Chao Cheng

Summary

Affiliation: Dartmouth Medical School
Country: USA

Publications

  1. doi request reprint E2F4 Program Is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer
    Chao Cheng
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
    Mol Cancer Res 13:1316-24. 2015
  2. pmc An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome
    Chao Cheng
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
    Genome Biol 16:63. 2015
  3. pmc Relating gene expression evolution with CpG content changes
    Huan Yang
    HB7400, Remsen 702, Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
    BMC Genomics 15:693. 2014
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. pmc Integrative analysis of survival-associated gene sets in breast cancer
    Frederick S Varn
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755, USA
    BMC Med Genomics 8:11. 2015
  10. pmc Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders
    Jie Tan
    Department of Genetics, Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
    Pac Symp Biocomput 20:132-43. 2015

Collaborators

Detail Information

Publications19

  1. doi request reprint E2F4 Program Is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer
    Chao Cheng
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
    Mol Cancer Res 13:1316-24. 2015
    ....
  2. pmc An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome
    Chao Cheng
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
    Genome Biol 16:63. 2015
    ..We also compare it to the regulatory network, finding that the phosphorylome is more hierarchical than the regulome. ..
  3. pmc Relating gene expression evolution with CpG content changes
    Huan Yang
    HB7400, Remsen 702, Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
    BMC Genomics 15:693. 2014
    ..Here we calculate the normalized CpG (nCpG) content in DNA regions around transcription start site (TSS) and transcription terminal site (TTS) of genes in nine organisms, and relate them with expression levels measured by RNA-seq...
  4. 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. ..
  5. 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. ..
  6. 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...
  7. 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...
  8. 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...
  9. pmc Integrative analysis of survival-associated gene sets in breast cancer
    Frederick S Varn
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755, USA
    BMC Med Genomics 8:11. 2015
    ..Identifying robust gene sets that are consistently predictive of a patient's clinical outcome has become one of the main challenges in the field...
  10. pmc Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders
    Jie Tan
    Department of Genetics, Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
    Pac Symp Biocomput 20:132-43. 2015
    ..In summary, we demonstrate that DAs effectively extract key biological principles from gene expression data and summarize them into constructed features with convenient properties. ..
  11. 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
    ....
  12. 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. ..
  13. doi request reprint Regulators associated with clinical outcomes revealed by DNA methylation data in breast cancer
    Matthew H Ung
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
    PLoS Comput Biol 11:e1004269. 2015
    ..Overall, this study provides a comprehensive analysis that links DNA methylation to TF binding to patient prognosis. ..
  14. doi request reprint Systematic analysis of hematopoietic gene expression profiles for prognostic prediction in acute myeloid leukemia
    Frederick S Varn
    Department of Genetics, Geisel School of Medicine at Dartmouth, 1 Rope Ferry Road, Hanover, New Hampshire 03755, USA
    Sci Rep 5:16987. 2015
    ..Finally, we validated our use of murine profiles by demonstrating similar results when applying our method to human profiles. ..
  15. doi request reprint Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles
    Frederick S Varn
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
    Nat Commun 7:10248. 2016
    ..When combined with routinely collected patient biopsy genomic data, this method can enable a richer understanding of the complex interplay between the host immune system and cancer. ..
  16. pmc E2F4 regulatory program predicts patient survival prognosis in breast cancer
    Sari S Khaleel
    Department of Genetics, Geisel School of Medicine at Dartmouth, 1 Rope Ferry Road, Hanover, NH, 03755, USA
    Breast Cancer Res 16:486. 2014
    ..A molecular signature that is prognostic across more clinical contexts would be a useful addition to current signatures...
  17. doi request reprint Integrative analysis of survival-associated gene sets in breast cancer
    Frederick S Varn
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755, USA
    BMC Med Genomics 8:86. 2015
    ..Identifying robust gene sets that are consistently predictive of a patient's clinical outcome has become one of the main challenges in the field...
  18. pmc p53 and ΔNp63α Coregulate the Transcriptional and Cellular Response to TGFβ and BMP Signals
    Amanda L Balboni
    Program in Experimental and Molecular Medicine, The Audrey and Theodor Geisel School of Medicine at Dartmouth, Hanover, New Hampshire Department of Pharmacology and Toxicology, The Audrey and Theodor Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
    Mol Cancer Res 13:732-42. 2015
    ..Collectively, these results establish an integrated gene network of SMADs, p53, and ΔNp63α that contribute to EMT and metastasis...
  19. doi request reprint Big data bioinformatics
    Casey S Greene
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
    J Cell Physiol 229:1896-900. 2014
    ..In addition to programming based solutions, we review webservers that allow users with limited or no programming background to perform these analyses on large data compendia...