Chun-Chi Liu

Chun-Chi Liu

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Chun-Chi Liu

Publications by authors named "Chun-Chi Liu"

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CMEP: a database for circulating microRNA expression profiling.

Bioinformatics 2019 Sep;35(17):3127-3132

Institute of Genomics and Bioinformatics.

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http://dx.doi.org/10.1093/bioinformatics/btz042DOI Listing
September 2019

Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells.

BMC Genomics 2018 Dec 27;19(1):966. Epub 2018 Dec 27.

Program in Medical Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist, Taichung City, 402, Taiwan.

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http://dx.doi.org/10.1186/s12864-018-5367-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307140PMC
December 2018

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

Nucleic Acids Res 2018 09;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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http://dx.doi.org/10.1093/nar/gky423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125664PMC
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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http://dx.doi.org/10.1186/s12864-017-4335-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780853PMC
January 2018

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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http://dx.doi.org/10.1186/s12864-016-3450-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223348PMC
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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http://dx.doi.org/10.1186/s12864-016-2963-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983039PMC
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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http://dx.doi.org/10.1038/srep29228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928112PMC
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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http://dx.doi.org/10.1016/j.ymeth.2015.07.016DOI Listing
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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http://dx.doi.org/10.1093/nar/gkv940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702939PMC
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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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv1258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702890PMC
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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http://dx.doi.org/10.1093/nar/gkv1282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702907PMC
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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https://linkinghub.elsevier.com/retrieve/pii/S10933263140020
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http://dx.doi.org/10.1016/j.jmgm.2014.11.014DOI Listing
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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http://dx.doi.org/10.1093/nar/gku1373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333414PMC
January 2015

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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http://dx.doi.org/10.1093/nar/gkt1362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973446PMC
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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http://dx.doi.org/10.1093/nar/gkt1254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965116PMC
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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http://dx.doi.org/10.1093/nar/gkt1266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965058PMC
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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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-14-504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750236PMC
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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http://dx.doi.org/10.1186/1471-2164-14-310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655836PMC
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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http://dx.doi.org/10.1093/bioinformatics/bts476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463121PMC
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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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gks725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479191PMC
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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http://dx.doi.org/10.1637/10047-122211-Reg.1DOI Listing
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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http://www.liebertpub.com/doi/10.1089/cmb.2012.0025
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http://dx.doi.org/10.1089/cmb.2012.0025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375651PMC
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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http://dx.doi.org/10.1016/j.cell.2011.10.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240866PMC
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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http://dx.plos.org/10.1371/journal.pcbi.1001106
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http://dx.doi.org/10.1371/journal.pcbi.1001106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116899PMC
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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http://www.pnas.org/cgi/doi/10.1073/pnas.0912043107
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http://dx.doi.org/10.1073/pnas.0912043107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872390PMC
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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008898PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813862PMC
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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http://dx.doi.org/10.1158/0008-5472.CAN-08-3114DOI Listing
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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http://dx.doi.org/10.1186/1471-2105-10-S1-S25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648756PMC
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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http://dx.doi.org/10.1158/1535-7163.MCT-07-2288DOI Listing
November 2008

MicroRNA signature predicts survival and relapse in lung cancer.

Cancer Cell 2008 Jan;13(1):48-57

Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan 100, Republic of China.

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http://dx.doi.org/10.1016/j.ccr.2007.12.008DOI Listing
January 2008

A five-gene signature and clinical outcome in non-small-cell lung cancer.

N Engl J Med 2007 Jan;356(1):11-20

National Taiwan University College of Public Health, National Taiwan University College of Medicine, Taipei, Taiwan.

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http://dx.doi.org/10.1056/NEJMoa060096DOI Listing
January 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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http://dx.doi.org/10.1093/nar/gkl583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557825PMC
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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http://dx.doi.org/10.1093/nar/gkl279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538777PMC
July 2006