Chun-Chi Liu

发表

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

P. Laird, Shihua Zhang, Chun-Chi Liu, 2012, Nucleic acids research.

Joint Genome-Wide Profiling of miRNA and mRNA Expression in Alzheimer's Disease Cortex Reveals Altered miRNA Regulation

Juan Nunez-Iglesias, Chun-Chi Liu, X. Zhou, 2010, PloS one.

Integrative disease classification based on cross-platform microarray data

Jianjun Hu, Mrinal Kalakrishnan, Chun-Chi Liu, 2009, BMC Bioinformatics.

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

Jeremy J. W. Chen, Chun-Chi Liu, Chih-Yi Chen, 2007, The New England journal of medicine.

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

Jeremy J. W. Chen, Chun-Chi Liu, Hsuan-Yu Chen, 2006, Nucleic acids research.

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

Shuli Kang, Chun-Chi Liu, Wenyuan Li, 2016, Methods.

MicroRNA signature predicts survival and relapse in lung cancer.

Sung-Liang Yu, Ching-Cheng Chiang, Ker-Chau Li, 2008, Cancer cell.

A new tumor suppressor DnaJ-like heat shock protein, HLJ1, and survival of patients with non-small-cell lung carcinoma.

Yuh-Shan Jou, Chun-Yi Wu, Wei J Chen, 2006, Journal of the National Cancer Institute.

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

Jianrong Li, Chun-Chi Liu, Wenyuan Li, 2015, Nucleic Acids Res..

IdentifyingMulti -LayerGeneRegula toryModulesfrom Multi-Dimensiona lGenomicData

Shihua Zhang, Chun-Chi Liu, X. Zhou, 2012 .

Identifyin gMulti-Layer Gen eRegulator yModule sfrom Multi-Dimensiona lGenomi cData

Shihua Zhang, Chun-Chi Liu, Wenyuan Li, 2012 .

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

Jeremy J. W. Chen, Chun-Chi Liu, Pan‐Chyr Yang, 2008, Molecular Cancer Therapeutics.

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

Jeremy J. W. Chen, Chun-Chi Liu, Chao Cheng, 2017, BMC Genomics.

Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation

Haifeng Li, Tong Zhang, Chun-Chi Liu, 2011, PLoS Comput. Biol..

Prediction of Specific 70-mer Oligonucleotide with Neural Network Model

Jeremy J. W. Chen, Chun-Chi Liu, Wen-Shyen E. Chen, 2006 .

Integrative analysis of cancer genes in a functional interactome

Chun-Chi Liu, Chao Cheng, M. Ung, 2016, Scientific Reports.

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

Andrey Rzhetsky, Chun-Chi Liu, Fengzhu Sun, 2014, Nucleic Acids Res..

Identifying Dynamic Network Modules with Temporal and Spatial Constraints

Yang Xiang, Ruoming Jin, Eivind Almaas, 2007, Pacific Symposium on Biocomputing.

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

Lee E. Edsall, Celso A. Espinoza, S. Grant, 2015, Nucleic acids research.

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

Hsien-Da Huang, Wen-Lian Hsu, Yu-Ling Lin, 2015, Nucleic Acids Res..

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

Hsien-Da Huang, Jianrong Li, Sheng-Da Hsu, 2015, Nucleic Acids Res..

Discovering chromatin motifs using FAIRE sequencing and the human diploid genome

Jeremy J. W. Chen, Chun-Chi Liu, Chao Cheng, 2013, BMC Genomics.

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

Hsien-Da Huang, Yu-Ling Lin, I-En Liao, 2013, Nucleic Acids Res..

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

Chun-Chi Liu, Chao Cheng, Mingzhu Zhu, 2013, BMC Genomics.

Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling

Chao Dai, Chun-Chi Liu, Wenyuan Li, 2012, J. Comput. Biol..

Topological-based classification using artificial gene networks

Pei-Chun Chang, Chun-Chi Liu, Wen-Shyen E. Chen, 2005, Fourth IEEE Conference on Cognitive Informatics, 2005. (ICCI 2005)..

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

Frank Alber, Wing Hung Wong, Xianghong Jasmine Zhou, 2018, Nucleic acids research.

IIIDB: a database for isoform-isoform interactions and isoform network modules

Shi-Hua Zhang, Chun-Chi Liu, Wenyuan Li, 2015, BMC Genomics.

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

Yan Liu, Xianghong Jasmine Zhou, Shihua Zhang, 2013, Nucleic acids research.

CRSD: a comprehensive web server for composite regulatory signature discovery

Pei-Chun Chang, Chun-Chi Liu, Wen-Shyen E. Chen, 2006, Nucleic Acids Res..

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

Shi-Hua Zhang, Chun-Chi Liu, Wenyuan Li, 2012, Bioinform..

CMEP: a database for circulating microRNA expression profiling

Chun-Chi Liu, Xianghong Jasmine Zhou, Jian-Rong Li, 2019, Bioinform..

cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA

Chun-Chi Liu, Wenyuan Li, X. Zhou, 2023, Nature Protocols.

Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer

C. Lajonchere, Fengzhu Sun, S. Dry, 2022, Nature Communications.

RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

Chun-Chi Liu, Wei-Ting Liu, Chih-Wen Wu, 2016, Database J. Biol. Databases Curation.

Optimal ranking in multi-label classification using local precision rates

Chun-Chi Liu, Ci-Ren Jiang, Xianghong Jasmine Zhou, 2014 .

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

Chun-Chi Liu, Xianghong Jasmine Zhou, Haiyan Huang, 2010, Proceedings of the National Academy of Sciences.

Discovering Causal and Temporal Relations in Biomedical Texts

Jerry R. Hobbs, Chun-Chi Liu, Rutu Mulkar-Mehta, 2009, AAAI Spring Symposium: Learning by Reading and Learning to Read.

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

Haiyan Huang, Chun-Chi Liu, X. Zhou, 2010, Proceedings of the National Academy of Sciences of the United States of America.

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

Shuli Kang, Chun-Chi Liu, Wenyuan Li, 2016, Methods.

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

I-En Liao, Chun-Chi Liu, Chao Cheng, 2013, Nucleic Acids Res..

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

Chao Cheng, Chun-Chi Liu, Chun-Chi Liu, 2013, BMC Genomics.

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

Jeremy J. W. Chen, M. Gerstein, Chun-Chi Liu, 2016, BMC Genomics.