Chao Cheng

Summary

Affiliation: Dartmouth Medical School
Country: USA

Publications

  1. pmc Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value
    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 14:332-43. 2016
  2. pmc 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
  3. 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
  4. 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
  5. 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 . 2014
  6. 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
  7. 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
  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 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
  10. 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

Publications28

  1. pmc Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value
    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 14:332-43. 2016
    ..A total of 259 gene sets were significantly associated with patient survival in liposarcoma, among which > 50% are involved in cell cycle and proliferation...
  2. pmc 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
    ....
  3. 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. ..
  4. 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...
  5. 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 . 2014
    ..The aim of this workshop is to bring together experimental and computational biologist to exchange ideas on non-coding RNA studies. ..
  6. 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. ..
  7. 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...
  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 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. ..
  10. 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
    ....
  11. 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...
  12. doi request reprint Systematic pan-cancer analysis reveals immune cell interactions in the tumor microenvironment
    Frederick S Varn
    Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth
    Cancer Res . 2017
    ..These results demonstrate the importance of personalized immune response profiles when studying the factors underlying tumor immunogenicity and immunotherapy response...
  13. 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...
  14. pmc 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. ..
  15. 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...
  16. 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. ..
  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 Integrative analysis of cancer genes in a functional interactome
    Matthew H Ung
    Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755 USA
    Sci Rep 6:29228. 2016
    ..In addition, our results align with current knowledge on the therapeutic actionability of GWAS and somatic mutant nodes, while demonstrating relationships between node classes from a global network perspective. ..
  19. pmc Adaptive immunity programmes in breast cancer
    Frederick S Varn
    Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
    Immunology 150:25-34. 2017
    ..Here, we review the literature pertaining to the adaptive immune response in breast cancer, summarize the primary findings relating to the breast tumour's biology, and discuss potential clinical immunotherapies...
  20. doi request reprint Application of pharmacologically induced transcriptomic profiles to interrogate PI3K-Akt-mTOR pathway activity associated with cancer patient prognosis
    Matthew H Ung
    Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755 USA
    Oncotarget 7:84142-84154. 2016
    ..With this approach, we predict prognosis and response to chemotherapy in cancer patients, and screen for potential pharmacological modulators of PI3K-Akt-mTOR pathway inhibitors...
  21. pmc In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics
    Matthew H Ung
    a Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
    Expert Opin Drug Discov 11:1213-1222. 2016
    ..Formal integration of these methodologies can accelerate and improve the efficiency of modern day anti-leukemic drug discovery and ease the economic and healthcare burden associated with it...
  22. pmc 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. ..
  23. pmc 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. ..
  24. pmc MYC Mediates mRNA Cap Methylation of Canonical Wnt/β-Catenin Signaling Transcripts By Recruiting CDK7 and RNA Methyltransferase
    Valeriya Posternak
    Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Lebanon, New Hampshire
    Mol Cancer Res . 2016
    ....
  25. pmc Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome
    Erik Andrews
    Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
    PLoS Comput Biol 13:e1005340. 2017
    ..We anticipate icTAIR will be of general use in contextually refining regulator target genes for discoveries across many contexts. The icTAIR algorithm can be downloaded from https://github.com/icTAIR...
  26. doi request reprint Insulin-mediated signaling facilitates resistance to PDGFR inhibition in proneural hPDGFB-driven gliomas
    Damian A Almiron Bonnin
    Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth
    Mol Cancer Ther . 2017
    ....
  27. 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...
  28. 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...