Chun-Chi Liu

Chun-Chi Liu

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Chun-Chi Liu

Chun-Chi Liu

Publications by authors named "Chun-Chi Liu"

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38Publications

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CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data.

Nucleic Acids Res 2018 Sep;46(15):e89

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.

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September 2018

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

BMC Genomics 2018 01 19;19(Suppl 1):958. Epub 2018 Jan 19.

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.

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January 2018

Improved n-butanol production via co-expression of membrane-targeted tilapia metallothionein and the clostridial metabolic pathway in Escherichia coli.

BMC Biotechnol 2017 04 11;17(1):36. Epub 2017 Apr 11.

Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.

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April 2017

Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data.

BMC Genomics 2017 01 10;18(1):61. Epub 2017 Jan 10.

Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.

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January 2017

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

BMC Genomics 2016 08 12;17(1):632. Epub 2016 Aug 12.

Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.

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August 2016

Integrative analysis of cancer genes in a functional interactome.

Sci Rep 2016 06 30;6:29228. Epub 2016 Jun 30.

Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755 USA.

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June 2016

Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level.

Methods 2016 Jan 31;93:110-8. Epub 2015 Jul 31.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. Electronic address:

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January 2016

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

Nucleic Acids Res 2016 Jan 7;44(D1):D209-15. Epub 2015 Oct 7.

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan

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January 2016

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

Nucleic Acids Res 2016 Jan 20;44(D1):D239-47. Epub 2015 Nov 20.

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan

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January 2016

Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells.

Nucleic Acids Res 2016 Jan 23;44(D1):D944-51. Epub 2015 Nov 23.

Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan PhD Program in Medical Biotechnology National Chung Hsing University, Taichung 402, Taiwan

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January 2016

Molecular recognition of CYP26A1 binding pockets and structure-activity relationship studies for design of potent and selective retinoic acid metabolism blocking agents.

J Mol Graph Model 2015 Mar 8;56:10-9. Epub 2014 Dec 8.

Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, PR China. Electronic address:

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March 2015

DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.

Nucleic Acids Res 2015 Jan 7;43(2):1268-82. Epub 2015 Jan 7.

Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA

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January 2015

DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.

Nucleic Acids Res 2014 Jul 3;42(Web Server issue):W137-46. Epub 2014 Jun 3.

Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA

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July 2014

High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method.

Nucleic Acids Res 2014 Apr 25;42(6):e39. Epub 2013 Dec 25.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan 40227, Republic of China, National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China and Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA.

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April 2014

DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data.

Nucleic Acids Res 2014 Jan 2;42(Database issue):D178-83. Epub 2013 Dec 2.

Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan, Department of Computer Science and Engineering, National Chung Hsing University, Taichung 402, Taiwan, Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA and Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.

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January 2014

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

Nucleic Acids Res 2014 Jan 4;42(Database issue):D78-85. Epub 2013 Dec 4.

Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan, Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan, Department of Computer Science and Engineering, National Chung Hsing University, Taichung 402, Taiwan, Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, Molecular Bioinformatics Center, National Chiao Tung University, Hsinchu 300, Taiwan, Graduate Department of Clinical Pharmacy, Taipei Medical University, Taipei 110, Taiwan, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan, Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 110, Taiwan, Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu 300, Taiwan, Mackay Medicine, Nursing and Management College, Taipei 112, Taiwan, Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.

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January 2014

REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer.

BMC Genomics 2013 Jul 26;14:504. Epub 2013 Jul 26.

Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA.

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July 2013

Discovering chromatin motifs using FAIRE sequencing and the human diploid genome.

BMC Genomics 2013 May 8;14:310. Epub 2013 May 8.

Institute of Molecular Biology, National Chung Hsing University, Taiwan, ROC.

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May 2013

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.

Bioinformatics 2012 Oct 3;28(19):2458-66. Epub 2012 Aug 3.

Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

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October 2012

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.

Nucleic Acids Res 2012 Oct 8;40(19):9379-91. Epub 2012 Aug 8.

Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

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October 2012

Identification and characterization of an RTX toxin-like gene and its operon from Avibacterium paragallinarum.

Avian Dis 2012 Sep;56(3):537-44

Graduate Institute of Microbiology and Public Health, National Chung Hsing University, Taichung 402, Taiwan.

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September 2012

Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling.

J Comput Biol 2012 Jun;19(6):710-30

Program in Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

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June 2012

Polycomb-repressed genes have permissive enhancers that initiate reprogramming.

Cell 2011 Dec;147(6):1283-94

Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

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December 2011

Integrative analysis of many weighted co-expression networks using tensor computation.

PLoS Comput Biol 2011 Jun 16;7(6):e1001106. Epub 2011 Jun 16.

Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.

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June 2011

Bayesian approach to transforming public gene expression repositories into disease diagnosis databases.

Proc Natl Acad Sci U S A 2010 Apr 1;107(15):6823-8. Epub 2010 Apr 1.

Department of Statistics, University of California, Berkeley, CA 94720, USA.

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April 2010

Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation.

PLoS One 2010 Feb 1;5(2):e8898. Epub 2010 Feb 1.

Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.

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February 2010

Identifying dynamic network modules with temporal and spatial constraints.

Pac Symp Biocomput 2009 :203-14

Department of Computer Science, Kent State University, Kent, OH, USA.

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March 2009

The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2.

Cancer Res 2009 Mar 3;69(6):2623-9. Epub 2009 Mar 3.

Department of Urology, Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.

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March 2009

Integrative disease classification based on cross-platform microarray data.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S25. Epub 2009 Jan 30.

Molecular and Computational Biology, University of Southern California, CA, USA.

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January 2009

Anticancer effects of tanshinone I in human non-small cell lung cancer.

Mol Cancer Ther 2008 Nov;7(11):3527-38

Institutes of Biomedical Sciences and Molecular Biology, National Chung-Hsing University, Taichung, Taiwan 40227, Republic of China.

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November 2008

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

BMC Bioinformatics 2007 May 22;8:164. Epub 2007 May 22.

Department of Computer Science, National Chung-Hsing University, Taichung, Taiwan, ROC.

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May 2007

Topology-based cancer classification and related pathway mining using microarray data.

Nucleic Acids Res 2006 16;34(14):4069-80. Epub 2006 Aug 16.

Department of Computer Science, National Chung-Hsing University, Taichung, Taiwan, ROC.

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September 2006

CRSD: a comprehensive web server for composite regulatory signature discovery.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W571-7

Department of Computer Science, National Chung-Hsing University, Taichung, Taiwan, ROC.

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July 2006