Publications

Journal Papers 

(2017)
  1. Ung MH, Sun CH, Weng CW, Huang CC, Lin CC*Liu CC*, Cheng C*. (2017) Integrated Drug Expression Analysis for leukemia: an integrated in silico and in vivo approach to drug discovery.  Pharmacogenomics J. 17, 351–359. (SCI, IF 4.229) (*corresponding author) [Abstract] [http://syslab5.nchu.edu.tw/IDEAL/]
  2. 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) (*corresponding author) [Abstract]
  3. Chin WC, Lin KH, Liu CC, Tsuge K, Huang CC. (2017) Improved n-butanol production via co-expression of membrane-targeted tilapia metallothionein and the clostridial metabolic pathway in Escherichia coli. BMC Biotechnol. 17:36. (SCI)
  4. (2016)
  5. Li JR, Sun CH, Li W, Chao RF, Huang CC, Zhou XJ, Liu CC*. (2016) Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. Nucleic Acids Research 44: D944-51. (SCI, IF 10.162) (*corresponding author)  [Abstract] [CancerRNA.org]
  6. Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, Liu CC*, Huang HD*. (2016) CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Research 44: D209-15. (SCI, IF 10.162) (*corresponding author) [Abstract] [http://syslab5.nchu.edu.tw/CircNet/]
  7. Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH, Yang CD, Hong HC, Wei TY, Tu SJ, Tsai TR, Ho SY, Jian TY, Wu HY, Chen PR, Lin NC, Huang HT, Yang TL, Pai CY, Tai CS, Chen WL, Huang CY, Liu CC, Weng SL, Liao KW, Hsu WL, Huang HD. (2016) miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Research 44: D239-47. (SCI, IF 10.162) [Abstract] [http://mirtarbase.mbc.nctu.edu.tw/]
  8. 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) (*corresponding author)
  9. Li WLiu 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) (co-first author)
  10. Ung MH, Liu CC, Cheng C. (2016) Integrative analysis of cancer genes in a functional interactome. Scientific Reports 6:29228. (SCI, IF 5.228) [Abstract]

  11. (2015)
  12. 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 3.867) (*corresponding author) [Abstract] [http://syslab.nchu.edu.tw/IIIDB
  13. Chen Y, Chen C, Zhang Z, Liu CC, Johnson ME, Espinoza CA, Edsall LE, Ren B, Zhou XJ, Grant SF, Wells AD, Chen L. (2015) DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions. Nucleic Acids Research 43:1268-82. (SCI, IF 10.162)
    (2014)
  14. 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 10.162) (*corresponding author) [Abstract] [http://disease-connect.org/] 
  15. 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 10.162) (*corresponding author) [PubMed] [http://syslab.nchu.edu.tw/DPRP/]
  16. 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 10.162) (*corresponding authors) [PubMed] [http://mirtarbase.mbc.nctu.edu.tw/(Cited by 457) 
  17. Li W, Kang S, Liu CC, Zhang S, Shi Y, Liu Y, Zhou XJ. (2014) High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method. Nucleic Acids Research 42: e39. (SCI, IF 10.162) [PubMed]
  18. Jiang CR, Liu CC, Zhou XJ, Huang H. (2014) Optimal Ranking in Multi-label Classification Using Local Precision Rates. Statistica Sinica 24: 1547-1570. (SCI)

  19. (2013)
  20. 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 4.04) (*corresponding author[Abstract]
  21. Zhu M, Liu CC, Cheng C. (2013) REACTIN: Regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. BMC Genomics 14:504 (SCI, IF 4.04) [Abstract]
  22. Chiang YT, Shien JH, Tan DH, Shieh MK, Liu CC, Chen YS, Chang PC. (2013) Identification of the lic1ABCD operon that controls the phase-variable expression of phosphorylcholine onlipopolysaccharide from Avibacterium paragallinarum. Avian Pathol. 42(1):72-8. (SCI)

    (2012)
  23. Zhang S, Liu CC, Li W, Shen H, Laird P, Zhou XJ. (2012) Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Research 40: 9379-9391. (SCI) [PubMed]
  24. Li W, Zhang S, Liu CC, Zhou XJ. (2012) Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. Bioinformatics 28: 2458-66. (SCI, IF 5.468)
  25. Li W, Dai C, Liu CC, and Zhou XJ. (2012) Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling. Journal of Computational Biology 19: 710-30. (SCI)
  26. Pan YC, Tan DH, Shien JH, Liu CC, He YS, Shen PC, Chang PC. (2012) Identification and characterization of an RTX toxin-like gene and its operon from Avibacterium paragallinarum. Avian Diseases 56: 537-544. (SCI)

    (2011)
  27. Taberlay PC, Kelly TK, Liu CC, You JS, De Carvalho DD, Miranda TB, Zhou XJ, Liang G, Jones PA. (2011) Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming. Cell 147: 1283-1294. (SCI, IF 32.4)  [Abstract(Cited by 118)
  28. Li W,  Liu CC, Zhang T, Li H, Waterman M, Zhou XJ. (2011) Integrative Analysis of Many Weighted Coexpression Networks Using Tensor Computation. PLoS Computational Biology 7: e1001106. (SCI, IF 5.8) [Abstract]

    (2010)
  29. Huang HLiu CC, Zhou XJ. (2010) Bayesian Approach to Transforming Public Gene Expression Repositories into Disease Diagnosis Databases. Proc. Natl. Acad. Sci. USA107: 6823-8. (SCI, IF 9.43) (co-first author) [Abstract(Cited by 43)
  30. Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, Zhou XJ. (2010) Joint Genome-Wide Profiling of miRNA and mRNA Expression in Alzheimer's Disease Cortex Reveals Altered miRNA Regulation. PLoS ONE 5: e8898.(SCI) 

    (2009)
  31. Liu CC, Hu J, Kalakrishnan M, Huang H, Zhou XJ. (2009) Integrative Disease Classification Based on Cross-platform Microarray Data. BMC Bioinformatics (APBC 2009) 10:S25. (SCI)
  32. Friedman JM, Liang G, Liu CC, Wolff EM, Tsai YC, Ye W, Zhou X, Jones PA. (2009) The Putative Tumor Suppressor microRNA-101 Modulates the Cancer Epigenome by Repressing the Polycomb Group Protein EZH2. Cancer Research 69:2623-9. (SCI, IF 7.514) [PubMed] (Cited by 294)

    (2008)
  33. Yu SL, Chen HY, Chang GC, Chen CY, Chen HW, Singh S, Cheng CC, Yu CJ, Lee YC, Chen HS, Su TJ, Chiang CC, Li HN, Hong QS, Su HY, Chen CC, Chen WJ, Liu CC, Chan WK, Chen WJ, Li KC, Chen JJ, Yang PC. (2008) MicroRNA Signature Predicts Survival and Relapse in Lung Cancer. Cancer Cell 13: 48-57. (SCI, IF 23.858[Abstract(Cited by 418)
  34. Lee CY, Sher HF, Chen HW, Liu CC, Chen CH, Lin CS, Yang PC, Tsay HS, Chen JJ. (2008) The anticancer effects of tanshinone I in human non-small-cell lung cancer. Molecular Cancer Therapeutics 7(11):3527-38. (SCI) 
  35. Chen HW, Liu CC, Chen JJ, Lee YM, Hwang JL, Tzeng CR. (2008) Combined differential gene expression profile and pathway enrichment analyses to elucidate the molecular mechanisms of uterineleiomyoma after gonadotropin-releasing hormone treatment. Fertility and Sterility 90:1219-1225. (SCI)

    (2007)
  36. Liu CC, Lin CC, Li KC, Chen WS, Chen JC, Yang MT, Yang PC, Chang PC, Chen JJ. (2007) Genome-wide identification of the specific oligonucleotides using artificial neural network and computational genomic analysis. BMC Bioinformatics 8:164. (SCI) 
  37. Chen HY, Yu SL, Chen CH, Chang GC, Chen CY, Yuan A, Cheng CL, Wang CH, Terng HJ, Kao SF, Chan WK, Li HN, Liu CC, Singh S, Chen WJ, Chen JJ, Yang PC. (2007) A Five-Gene Signature and Clinical Outcome in Non–Small-Cell Lung Cancer. New England Journal of Medicine 356:11-20. (SCI, IF 52.589[Abstract](Cited by 559)

    (2006)
  38. Liu CC, Chen WS, Lin CC, Liu HC, Chen HY, Yang PC, Chang PC, Chen JJ. (2006) Topology-based cancer classification and related pathway mining using microarray data. Nucleic Acids Research 34: 4069-4080. (SCI) [Abstract
  39. Liu CC, Lin CC, Chen WS, Chen HY, Chang PC, Chen JJ, Yang PC. (2006) CRSD: a comprehensive web server for composite regulatory signature discovery. Nucleic Acids Research 34: W571-W577. (SCI) [Abstract] 
  40. Tsai MF, Wang CC, Chang GC, Chen CY, Chen HY, Cheng CL, Yang YP, Wu CY, Shih FY, Liu CC, Lin HP, Jou YS, Lin SC, Lin CW, Chen WJ, Chan WK, Chen JJ, Yang PC. (2006) A New Tumor Suppressor DnaJ-like Heat Shock Protein HLJ1 and Survival of Patients with Non-Small-Cell Lung Carcinoma. Journal of the National Cancer Institute 98: 825-838. (SCI)

Conference Papers

  1. 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. The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). January 21-23, 2015. HsinChu, Taiwan.
  2. Li W, Dai C, Liu CC, and Zhou XJ. (2012) Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling. The computational biology symposium at USC to celebrate the 70th birthday of Professor Michael Waterman and the 60th birthday of Simon Tavare. March 30th - April 1st, 2012. University of Southern California, Los Angeles, USA.
  3. Chun-Chi Liu, Jianjun Hu, Mrinal Kalakrishnan, Haiyan Huang, and Xianghong Jasmine Zhou. (2009) Integrative Disease Classification Based on Cross-platform Microarray Data. The Seventh Asia Pacific Bioinformatics Conference (APBC 2009). January 13-16, 2009. Beijing, China.
  4. Ruoming Jin, Scott McCallen, Chun-Chin Liu, Yang Xiang, Eivind Almaas, and Xianghong Jasmine Zhou. (2009) Identifying Dynamic Network Modules with Temporal and Spatial Constraints. Pacific Symposium on Biocomputing (PSB 2009). January 5-9, 2009. Big Island, Hawaii, USA.
  5. Rutu Mulkar-Mehta, Jerry R. Hobbs, Chun-Chi Liu, Xianghong Jasmine Zhou. (2009) Discovering Causal and Temporal Relations in Biomedical Texts. AAAI Spring Symposium 2009, Stanford, California, USA.
  6. Chun-Chi Liu, Wen-Shyen E. Chen, Pei-Chun Chang* and Jeremy J.W. Chen*. (2005)Topological-based Classification Using Artificial Gene Networks. The 4th IEEE International Conference on Cognitive Informatics (ICCI 2005). August 8-10, 2005. University of California, Irvine, USA.
  7. Chun-Chi Liu, Wen-Shyen E. Chen, Gwoboa Horng, Jeremy J.W. Chen*, and Pei-Chin Chang*. (2004) Prediction of Specific 70-mer Oligonucleotide with Neural Network Model. The 21st Workshop on Combinatorial Mathematics and Computational Theory, Taichung Healthcare and Management University.



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