Chao Cheng

Summary

Affiliation: Dartmouth Medical School
Country: USA

Publications

  1. pmc Applications of bioinformatics to non-coding rnas in the era of next-generation sequencing
    Chao Cheng
    Department of Genetics, Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
    Pac Symp Biocomput 19:412-6. 2014
  2. pmc Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs
    Chao Cheng
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
    PLoS Comput Biol 9:e1003132. 2013
  3. pmc Discovering chromatin motifs using FAIRE sequencing and the human diploid genome
    Chia Chun Yang
    Institute of Molecular Biology, National Chung Hsing University, Taiwan, ROC
    BMC Genomics 14:310. 2013
  4. pmc REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer
    Mingzhu Zhu
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
    BMC Genomics 14:504. 2013
  5. pmc Identification of yeast cell cycle regulated genes based on genomic features
    Chao Cheng
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
    BMC Syst Biol 7:70. 2013
  6. pmc Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
    Gavin D Grant
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
    Mol Biol Cell 24:3634-50. 2013
  7. pmc DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data
    David T W Tzeng
    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
    Nucleic Acids Res 42:D178-83. 2014

Collaborators

Detail Information

Publications7

  1. pmc Applications of bioinformatics to non-coding rnas in the era of next-generation sequencing
    Chao Cheng
    Department of Genetics, Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
    Pac Symp Biocomput 19:412-6. 2014
    ..The aim of this workshop is to bring together experimental and computational biologist to exchange ideas on non-coding RNA studies. ..
  2. pmc Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs
    Chao Cheng
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
    PLoS Comput Biol 9:e1003132. 2013
    ..The model we propose here provides not only a practical tool for identifying novel cell cycle genes with high accuracy, but also new insights on cell cycle regulation by TFs and cis-regulatory elements. ..
  3. pmc Discovering chromatin motifs using FAIRE sequencing and the human diploid genome
    Chia Chun Yang
    Institute of Molecular Biology, National Chung Hsing University, Taiwan, ROC
    BMC Genomics 14:310. 2013
    ..The gene regulatory elements are intrinsically dynamic and alternate between inactive and active states through the recruitment of DNA binding proteins, such as chromatin-remodeling proteins...
  4. pmc REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer
    Mingzhu Zhu
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
    BMC Genomics 14:504. 2013
    ..Gene expression data from microarray or RNA-seq experiments can capture the expression change of genes, however, it is still challenge to reveal the activity change of TFs...
  5. pmc Identification of yeast cell cycle regulated genes based on genomic features
    Chao Cheng
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
    BMC Syst Biol 7:70. 2013
    ..To complement microarray experiments, we propose a computational method to predict cell cycle regulated genes based on their genomic features - transcription factor binding and motif profiles...
  6. pmc Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors
    Gavin D Grant
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
    Mol Biol Cell 24:3634-50. 2013
    ..These data identify the cell cycle-regulated genes in a second cancer-derived cell line and provide a comprehensive picture of the transcriptional regulatory systems controlling periodic gene expression in the human cell division cycle. ..
  7. pmc DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data
    David T W Tzeng
    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
    Nucleic Acids Res 42:D178-83. 2014
    ....