69:138-146  

• Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi

  Y.C. Liu, W.L. Chen, W.H. Kung, H.D. Huang*
  BMC Genomics. 2017 Mar 14;18  

• Identification of novel mutations in endometrial cancer patients by whole-exome sequencing

  Y.S. Chang, H.D. Huang, K.T. Yeh, J.G. Chang*
  Int J Oncol. 2017 May;50(5):1778-1784.  

• Diversity and enterotype in gut bacterial community of adults in Taiwan

  C. Liang, H.C. Tseng, H.M. Chen, W.C. Wang, C.M. Chiu, J.Y. Chang, K.Y. Lu, S.L. Weng, T.H. Chang, C.H.Chang, C.T. Weng, H.M. Wang, H.D. Huang*
  BMC Genomics. 2017 Jan 25;18(Suppl 1):932.   

• Haptoglobin expression correlates with tumor differentiation and five-year overall survival rate in hepatocellular carcinoma.

  C.S. Tai, Y.R. Lin, T.H. Teng, P.Y. Lin, S.J. Tu, C.H. Chou, Y.R. Huang, W.C. Huang, S.L. Weng, H.D. Huang, Y.L. Chen, W.L. Chen
  PLoS One. 2017 Feb 3;12(2):e0171269.  

• Characterization of the Drug Resistance Profiles of Patients Infected with CRF07_BC Using Phenotypic Assay and Ultra-Deep Pyrosequencing

  S.W. Huang, W.Y. Li, W.H. Wang, Y.T. Lin, C.H. Chou, M. Chen, H.D. Huang, Y.H. Chen, P.L. Lu, S.F. Wang, S. Oka, Y.A.Chen*
  PLoS One. 2017 Jan 20;12(1):e0170420.  

• Honeysuckle aqueous extract and induced let-7a suppress dengue virus type 2 replication and pathogenesis

  Y.R. Lee, S.F. Yeh, X.M. Ruan, H. Zhang, S.D. Hsu, H.D. Huang, C.C. Hsieh, Y.S. Lin, T.M. Yeh, H.S. Liu*, D.D. Gan*
  J Ethnopharmacol. 2017 Feb 23;198:109-121  

• PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms

  R.C. Gan, T.W. Chen, T.H. Wu, P.J. Huang, C.C. Lee, Y.M. Yeh, C.H. Chiu, H.D. Huang*, P. Tang*
  BMC Bioinformatics. 2016 Dec 22;17(Suppl 19):513.  

• Adipocyte-specific loss of PPARγ attenuates cardiac hypertrophy

  X. Fang, M.J. Stroud, K. Quyang, L. Fang. J.L. Zhang, N.D. Dalton, Y. Gu, T. Wu, K.L. Peterson, H.D. Huang, J. Chen*, N. Wang*
  JCI Insight. 2016 Oct 6;1(16):e89908.  

• Bidirectional cross-kingdom RNAi and fungal uptake of external RNAs confer plant protection

  M. Wang, A. Weiberg, F.M. Lin, B.P.H.J. Thomma, H.D. Huang, H. Jin*
  Nature Plants. 2016 Sep 19;2:16151  

• Circulating miR-148b-3p and miR-409-3p as biomarkers for heart failure in patients with mitral regurgitation

  M.C. Chen*, T.H. Chang, J.P. Chang, H.D. Huang, W.C. Ho, Y.S. Lin, K.L. Pan, W.H. Liu, Y.K. Huang
  International Journal of Cardiology. 2016 Nov 1;222:148-54.  

• Long noncoding RNA TUG1 is downregulated in non-small cell lung cancer and can regulate CELF1 on binding to PRC2

  P.C. Lin, H.D. Huang, C.C. Chang, Y.S. Chang, J.C. Yen, C.C. Lee, W.H. Chang, T.C. Liu*, J.G. Chang*
  BMC Cancer. 2016 Aug 2;16:583  

• DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma

  H.K. Li, R.T. Mai, H.D. Huang, C.H. Chou, Y.A. Chang, Y.M. Chang, L.R. You, C.M. Chen, Y.H. Lee*
  Scientific Reports. 2016 Jun 27;6:28637  

• Single-Tube Reaction Using Perfluorocarbons: A Prerequisite Step Leading to the Whole-Slide In Situ Technique on Histopathological Slides

  Y.C. Chen, T.H. Teng, J.S. Tsai, H.D. Huang, Y.L. Cheng, C.W. Liang*
  PLoS One. 2016 Jun 23;11(6):e0158018  

• Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome

  Y.C. Liu, S.D. Hsu, C.H. Chou, W.Y. Huang, Y.H. Chen, C.Y. Liu, G.J. Lyu, S.Z. Huang, S. Aganezov, M.A. Alekseyev, C.D. Hsiao*, H.D. Huang*
  BMC Genomics. 2016 Jan 11;17 Suppl 1:13.  

• Genetic alterations in endometrial cancer by targeted next-generation sequencing

  Y.S. Chang, H.D. Huang, K.T. Yeh, J.G. Chang*
  Exp Mol Pathol. 2016 Feb;100(1):8-12.  

• miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database

  C.H. Chou, N.W. Chang, S. Shrestha, S.D. Hsu, Y.L. Lin, W.H. Lee, C.D. Yang, H.C. Hong, T.Y. Wei, S.J. Tu, T.R. Tsai, S.Y. Ho, T.Y. Jian, H.Y. Wu, P.R. Chen, N.C. Lin, H.T. Huang, T.L. Yang, C.Y. Pai, C.S. Tai, W.L. Chen, C.Y. Huang, C.C. Liu, S.L. Weng, K.W. Liao, W.L. Hsu*, H.D. Huang*
  Nucleic Acids Res. 2016 Jan 4;44(D1):D239-47.  

• dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins

  K.Y. Huang, M.G. Su, H.J. Kao, Y.C. Hsieh, J.H. Jhong, K.H. Cheng, H.D. Huang*, T.Y. Lee*
  Nucleic Acids Res. 2016 Jan 4;44(D1):D435-46.  

• PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants

  C.N. Chow, H.Q. Zheng, N.Y. Wu, C.H. Chien, H.D. Huang, T.Y. Lee, Y.F. Chiang-Hsieh, P.F. Hou, T.Y. Yang, W.C. Chang*
  Nucleic Acids Res. 2016 Jan 4;44(D1):D1154-60.  

• CircNet: a database of circular RNAs derived from transcriptome sequencing data

  Y.C. Liu, J.R. Li, C.H. Sun, E. Andrews, R.F. Chao, F.M. Lin, S.L. Weng, S.D. Hsu, C.C. Huang, C. Cheng, C.C. Liu*, H.D. Huang*
  Nucleic Acids Res. 2016 Jan 4;44(D1):D209-15.  

• Exploring Regulatory Mechanisms of Atrial Myocyte Hypertrophy of Mitral Regurgitation through Gene Expression Profiling Analysis: Role of NFAT in Cardiac Hypertrophy

  T.H. Chang, M.C. Chen*, J.P. Chang, H.D. Hunag, W.C. Ho, Y.S. Lin, K.L. Pan, Y.K. Huang, W.H. Liu, C.C. Wu
  PLoS One. 2016 Dec 1;11(12):e0166791.   

• Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS

  X. Tian*, W.C. Liang*, Y. Feng*, J. Wang, V.W. Zhang, C.H. Chou, H.D. Huang, C.W. Lam, Y.Y. Hsu, T.S. Lin, W.T. Chen, L.J. Wong, and Y.J. Jong
  Neurology Genetics 2015 Aug 13;1(2) e14  

• The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli

  M.J. McDonald, C.H. Chou, K.B. Swamy, H.D. Huang, J.Y. Leu*
  BMC Evol Biol. 2015 Aug 19;15:163.  

• Urokinase-type plasminogen activator resulting from endometrial carcinogenesis enhances tumor invasion and correlates with poor outcome of endometrial carcinoma patients

  C.Y. Huang, M.C. Chang, W.Y. Huang, C.T. Huang, Y.C. Tang, H.D. Huang, K.T. Kuo, C.A. Chen, W.F. Cheng*
  Sci Rep. 2015 Jun 2;5:10680.  

• GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes.

  Y.H. Chen, C.D. Yang, C.P. Tseng, H.D. Huang, S.Y. Ho*
  Bioinformatics. 2015 Feb 24. pii: btv075.  

• Oxidative Stress Activates Endothelial Innate Immunity via Sterol Regulatory Element Binding Protein 2 (SREBP2) Transactivation of MicroRNA-92a.

  Z. Chen*, L. Wen, M. Martin, C.Y. Hsu, L. Fang, F.M. Lin, T.Y. Lin, M.J. Geary, G.G. Geary, Y. Zhao, D.A. Johnson, J.W. Chen, S.J. Lin, S. Chien, H.D. Huang, Y.I. Miller, P.H. Huang, J.Y. Shyy*
  Circulation. 2015 Mar 3;131(9):805-14.  

• Unraveling regulatory mechanisms of atrial remodeling of mitral regurgitation pigs by gene expression profiling analysis: role of type I angiotensin II receptor antagonist.

  M.C. Chen*, J.P. Chang, T.H. Chang, S.D. Hsu, H.D. Huang, W.C. Ho, F.S. Wang, C.C. Hsiao, W.H. Liu
  Transl Res. 2015 May;165(5):599-620.  

• MethHC: a database of DNA methylation and gene expression in human cancer.

  W.Y. Huang, S.D. Hsu, H.Y. Huang, Y.M. Sun, C.H. Chou, S.L. Weng, H.D. Huang*
  Nucleic Acids Res. 2015 Jan;43(Database issue):D856-61.  

• RNAcentral: an international database of ncRNA sequences.

  A.I. Petrov, S.J. Kay, R. Gibson, E. Kulesha, D. Staines, E.A. Bruford, M.W. Wright, S. Burge, R.D. Finn, .P.J Kersey , G. Cochrane , A. Bateman*, S. Griffiths-Jones, J. Harrow , P.P. Chan , T.M. Lowe , C.W. Zwieb , J. Wower , K.P. Williams , C.M. Hudson
  Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9.  

• Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.

  S.L. Weng, C.M. Chiu, F.M Lin,W.C Huang, C. Liang, T. Yang, T.L. Yang, C.YC Liu, W.Y. Wu, Y.A. Chang, T.H. Chang*, H.D. Huang*
  PLoS One. 2014 Oct 23;9(10):e110152.  

• Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches.

  C.M. Chiu, W.C. Huang, S.L. Weng, H.C. Tseng, C.Liang, W.C. Wang, T. Yang, T.L. Yang, C.T. Weng, T.H. Chang*, and H.D. Huang*
  BioMed Research International. Volume. 2014;2014:906168.  

• Large-Scale Investigation of Human TF-miRNA Relations Based on Coexpression Profiles.

  C.H. Chien , Y.F. Chiang-Hsieh , A.P. Tsou , S.L. Weng , W.C. Chang*, H.D. Huang*
  Biomed Research International. 2014;2014:623078.   

• A systematic review of microRNA expression profiling studies in human gastric cancer.

  S. Shrestha, S.D. Hsu, W.Y. Huang, H.Y. Huang, W. Chen, S.L. Weng, H.D. Huang*.
  Cancer Medicine. 2014 Aug;3(4):878-88.  

• RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.

  K.Y. Huang, H.Y. Wu, Y.J. Chen, C.T. Lu, M.G. Su, Y.C. Hsieh, C.M. Tsai, K.I. Lin, H.D. Huang, T.Y. Lee*, Y.J. Chen*.
  Database (Oxford). 2014 Apr 25;2014(0):bau034.  

• Investigating microRNA-target interaction-supported tissues in human cancer tissues based on miRNA and target gene expression profiling.

  W.J. Hsieh, F.M. Lin, H.D. Huang*, H. Wang*.
  PLoS One. 2014 Apr 22;9(4):e95697.  

• CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication.

  C.D. Yang, Y.H. Chen, H.Y. Huang, H.D. Huang, C.P. Tseng*.
  Molecular Microbiology. 2014 Jun;92(5):1072-91.  

• lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome

  W.L. Chan, H.D. Huang* and J.G. Chang*
  Computational Biology and Chemistry. 2014 Jun;50:41-9.  

• The effects of actin cytoskeleton perturbation on keratin intermediate filament formation in mesenchymal stem/stromal cells

  T.H. Chang, H.D. Huang, W.K. Ong, Y.J. Fu, O.K. Lee, S. Chien, J.H. Ho*.
  Biomaterials. 2014 Apr;35(13):3934-44.  

• Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing

  C.M Chiu, F.M. Lin, T.H. Chang, W.C. Huang, C. Liang, T. Yang, W.Y. Wu, T.L. Yang, S.L. Weng*, H.D. Huang*.
  Journal of Clinical Bioinformatics. 2014 Jan 13;4(1):1.  

• miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

  S.D. Hsu, Y.T. Tseng, S. Shrestha, Y.L. Lin, A. Khaleel, C.H. Chou, C.F. Chu, H.Y. Huang, C.M. Lin, S.Y. Ho, T.Y. Jian, F.M. Lin, T.H. Chang, S.L. Weng, K.W. Liao, I.E. Liao, C.C. Liu*, H.D. Huang*.
  Nucleic Acids Research. 2014 Jan;42(Database issue):D78-85.  

• Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways.

  A. Weiberg, M. Wang, F.M. Lin, H.W. Zhao, Z.H. Zhang, I. Kaloshian, H.D. Huang, and H. Jin*
  Science. 2013 Oct 4;342(6154):118-23.  

• YjcC, a c-di GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43

  C.J. Huang, Z.C. Wang, H.Y. Huang, H.D. Huang, and H.L. Peng*
  PLoS One. 2013 Jul 23;8(7):e66740.  

• COL11A1 Promotes Tumor Progression, and Predicts Poor Clinical Outcome in Ovarian Cancer

  Y.H. Wu, T.H. Chang, Y.F. Huang, H.D. Huang* and C.Y. Chou*
  Oncogene. 2014 Jun 26;33(26):3432-40.  

• Sterol Regulatory Element Binding Protein 2 Activation of NLRP3 Inflammasome in Endothelium Mediates Hemodynamic-Induced Atherosclerosis Susceptibility

  H. Xiao, M. Lu, T.Y. Lin, Z. Chen, G. Chen, W.C. Wang, T. Marin, T.P. Shentu, L. Wen, B. Gongol, W. Sun, X. Liang, J. Chen, H.D. Huang, J.H. Pedra, D.A. Johnson, and J.Y. Shyy*
  Circulation. 2013 Aug 6;128(6):632-42.  

• Histone Demethylase RBP2 Promotes Lung Tumorigenesis and Cancer Metastasis

  Y.C. Tseng, C.F. Lee, Y.S. Li, Y.R. Chen, P.W. Hsiao, M.Y. Chan, F.M. Lin, H.D. Huang, Y.T. Chen, Y.M. Jeng, C.H. Hsu, Q. Yan, M.D. Tsai, and L.J. Juan*
  Cancer Research. 2013 Aug 1;73(15):4711-21.  

• Hypoxia-responsive miRNAs target argonaute 1 to promote angiogenesis

  Z. Chen, W.C. Wang, H. Xiao, Y.T. Wang, F.M. Lin, W. Sun, T.C. Lai, Y.H. Jan, Y.S. Li, X. Cui, T. Fang, H. Zhao, C. Padmanabhan, R. Sun, D.L. Wang, H. Jin, H.D. Huang, M. Hsiao and J. Y.J. Shyy*
  Journal of Clinical Investigation. 2013 Mar 1;123(3):1057-67.  

• pseudoMap: a novel method and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes

  W.L. Chan, W.K. Yang, H.D. Huang*, and J.G. Chang*
  Database. 2013 Feb 8;2013:bat001.  

• Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma

  W.L. Chan, C.Y. Yuo, W.K. Yang, S.Y. Huang, Y.S. Chang, C.C. Chiu, K.T. Yeh, H.D. Huang*, J.G. Chang*
  Nucleic Acids Research. 2013 Apr 1;41(6):3734-47.  

• An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs

  T.H. Chang, H.Y. Huang, J. B.K. Hsu, S.L. Weng, J.T. Horng* and H.D. Huang*
  BMC Bioinformatics. 2013;14 Suppl 2:S4.  

• A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing

  C.H. Chou, F.M. Lin, M.T. Chou, S.D. Hsu, T.H. Chang, S.L. Weng, S. Shrestha, C.C. Hsiao, J.H. Hung* and H.D. Huang*
  BMC Genomics. 2013;14 Suppl 1:S2.  

• EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou’s PseAAC

  T.H. Chang, L.C. Wu, T.Y. Lee, S.P. Chen, H.D. Huang* and J.T. Horng*
  Journal of Computer-Aided Molecular Design, 2013 Jan;27(1):91-103.   

• A new method for post Genome-Wide-Association-Study (GWAS) analysis of colorectal cancer in Taiwan

  H.M. Wang, T.H. Chang, F.M. Lin, T.H. Chao, W.C. Huang, C. Liang, C.M. Chiu, W.Y. Wu, M.C. Chen, C.T. Weng, S.L. Weng, F.F. Chiang*, and H.D. Huang*
  Gene. 2013 Apr 10;518(1):107-13.  

• The activation of directional stem cell motility by green light-emitting diode irradiation

  W.K. Ong, H.F. Chen, C.T. Tsai, Y.J. Fu, Y.S. Wong, D.J. Yen, T.H. Chang, H.D. Huang, O. K.S. Lee, S. Chien, and J. H.C. Ho*
  Biomaterials. 2013 Mar;34(8):1911-20.   

• dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

  C.T. Lu, K.Y. Huang, M.G. Su, T.Y. Lee*, N. A. Bretaña, W.C. Chang, Y.J. Chen, and H.D. Huang*
  Nucleic Acids Research. 2013 Jan;41(Database issue):D295-305.  

• Phosphoproteome profiling of the sexually transmitted pathogen Trichomonas vaginalis

  Y.M. Yeh, K.Y. Huang, R.R.C. Gan, H.D. Huang, T.C. Wang, and P. Tang*
  Journal of Microbiology, Immunology and Infection. 2013 Oct;46(5):366-73.  

• Functional analyses of endometriosis-related polymorphisms in the estrogen synthesis and metabolism-related genes

  H.S. Wang, H.M. Wu, B.H. Cheng, C.F. Yen, P.Y. Chang, A. Chao, Y.S. Lee, H.D. Huang*, T.H. Wang*
  PLoS One. 2012;7(11):e47374.  

• TET1 Suppresses Cancer Invasion by Activating the Tissue Inhibitors of Metalloproteinases

  C.H. Hsu, K.L. Peng, M.L. Kang, Y.R. Chen, Y.C. Yang, C.H. Tsai, C.S. Chu, Y.M. Jeng, Y.T. Chen, F.M. Lin, H.D. Huang, Y.Y. Lu, Y.C. Teng, S.T. Lin, R.K. Lin, F.M. Tang, S.B. Lee, H. M. Hsu, J.C. Yu *, P.W. Hsiao*, L.J. Juan*
  Cell Reports. 2012 Sep 27;2(3):568-79.  

• Identifying cancer highly-expressed membrane receptors for targeted drug delivery

  W.C. Huang, F.M. Lin, T.H. Chang, K.W. Liao, H.D. Huang*
  International Journal of Bioinformatics Research and Applications. 2012;8(3-4):192-209.  

• MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis

  W.C. Tsai, S.D. Hsu, C.S. Hsu, T.C. Lai, S.J. Chen, R. Shen, Yi Huang, H.C. Chen, C.H. Lee, T.F. Tsai, M.T. Hsu, J.C. Wu, H.D. Huang*, M.S. Shiao*, M. Hsiao*, A.P. Tsou*
  Journal of Clinical Investigation. 2012 Aug 1;122(8):2884-97.   

• Very long non-coding RNA and human disease

  W.L. Chan, Y.S. Chang, W.K. Yang, H.D. Huang, and J.G. Chang
  Biomedicine. 2012 Aug;40(4):902-6.  

• dbSNO: a database of cysteine S-Nitrosylation

  T.Y. Lee, Y.J. Chen, C.T. Lu, W.C. Ching, Y.C. Teng, H.D. Huang and Y.J. Chen*
  Bioinformatics. 2012 Sep 1;28(17):2293-5.  

• miR-103/107 promote metastasis of colorectal cancer by targeting the metastasis suppressors DAPK and KLF4

  H.Y. Chen, Y.M. Lin, H.C. Chung, Y.D. Lang, C.J. Lin, J. Huang, W.C. Wang, F.M. Lin, Z. Chen, H.D. Huang, J. Y.J. Shyy, J.T. Liang, and R.H. Chen*
  Cancer Research. 2012 Jul 15;72(14):3631-41.  

• Let-7b is a novel regulator of hepatitis C virus replication

  J.C. Cheng, Y.J. Yeh, C.P. Tseng, S.D. Hsu, Y.L. Chang, N. Sakamoto, H.D. Huang*
  Cellular and Molecular Life Sciences. 2012 Aug;69(15):2621-33.  

• Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans

  J.B.K. Hsu, T.Y. Lee*, N.A. Bretaña, and H.D Huang*
  PLoS One. 2011;6(11):e27567.  

• RNAcentral: A vision for an international database of RNA sequences

  Bateman A*, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD,
  RNA. 2011 Nov;17(11):1941-6.  

• Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data

  C.H. Chien, Y.M. Sun, W.C. Chang, P.Y. Chiang-Hsieh, T.Y. Lee, W.C. Tsai, J.T. Horng, A.P. Tsou*, H.D. Huang*
  Nucleic Acids Research. 2011 Nov;39(21):9345-56.   

• miRTar: an integrated system for identifying miRNA-target interactions in Human

  J.B.K. Hsu, C.M. Chiu, S.D. Hsu, W.Y. Huang, C.H. Chien, T.Y. Lee and H.D. Huang*
  BMC Bioinformatics. 2011 Jul 26;12:300.  

• SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity

  T.Z. Lee, Yi-Ju Chen, T.C. Lu, H.D. Huang, and Y.J. Chen*
  PLoS One. 2011;6(7):e21849.  

• Flow-Dependent Regulation of Kruppel-Like Factor 2 Is Mediated by MicroRNA-92a

  W. Wu, H. Xiao, A. Laguna-Fernandez, G. Villarreal, K.C. Wang, G.G. Geary, W.C. Wang, H.D. Huang, J. Zhou, Y.S. Li, S. Chien, G. Garcia-Cardena, J.Y-J. Shyy*
  Circulation. 2011 Aug 2;124(5):633-41.  

• Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences

  M. McDonald, W.C. Wang, H.D. Huang*, and J.Y. Leu*
  PLoS Biology. 2011 Jun;9(6):e1000622.   

• Small molecule amiloride modulates oncogenic RNA alternative splicing to devitalize human cancer cells

  J.G. Chang*, D.M. Yang, W.H. Chang, L.P. Chow, W.L. Chan, H.H. Lin, H.D. Huang, Y.S. Chang, C.H. Hung, and W.K. Yang*
  PLoS One. 2011;6(6):e18643.  

• Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393*-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB12

  X. Zhang, H. Zhao, S. Gao, W.C. Wang, S. Katiyar-Agarwal, H.D. Huang, N. Raikhel and H. Jin*
  Molecular Cell. 2011 May 6;42(3):356-66.  

• Characterization and prediction of mRNA polyadenylation sites in human genes

  T.H. Chang, L.C. Wu, Y.T. Chen, H.D. Huang, B.J. Liu, K.F. Cheng, J.T. Horng*
  Medical & Biological Engineering & Computing. 2011 Apr;49(4):463-72.  

• miRTarBase: a database curates experimentally validated microRNA-target interactions

  S.D. Hsu, F.M. Lin, W.Y. Wu, C. Liang, W.C. Huang, W.L. Chan, W.T. Tsai, G.Z. Chen, C.J. Lee, C.M. Chiu, C.H. Chien, C.Y. Huang, A.P. Tsou and H.D. Huang*
  Nucleic Acids Res. 2011 Jan;39(Database issue):D163-9.  

• RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans

  T.Y. Lee, J. B.K. Hsu, W.C. Chang* and H.D. Huang*
  Nucleic Acids Research. 2011 Jan;39(Database issue):D777-87.  

• N-Ace: using solvent accessibility and physicochemical properties to identify protein N-Acetylation sites

  T.Y. Lee, J.B.K. Hsu, F.M. Lin, W.C. Chang*, P.C. Hsu, and H.D. Huang*
  Journal of Computational Chemistry. 2010 Nov 30;31(15):2759-71.  

• Global analyses of small interfering RNAs derived from Bamboo mosaic virus and its associated satellite RNAs in different plants

  K.Y. Lin, C.P. Cheng , B. Chang , W.C. Wang , Y.W. Huang , Y.S. Lee, H.D. Huang, Y.H. Hsu, N.S. Lin*
  PLoS One. 2010 Aug 2;5(8):e11928.  

• A novel role of CPEB3 in regulating EGFR gene transcription via association with Stat5b in neurons

  S.C. Peng, Y.T. Lai, H.Y. Huang, H.D. Huang, and Y.S. Huang*
  Nucleic Acids Research. 2010 Nov;38(21):7446-57.  

• MicroRNA: a master regulator of cellular processes for bioengineering systems

  W. Sun, Y.S.J. Li, H.D. Huang, J. Y-J. Shyy*, S. Chien*
  Annual Review of Biomedical Engineering. 2010 Aug 15;12:1-27.  

• An expert system to identify co-regulated gene groups from time-lagged gene clusters using cell cycle expression data

  L.C. Wu, J.L. Huang, J.T. Horng*, H.D. Huang
  Expert Systems with Applications. 2010, Vol. 37, No. 3, pp. 2202-2213.   

• Prediction of small non-coding RNA in bacterial genomes using support vector machines

  T.H. Chang, L.C. Wu, J.H. Lin, H.D. Huang, B.J. Liu, K.F. Cheng, J.T. Horng*
  Expert Systems with Applications. 2010, Vol. 37, No. 8, pp. 5549-5557.   

• miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

  W.C. Wang, F.M. Lin, W.C. Chang, K.Y. Lin, H.D. Huang*, and N.S. Lin*
  BMC Bioinformatics. 2009 Oct 12;10:328.  

• A Comprehensive Resource for Integrating and Displaying Protein Post-Translational Modifications

  T.Y. Lee, J.B.K. Hsu, W.C. Chang, T.Y. Wang, P.C. Hsu, and H.D. Huang*.
  BMC Research Notes. 2009 Jun 23;2:111.  

• Computational Identification of riboswitches based on RNA conserved functional sequences and conformations

  T.H. Chang, H.D. Huang*, L.C. Wu, C.T. Yeh, B.J. Liu, J.T. Horng*
  RNA. 2009 Jul;15(7):1426-30.  

• FMM: a web server for metabolic pathway reconstruction and comparative analysis

  C.H. Chou†, W.C. Chang†, C.M. Chiu, C.C. Huang, and H.D. Huang*
  Nucleic Acids Research. 2009 Jul;37(Web Server issue):W129-34.  

• Incorporating support vector machine for identifying protein tyrosine sulfation sites

  W.C. Chang, T.Y. Lee, D.M. Shien, J. B.K. Hsu, P.C. Hsu, T.Y. Wang, J.T. Horng, H.D. Huang* and R.L. Pan*
  Journal of Computational Chemistry. 2009 Nov 30;30(15):2526-37.  

• MicoRNA-122, a tumor suppressor microRNA that regulates intra-hepatic metastasis of hepatocellular carcinoma

  W.C. Tsai†, Paul W.C. Hsu†, T.C. Lai†, G.Y. Chau, C.W. Lin, C.M. Chen, C.D. Lin, Y.L. Liao, J.L. Wang, Y.P. Chau, M.T. Hsu, M. Hsiao*, H.D. Huang*, A.P. Tsou*.
  Hepatology. 2009 May;49(5):1571-82.  

• Incorporating structural characteristics for identification of protein methylation sites

  D.M. Shien†, T.Y. Lee†, W.C. Chang, J.B.K. Hsu, J.T. Horng, P.C. Hsu, T.Y. Wang and H.D. Huang*.
  Journal of Computational Chemistry. 2009 Jul 15;30(9):1532-43.  

• sRNAMap: Genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes

  H.Y. Huang, H.Y. Chang, C.H. Chou, C.P. Tseng, S.Y. Ho, C.D. Yang, Y.W. Ju, H.D. Huang
  Nucleic Acids Research. 2009 Jan;37(Database issue):D150-4.  

• Detecting LTR structures in human genomic sequences using profile hidden Markov models

  L.C. Wu, H.D. Huang, Y.C. Chang, Y.C. Lee, J.T. Horng*.
  Expert Systems with Applications. 2009, Vol. 36, No. 1, pp. 668-674.   

• An expert system to predict protein thermostability using decision tree

  L.C. Wu, J.X. Lee, H.D. Huang, B.J. Liu, J.T. Horng*.
  Expert Systems with Applications. 2009, Vol. 36, No. 5, pp. 9007-9014.   

• PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group

  W.C. Chang, T.Y. Lee, H.D. Huang*, H.Y. Huang, R.L. Pan*.
  BMC Genomics. 2008 Nov 26;9:561.  

• Identifying discriminative amino acids within the hemagglutinin of human influenza A H5N1 virus using a decision tree

  L.C. Wu, J.T. Horng*, H.D. Huang, W.L. Chen,
  IEEE Transactions on Information Technology in Biomedicine. 2008 Nov;12(6):689-95.  

• RNALogo: a new approach to display structural RNA alignment

  T.H. Chang, J.T. Horng, and H.D. Huang*
  Nucleic Acids Research. 2008 Jul 1;36(Web Server issue):W91-6.   

• miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes

  S.D. Hsu, C.H. Chu, A.P. Tsou, S.J. Chen, H.C. Chen, Paul W.C. Hsu, Y.H. Wong, Y.H. Chen, G.H. Chen, and H.D. Huang*
  Nucleic Acids Research. 2008 Jan;36(Database issue):D165-9.  

• KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns

  Y.H. Wong, T.Y. Lee, H.K. Liang, C.M. Huang, Y.H. Yang, C.H. Chu, H.D. Huang* , M.T. Ko, and J.K. Hwang
  Nucleic Acids Research. 2007 Jul;35(Web Server issue):W588-94.  

• ViTa: a database of host microRNA targets on viruses

  Paul W.C. Hsu, L.Z. Lin, S.D. Hsu, H.D. Huang*
  Nucleic Acids Research. 2007 Jan;35(Database issue):D381-5.  

• Primer Design for Multiplex PCR Using a Genetic Algorithm

  L.C. Wu, J.Z. Horng, H.Y. Huang, F.M. Lin, H.D. Huang, and M.F. Tsai
  Soft Computing. 2007, Vol. 11, No. 9, 855-863.   

• miRNAMap: genomic maps for miRNA genes and their target genes in vertebrate genomes

  W.C. Hsu†, H.D. Huang†*, S.D. Hsu, L.Z. Lin, A.P. Tsou, C.P. Tseng, P.F. Stadler, S. Washietl, and I.L. Hofacker.
  Nucleic Acids Research. 2008 Jan;36(Database issue):D165-9.  

• RINGdb: An integrated database for G protein-coupled receptors and regulators of G protein signaling

  Y.C. Fang, W.H. Sun, L.C. Wu, H.D. Huang, H.F. Juan, J.T. Horng.
  BMC Genomics. 2006 Dec 16;7:317.  

• Database to dynamically aid probe design for virus identification

  F.M. Lin, H.D. Huang, P.L. Chan, Y.C. Chang, and J.T. Horng,
  IEEE Transactions on Information Technology in Biomedicine. 2006 Oct;10(4):705-13.  

• Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data

  A.P. Tsou, Y.M. Sun, C.L. Liu, H.D. Huang*, and J.T. Horng*.
  IEEE Transactions on Information Technology in Biomedicine. 2006 Jul;10(3):550-8.  

• ProKware: an integrated software for presenting protein structural properties in protein tertiary structures

  J.H. Hung†, H.D. Huang†*, and T.Y. Lee,
  Nucleic Acids Research. 2006 Jul 1;34(Web Server issue):W89-94.  

• RegRNA: A regulatory RNA motifs and elements finder

  H.Y. Huang, C.H. Chien, and K.H. Jen, H.D. Huang*
  Nucleic Acids Research. 2006 Jul 1;34(Web Server issue):W429-34.  

• RNAMST: An efficient and flexible search tool for RNA structural homologs

  T.H. Chang†, H.D. Huang†* , Zi-Neng Chung, and J.T. Horng,
  Nucleic Acids Research. 2006 Jul 1;34(Web Server issue):W423-8.  

• An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints

  T.Y. Lee, J.T. Horng, H.F. Juan, H.D. Huang, L.C. Wu, and F.M. Lin.
  Journal of Computational Chemistry. 2006 Jul 15;27(9):1020-32.  

• Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures

  Li-Cheng Wu, J.T. Horng, S.L. Huang and H.D. Huang,
  Journal of Computational Chemistry. 2006 Apr 30;27(6):798-808.  

• dbPTM: An information repository of protein post-translational modification

  T.Y. Lee†, H.D. Huang†*, J.H. Hung, H.Y. Huang, Y.S. Yang, and T.H. Wang*.
  Nucleic Acids Research. 2006 Jan 1;34(Database issue):D622-7.  

• KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites

  H.D. Huang*, T.Y. Lee, S.W. Tseng, and J.T. Horng.
  Nucleic Acids Research. 2005 Jul 1;33(Web Server issue):W226-9.  

• MultiProtIdent: identifying proteins using database search and protein-protein interactions

  H.D. Huang, T.Y. Lee, L.C. Wu, F.M. Lin, J.T. Horng, and A.P. Tsou.
  Journal of Proteome Research. 2005 May-Jun;4(3):690-7.  

• Incorporating Hidden Markov Model for identifying protein kinase-specific phosphorylation sites

  H.D. Huang*, T.Y. Lee, S.W. Tseng, L.C. Wu, J.T. Horng, and A.P. Tsou.
  Journal of Computational Chemistry. 2005 Jul 30;26(10):1032-41.  

• SpliceInfo: An information repository for mRNA alternative splicing in human genome

  H.D. Huang, J.T. Horng, F.M. Lin, Y.C. Chang, and C.C. Huang.
  Nucleic Acids Research. 2005 Jan 1;33(Database issue):D80-5.  

• Discovering common of structural motifs from SSU 16 S ribosomal RNA secondary structures

  H.D. Huang*, J.T. Horng, and S.F. Fang.
  International Journal on Artificial Intelligence Tools. 2005, Vol. 14, No. 4, pp. 621-639.   

• A probabilistic method to correlate ion-pairs with protein thermostability

  S.L. Huang, LC. Wu, H.D. Huang, H.K. Liang, M.T. Ko, and J.T. Horng.
  Applied Bioinformatics. 2004;3(1):21-9.  

• i-Genome: A database to summarize oligonucleotide data in genomes

  F.M. Lin, H.D. Huang, YC, Chang, J.T. Horng.
  BMC Genomics. 2004 Oct 9;5:78.  

• Identification of the combination of susceptibility genetic factors for cervical cancer

  J.T. Horng, K. C. Hu, L. C. Wu, H. D. Huang, F. M. Lin, H. C. Lai, and T. Y Chu.
  IEEE Trans Inf Technol Biomed. 2004 Mar;8(1):59-66.  

• Identifying transcriptional regulatory sites in the human genome using an integrated system

  H.D Huang, J.T. Horng, Y.M. Sun, and A.P. Tsou.
  Nucleic Acids Research. 2004 Mar 29;32(6):1948-56.  

• A computational approach to discover differential cooperation of regulatory sites in functionally related genes in yeast genome

  J.T. Horng, H.D. Huang, T.S. Tsou, J.Y. Hong, and B.J. Liu.
  Journal of Information Science and Engineering. 2004, Vol. 20, No. 6, pp. 1141- 1159.   

• A biological data warehousing, analyzing and mining system for identifying transcriptional regulatory sites in human genome

  Y.M. Sun, H.D. Huang, J.T. Horng, A.P. Tsou, and S.L. Huang.
  Lecture Notes in Computer Sciences. 2004, 3180: 751-760.   

• Computing motif correlations in proteins

  J.T. Horng, H.D. Huang, S.H. Wang, M.Y. Chen, J.K. Hwang, and S.L. Huang.
  Journal of Computational Chemistry. 2003 Dec;24(16):2032-43.   

• Database of repetitive elements in complete genomes and data mining using transcription factor binding sites

  J.T. Horng, F.M. Lin, J.H. Lin, H.D. Huang, and B.J. Liu.
  IEEE Trans Inf Technol Biomed. 2003 Jun;7(2):93-100.  

• ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag data,

  H.D. Huang, J.T. Horng, C.C. Lee, and B.J. Liu.
  Genome Biology. 2003;4(4):R29.  

• A data mining method to predict transcriptional regulatory sites based on differentially expressed genes in human genome

  H.D. Huang, H.L. Chang, T.S. Tsou, B.J. Liu, and J.T. Horng.
  Journal of Information Science and Engineering, 2003, Vol. 19, No. 6, pp. 923-942.   

• Mining correlations of tissue gene expression from digital expression profiles of human tissues

  J.T. Horng, H.D. Huang, K.Y. Tseng, T.S. Tsou, and B.J. Liu.
  Journal of Information Science and Engineering. 2003, Vol. 19, No. 6, pp. 909-921.   

• Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae

  J.T. Horng, H.D. Huang, S.L. Huang, U.C. Yang, and Y.C. Chang.
  In Silico Biology. 2002;2(3):263-73.  

• The repetitive sequence database and mining putative regulatory elements in gene promoter regions

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