Integrative System Biology Laboratory

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Publications »  2016

• 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.