Members

Associate Professor
Institute of Genomics and Bioinformatics, National Chung Hsing University
E-mail: jimliu {at} nchu.edu.tw
Office Tel: 04-22840338 # 7031
 


Ph.D. Students (博士生)

Jeff (翁嘉偉Chia-Wei Weng


E-mail: cwweng060304 {at} gmail.com
PhD student since Sep 2013

Research topics:
  1. Computer-aided drug discovery
  2. Resequencing data analysis and variation detection
  3. Transcriptome-based drug discovery

Publication:

  1. Ung MH, Sun CH, Weng CW, Huang CC, Lin CC*, Liu CC*, Cheng C*. (2016) Integrated Drug Expression Analysis for leukemia: an integrated in silico and in vivo approach to drug discovery. Pharmacogenomics J. in press. (SCI, IF 4.229) 

Conference:

  • Yu-Ting TsengChia-Wei Weng, Te-Wei Tzeng, Chia-Chun Yang, I-En Liao, Jeremy J.W. Chen, Chao Cheng, Chun-Chi Liu. (2013) KeyNet: Dynamic Keyword Network Web Server Using PubMed Database. Intelligent Systems for Molecular Biology (ISMB 2013) July 19-23, 2013. Berlin, Germany. F1000Posters 2013, 4: 885 [Poster]


Jalen (李建融) Jian-Rong Li


E-mail: fanicesiza {at} gmail.com
PhD student since Sep 2015

Research topics:
  1. Construction of cancer RNA-seq database
  2. Construction of circular RNA database
  3. The function study of tissue-specific circRNA modules
Publications:
  1. Jian-Rong Li, Chuan-Hu Sun, Wenyuan Li, Rou-Fang Chao, Chieh-Chen Huang, Xianghong Jasmine Zhou, Chun-Chi Liu. Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. Nucleic Acids Research 44: D944-51. (SCI, IF 9.112) [Abstract] [http://syslab4.nchu.edu.tw/CRN/]
  2. Yu-Chen Liu, Jian-Rong Li, Chuan-Hu Sun, Erik Andrews, Rou-Fang Chao, Feng-Mao Lin, Shun-Long Weng, Sheng-Da Hsu, Chieh-Chen Huang, Chao Cheng, Chun-Chi Liu*, and Hsien-Da Huang*. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Research 44: D209-15. (SCI, IF 9.112) [Abstract] [http://syslab5.nchu.edu.tw/CircNet/]
  3. Li W, Liu CC, Kang S, Li JR, Tseng YT, Zhou XJ. (2016) Pushing the Annotation of Cellular Activities to a Higher Resolution: Predicting Functions at the Isoform Level. Methods 93: 110-118. (SCI, IF 3.645)

Conference:

  • Yu-Chen Liu, Chuan-Hu Sun, Jian-Rong Li, Chun-Chi Liu and Hsien-Da Huang. (2015) Ouroboros-like double negative feedback loops in circular RNAs. The 2nd Bilateral Israel-Taiwan Life Sciences Conference. June 7-9, 2015. Tel Aviv University, Tel Aviv, Israel.




Research Assistants (研究助理)

Sac (孫全滸
Chuan-Hu Sun

E-mail: s39676536

{at}

gmail.com
Office Tel: 04-22840338 # 7051

Research topics:
  1. Construction of cancer RNA-seq database
  2. Construction of circular RNA database
  3. The function study of tissue-specific circRNA modules
Publications:
  1. Jian-Rong Li, Chuan-Hu Sun, Wenyuan Li, Rou-Fang Chao, Chieh-Chen Huang, Xianghong Jasmine Zhou, Chun-Chi Liu. Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. Nucleic Acids Research 44: D944-51. (SCI, IF 9.112) [Abstract] [http://syslab4.nchu.edu.tw/CRN/]
  2. Yu-Chen Liu, Jian-Rong Li, Chuan-Hu Sun, Erik Andrews, Rou-Fang Chao, Feng-Mao Lin, Shun-Long Weng, Sheng-Da Hsu, Chieh-Chen Huang, Chao Cheng, Chun-Chi Liu*, and Hsien-Da Huang*. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Research 44: D209-15. (SCI, IF 9.112) [Abstract] [http://syslab5.nchu.edu.tw/CircNet/] 
  3. Ung MH, Sun CH, Weng CW, Huang CC, Lin CC*, Liu CC*, Cheng C*. (2016) Integrated Drug Expression Analysis for leukemia: an integrated in silico and in vivo approach to drug discovery. Pharmacogenomics J. in press. (SCI, IF 4.229) 
Conference:
  1. Yu-Chen Liu, Chuan-Hu Sun, Jian-Rong Li, Chun-Chi Liu and Hsien-Da Huang. (2015) Ouroboros-like double negative feedback loops in circular RNAs. The 2nd Bilateral Israel-Taiwan Life Sciences Conference. June 7-9, 2015. Tel Aviv University, Tel Aviv, Israel.

Joyce (趙柔芳Rou-Fang Chao

E-mail: roufangchao 

{at} gmail.com

Office Tel: 04-22840338 # 7051

Research topics: 
  1. Construction of cancer RNA-seq database
  2. Construction of circular RNA database
  3. The function study of tissue-specific circRNA modules
Publications
  1. Jian-Rong Li, Chuan-Hu Sun, Wenyuan Li, Rou-Fang Chao, Chieh-Chen Huang, Xianghong Jasmine Zhou, Chun-Chi Liu. Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. Nucleic Acids Research 44: D944-51. (SCI, IF 9.112) [Abstract][http://syslab4.nchu.edu.tw/CRN/]
  2. Yu-Chen Liu, Jian-Rong Li, Chuan-Hu Sun, Erik Andrews, Rou-Fang Chao, Feng-Mao Lin, Shun-Long Weng, Sheng-Da Hsu, Chieh-Chen Huang, Chao Cheng, Chun-Chi Liu*, and Hsien-Da Huang*. CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Research 44: D209-15. (SCI, IF 9.112) [Abstract] [http://syslab5.nchu.edu.tw/CircNet/]

M.S. Students (碩士生)



Former M.S. Students

Year 2011

  • Ken (袁偉勝) E-mail: skyblue750202 {at} gmail.com
  • Ting (曾毓婷) E-mail: ting0514 {at} gmail.com (Current position: Post-doctoral associate, UCLA)

Year 2012   

  • Dora (陳怡穎) E-mail: dorayea {at} gmail.com (現況:矽品精密工業股份有限公司 工程師)
  • Wayne (洪偉欣) E-mail: weisinhong {at} gmail.com (現況:中山科學研究院 研發替代役)

Year 2014

  • David (曾德維) E-mail: allqwdd {at} gmail.com      

Publications: 

  • Tzeng DT, Tseng YT, Ung M, Liao IE, Liu CC, Cheng C. (2014) DPRP: A database of phenotype-specific regulatory programs derived from transcription factor binding data. Nucleic Acids Research 42: D178-183. (SCI, IF 9.112) [PubMed]


  

Year 2015

  • Jalen (李建融) Jian-Rong Li (Current position: PhD. student, NCHU, Taiwan)

Year 2016

  • Kelly (蕭函容) E-mail: st30393 {at} gmail.com
  • Ron (邱于榮) E-mail: kim38026 {at} gmail.com
  • Joyce (趙柔芳) Rou-Fang Chao E-mail: roufangchao {at} gmail.com


Former Ph.D. Student

Ting (曾毓婷) Yu-Ting Tseng (Jan 2012 ~ July 2014)

Current position: Post-doctoral associate, UCLA
E-mail: ting0514 {at} gmail.com
Publications: 

  • Liu CC , Tseng YT , Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M, Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ. (2014) DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acids Research 42: W137-146. (SCI, IF 9.112) (co-first authors) [Abstract]

  • Tzeng DT , Tseng YT , Ung M, Liao IE, Liu CC*, Cheng C*. (2014) DPRP: A database of phenotype-specific regulatory programs derived from transcription factor binding data. Nucleic Acids Research 42: D178-183. (SCI, IF 9.112) (co-first authors) [PubMed]
  • Hsu SD, Tseng YT , Shrestha S, Lin YL, Khaleel A, Chou CH, Chu CF, Huang HY, Lin CM, Ho SY, Jian TY, Lin FM, Chang TH, Weng SL, Liao KW, Liao IE, Liu CC*, Huang HD*. (2014) miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Research 42: D78-85. (SCI, IF 9.112) (co-first authors) [PubMed]
  • Tseng YT, Li W, Chen CH, Zhang S, Chen JJ, Zhou XJ and Liu CC*. (2015) IIIDB: a database for isoform-isoform interactions and isoform network modules. BMC Genomics 16: S10. (SCI, IF 4.04) (*corresponding author) [Abstract]
  • Li W, Liu CC, Kang S, Li JR, Tseng YT, Zhou XJ. (2016) Pushing the Annotation of Cellular Activities to a Higher Resolution: Predicting Functions at the Isoform Level. Methods 93: 110-118. (SCI, IF 3.645)

Conference:

  • Yu-Ting Tseng, Chia-Wei Weng, Te-Wei Tzeng, Chia-Chun Yang, I-En Liao, Jeremy J.W. Chen, Chao Cheng, Chun-Chi Liu. (2013) KeyNet: Dynamic Keyword Network Web Server Using PubMed Database. Intelligent Systems for Molecular Biology (ISMB 2013) July 19-23, 2013. Berlin, Germany. F1000Posters 2013, 4: 885 [Poster]


  


Kohler (楊家俊Chia-Chun Yang (Sep 2009 ~ Jan 2016)

E-mail: biohomeg {at} gmail.com

Research topics: 
  1. Haplotype and chromatin status 
  2. Develop gene regulation database
  3. Discovering chromatin motifs
Publication: 
  • Yang CC, Buck MJ, Chen MH, Chen YF, Lan HC, Chen JJ, Cheng C, Liu CC. (2013) Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. BMC Genomics 14:310. (SCI, IF 3.867) [Abstract]
  • Yang CC, Andrews E, Chen MH, Wang WY, Chen JJ, Gerstein M, Liu CC, Cheng C*. (2016) iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data. BMC Genomics 17:632. (SCI, IF 3.867)
  • Yang CC, Chen MH, Lin SY, Andrews EH, Cheng C*, Liu CC*, Chen JJ*. (2017) Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. BMC Genomics 18:61. (SCI, IF 3.867) [Abstract]


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