Andrew E Teschendorff

Summary

Affiliation: University College London
Country: UK

Publications

  1. doi request reprint Phenotypic and functional characterisation of the luminal cell hierarchy of the mammary gland.
    Mona Shehata
    Breast Cancer Res 14:R134. 2012
  2. doi request reprint ChAMP: Updated Methylation Analysis Pipeline for Illumina BeadChips
    Yuan Tian
    CAS Key Lab of Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
    Bioinformatics . 2017
  3. pmc The multi-omic landscape of transcription factor inactivation in cancer
    Andrew E Teschendorff
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
    Genome Med 8:89. 2016
  4. pmc Stochastic epigenetic outliers can define field defects in cancer
    Andrew E Teschendorff
    CAS Key Lab of Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    BMC Bioinformatics 17:178. 2016
  5. pmc HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer
    Andrew E Teschendorff
    Statistical Genomics Group, UCL Cancer Institute, University College London, London, UK
    Genome Med 7:108. 2015
  6. doi request reprint Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data
    Andrew E Teschendorff
    CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai 200031, China Statistical Cancer Genomics, Paul O Gorman Building, UCL Cancer Institute, University College London, London WC1E 6BT, UK Electronic address
    Methods 67:282-93. 2014
  7. doi request reprint Epigenetic aging: insights from network biology.
    Andrew E Teschendorff
    Statistical Cancer Genomics, UCL Cancer Institute
    Aging (Albany NY) 5:719-20. 2013
  8. doi request reprint Age-associated epigenetic drift: implications, and a case of epigenetic thrift?
    Andrew E Teschendorff
    Hum Mol Genet 22:R7-R15. 2013
  9. pmc A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
    Andrew E Teschendorff
    Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Bioinformatics 29:189-96. 2013
  10. pmc Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation
    Andrew E Teschendorff
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    Genome Med 4:24. 2012

Detail Information

Publications60

  1. doi request reprint Phenotypic and functional characterisation of the luminal cell hierarchy of the mammary gland.
    Mona Shehata
    Breast Cancer Res 14:R134. 2012
    ..An understanding of these cells will be essential for understanding the origins and the cellular context of human breast tumours...
  2. doi request reprint ChAMP: Updated Methylation Analysis Pipeline for Illumina BeadChips
    Yuan Tian
    CAS Key Lab of Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
    Bioinformatics . 2017
    ..Many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis, and a series of interactive graphical user interfaces...
  3. pmc The multi-omic landscape of transcription factor inactivation in cancer
    Andrew E Teschendorff
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
    Genome Med 8:89. 2016
    ..However, the biological significance of this observation for carcinogenesis is unclear given that most of these transcription factors are not expressed in any given normal tissue...
  4. pmc Stochastic epigenetic outliers can define field defects in cancer
    Andrew E Teschendorff
    CAS Key Lab of Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    BMC Bioinformatics 17:178. 2016
    ....
  5. pmc HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer
    Andrew E Teschendorff
    Statistical Genomics Group, UCL Cancer Institute, University College London, London, UK
    Genome Med 7:108. 2015
    ..Long non-coding RNA HOTAIR (HOX transcript antisense intergenic RNA) is involved in mesenchymal stem cell fate and cancer biology...
  6. doi request reprint Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data
    Andrew E Teschendorff
    CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai 200031, China Statistical Cancer Genomics, Paul O Gorman Building, UCL Cancer Institute, University College London, London WC1E 6BT, UK Electronic address
    Methods 67:282-93. 2014
    ....
  7. doi request reprint Epigenetic aging: insights from network biology.
    Andrew E Teschendorff
    Statistical Cancer Genomics, UCL Cancer Institute
    Aging (Albany NY) 5:719-20. 2013
  8. doi request reprint Age-associated epigenetic drift: implications, and a case of epigenetic thrift?
    Andrew E Teschendorff
    Hum Mol Genet 22:R7-R15. 2013
    ....
  9. pmc A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
    Andrew E Teschendorff
    Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Bioinformatics 29:189-96. 2013
    ..A key statistical issue is therefore how best to adjust for the two different probe designs...
  10. pmc Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation
    Andrew E Teschendorff
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    Genome Med 4:24. 2012
    ..We aimed to demonstrate that epigenetic changes in normal cells, collected years in advance of the first signs of morphological transformation, can predict the risk of such transformation...
  11. doi request reprint Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions
    Andrew E Teschendorff
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London, UK
    Bioinformatics 28:1487-94. 2012
    ....
  12. pmc An epigenetic signature in peripheral blood predicts active ovarian cancer
    Andrew E Teschendorff
    Medical Genomics Group, University College London Cancer Institute, University College London, London, United Kingdom
    PLoS ONE 4:e8274. 2009
    ..However, to date no study has evaluated the diagnostic and predictive potential of such markers in a large case control cohort and on a genome-wide basis...
  13. pmc Increased entropy of signal transduction in the cancer metastasis phenotype
    Andrew E Teschendorff
    Medical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    BMC Syst Biol 4:104. 2010
    ..However, relatively little is known as to what network features differ between the cancer and normal cell physiologies, or between different cancer cell phenotypes...
  14. pmc Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Department of Oncology University of Cambridge, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    BMC Cancer 10:604. 2010
    ..However, relatively few strategies for estimating pathway activity from such model signatures exist and only few studies have used activation patterns of pathways to refine molecular classifications of cancer...
  15. pmc Prognostic gene network modules in breast cancer hold promise
    Andrew E Teschendorff
    Medical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Breast Cancer Res 12:317. 2010
    ..We envisage that further improvements and insights may come from integrative expression pathway analyses that dissect prognostic signatures into modules related to cancer hallmarks...
  16. doi request reprint Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies
    Andrew E Teschendorff
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, London WC1E 6BT, UK
    Bioinformatics 27:1496-505. 2011
    ..To deal with these difficulties, an algorithmic framework known as Surrogate Variable Analysis (SVA) was recently proposed...
  17. pmc An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways
    James West
    Statistical Cancer Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    Sci Rep 3:1630. 2013
    ..The proposed algorithm will be useful to any study seeking to identify interactome hotspots associated with common phenotypes...
  18. pmc A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform
    Joanna Zhuang
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    BMC Bioinformatics 13:59. 2012
    ....
  19. pmc Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer
    Andrew E Teschendorff
    University College London, London WC1E 6BT, UK
    Genome Res 20:440-6. 2010
    ..These findings shed substantial novel insights into the epigenetic effects of aging and support the view that age may predispose to malignant transformation by irreversibly stabilizing stem cell features...
  20. pmc High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
    Suet F Chin
    Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R215. 2007
    ..To date, most genome-wide array comparative genomic hybridization studies have used tumor panels of relatively large tumor size and high Nottingham Prognostic Index (NPI) that are not as representative of breast cancer demographics...
  21. pmc The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer
    Joanna Zhuang
    Department of Women s Cancer, University College London Elizabeth Garrett Anderson Institute for Women s Health, London, UK
    PLoS Genet 8:e1002517. 2012
    ..These findings have major implications for cancer and embryonic stem cell biology and establish the importance of systemic DNA hypomethylation for predicting prognosis in a wide range of different cancers...
  22. pmc Cellular network entropy as the energy potential in Waddington's differentiation landscape
    Christopher R S Banerji
    1 Statistical Cancer Genomics, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom 2 Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E6BT United Kingdom
    Sci Rep 3:3039. 2013
    ..In summary, network entropy provides a quantitative measure of a cell's undifferentiated state, defining its elevation in Waddington's landscape. ..
  23. pmc Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
    Andrew Feber
    Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    Genome Res 21:515-24. 2011
    ..This study establishes MeDIP-seq as an effective method to analyze cancer methylomes...
  24. pmc Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus
    Christopher G Bell
    Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    PLoS ONE 5:e14040. 2010
    ....
  25. pmc Correlation of an epigenetic mitotic clock with cancer risk
    Zhen Yang
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
    Genome Biol 17:205. 2016
    ..To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk...
  26. pmc Role of DNA methylation and epigenetic silencing of HAND2 in endometrial cancer development
    Allison Jones
    Department of Women s Cancer, UCL Elizabeth Garrett Anderson Institute for Women s Health, University College London, London, United Kingdom
    PLoS Med 10:e1001551. 2013
    ..The objective of this study was to determine the functional role of epigenetic factors in endometrial cancer development...
  27. pmc Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus
    Christopher G Bell
    Medical Genomics, UCL Cancer Institute, University College London, London, UK
    BMC Med Genomics 3:33. 2010
    ..Cases had T1D and nephropathy whereas controls had T1D but no evidence of renal disease...
  28. pmc A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancer
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, CB2 0RE, UK
    Breast Cancer Res 10:R73. 2008
    ..However, identification of such patients with a good prognosis remains difficult and at present is only possible through examining histopathological factors...
  29. pmc Elucidating the altered transcriptional programs in breast cancer using independent component analysis
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, United Kingdom
    PLoS Comput Biol 3:e161. 2007
    ..Adopting ICA as the analysis tool of choice will help understand the phenotype-pathway relationship and thus help elucidate the molecular taxonomy of heterogeneous cancers and of other complex genetic diseases...
  30. doi request reprint Correlation of Smoking-Associated DNA Methylation Changes in Buccal Cells With DNA Methylation Changes in Epithelial Cancer
    Andrew E Teschendorff
    Statistical Genomics Group at the University College London Cancer Institute, London, United Kingdom2CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biol
    JAMA Oncol 1:476-85. 2015
    ..Given the direct exposure of buccal cells to potent carcinogens such as smoke, epigenetic changes in these cells may provide insights into the development of smoke-related cancers...
  31. pmc DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference
    Yan Jiao
    Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    BMC Bioinformatics 12:403. 2011
    ..g protein interaction networks) or more generally with prior knowledge pathway databases. However, it is unclear how best to use the pathway knowledge information in the context of molecular profiles of any given study...
  32. pmc ChAMP: 450k Chip Analysis Methylation Pipeline
    Tiffany J Morris
    Medical Genomics, and Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden
    Bioinformatics 30:428-30. 2014
    ..Here we present an integrated analysis pipeline offering a choice of the most popular normalization methods while also introducing new methods for calling differentially methylated regions and detecting copy number aberrations...
  33. pmc Corruption of the intra-gene DNA methylation architecture is a hallmark of cancer
    Thomas E Bartlett
    CoMPLEX, University College London, London, United Kingdom
    PLoS ONE 8:e68285. 2013
    ..Our findings strongly support the view that intra-gene methylation architecture has great clinical potential for the development of DNA-based cancer biomarkers...
  34. pmc Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
    Caryn S Ross-Innes
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Nature 481:389-93. 2012
    ..By establishing transcription-factor mapping in primary tumour material, we show that there is plasticity in ER-binding capacity, with distinct combinations of cis-regulatory elements linked with the different clinical outcomes...
  35. pmc An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer
    Andrew E Teschendorff
    Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R157. 2007
    ..Reliable identification of ER-negative tumors that have a good prognosis is not yet possible...
  36. ncbi request reprint PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
    Andrew E Teschendorff
    Cancer Genomics Program, Department of Oncology University of Cambridge, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK
    Bioinformatics 22:2269-75. 2006
    ..Feature selection methods that can identify relevant classifiers or that can remove likely false positives prior to supervised analysis are therefore desirable...
  37. pmc Increased signaling entropy in cancer requires the scale-free property of protein interaction networks
    Andrew E Teschendorff
    1 Statistical Cancer Genomics, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom 2 CAS Key Lab for Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
    Sci Rep 5:9646. 2015
    ..In summary, this work exposes a deep connection between cancer, signaling entropy and interaction network topology. ..
  38. pmc Differential network entropy reveals cancer system hallmarks
    James West
    Statistical Cancer Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    Sci Rep 2:802. 2012
    ..These findings may have potential implications for identifying novel drug targets...
  39. pmc Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2
    Paul Guilhamon
    Medical Genomics, UCL Cancer Institute, University College London, London, UK
    Nat Commun 4:2166. 2013
    ....
  40. pmc MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype
    Cherie Blenkiron
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R214. 2007
    ..MicroRNAs (miRNAs), a class of short non-coding RNAs found in many plants and animals, often act post-transcriptionally to inhibit gene expression...
  41. pmc Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer
    Kerstin B Meyer
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom
    PLoS Biol 6:e108. 2008
    ..We propose a model in which the Oct-1/Runx2 and C/EBPbeta binding sites in the disease-associated allele are able to lead to an increase in FGFR2 gene expression, thereby increasing the propensity for tumour formation...
  42. doi request reprint Epigenetics makes its mark on women-specific cancers--an opportunity to redefine oncological approaches?
    Martin Widschwendter
    Department of Women s Cancer, UCL Elizabeth Garrett Anderson Institute for Women s Health, University College London, UK
    Gynecol Oncol 128:134-43. 2013
    ..This review focuses attention on DNA methylation-a core epigenetic mechanism that can be readily detected in body fluids and has the potential to substantially reform cancer screening and treatment...
  43. pmc The breast cancer somatic 'muta-ome': tackling the complexity
    Andrew E Teschendorff
    Medical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, London, UK
    Breast Cancer Res 11:301. 2009
    ....
  44. pmc An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer
    Zhen Yang
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
    Genome Biol 16:140. 2015
    ..Little is known, however, as to whether these genes exhibit patterns of epigenomic deregulation that transcend cancer types...
  45. pmc Intra-tumour signalling entropy determines clinical outcome in breast and lung cancer
    Christopher R S Banerji
    Statistical Cancer Genomics, Paul O Gorman Building, UCL Cancer Institute, University College London, London WC1E 6BT, UK Department of Computer Science, University College London, London WC1E 6BT, UK Centre of Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E 6BT, UK
    PLoS Comput Biol 11:e1004115. 2015
    ..In summary, by approximating both stemness and intra-tumour heterogeneity, signalling entropy provides a powerful prognostic measure across different epithelial cancers. ..
  46. ncbi request reprint Network transfer entropy and metric space for causality inference
    Christopher R S Banerji
    Department of Computer Science, University College London, London WC1E 6BT, United Kingdom
    Phys Rev E Stat Nonlin Soft Matter Phys 87:052814. 2013
    ....
  47. pmc Distinctive topology of age-associated epigenetic drift in the human interactome
    James West
    Statistical Cancer Genomics, University College London Cancer Institute, University College London, London WC1E 6BT, United Kingdom
    Proc Natl Acad Sci U S A 110:14138-43. 2013
    ..Thus, these results point toward a potentially distinct mechanistic and biological role of DNA methylation in dictating the complex aging and disease phenotypes. ..
  48. pmc Comments on: Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed paraffin-embedded paired tumor and normal tissue
    Christina Thirlwell
    Medical Genomics Laboratory, UCL Cancer Institute, 72, Huntley Street, London WC1E 6BT, UK
    BMC Res Notes 5:631. 2012
    ..Moreover, we continue to analyse genome-wide methylation data from DNA extracted from FFPE tissue successfully on both the HumMeth27 and 450 K arrays...
  49. pmc Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer
    Yuting Chen
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049 People s Republic of China
    Epigenetics Chromatin 9:10. 2016
    ..In addition, it is unknown which factors determine the patterns of aberrant DNA methylation in cancer...
  50. doi request reprint Epigenetic drift, epigenetic clocks and cancer risk
    Shijie C Zheng
    CAS Key Lab of Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Epigenomics 8:705-19. 2016
    ....
  51. pmc DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer
    Andrew E Teschendorff
    Department of Women s Cancer, University College London, Medical School Building, Room 340, 74 Huntley Street, London WC1E 6AU, UK
    Nat Commun 7:10478. 2016
    ..Our data support a model where clonal epigenetic reprogramming towards reduced differentiation in normal tissue is an important step in breast carcinogenesis. ..
  52. pmc An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging
    Tian Yuan
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai, China
    PLoS Genet 11:e1004996. 2015
    ..Integration of Illumina 450k with appropriate ENCODE data may represent a fruitful approach to identify transcription factors with key roles in aging and disease. ..
  53. pmc The dynamics of DNA methylation covariation patterns in carcinogenesis
    Andrew E Teschendorff
    CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai, China Statistical Genomics Group, UCL Cancer Institute, University College London, London, United Kingdom
    PLoS Comput Biol 10:e1003709. 2014
    ..The model and algorithm proposed here may allow, in future, network biomarkers predicting the risk of neoplastic transformation to be identified. ..
  54. pmc Expression profiling of nuclear receptors in breast cancer identifies TLX as a mediator of growth and invasion in triple-negative breast cancer
    Meng Lay Lin
    Department of Surgery and Cancer, Imperial College London, London, UK
    Oncotarget 6:21685-703. 2015
    ..Functional studies demonstrated the importance of TLX in regulating growth and invasion in ERα-negative breast cancer cells. ..
  55. pmc Denoising perturbation signatures reveal an actionable AKT-signaling gene module underlying a poor clinical outcome in endocrine-treated ER+ breast cancer
    Andrew E Teschendorff
    CAS Key Laboratory of Computational Biology, Chinese Academy of Sciences Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
    Genome Biol 16:61. 2015
    ....
  56. pmc eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data
    Charles E Breeze
    UCL Cancer Institute, University College London, London WC1E 6BT, UK Electronic address
    Cell Rep 17:2137-2150. 2016
    ..Our approach bridges the gap between large-scale epigenomics data and EWAS-derived target selection to yield insight into disease etiology...
  57. pmc dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers
    Zhen Yang
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai 200031, China
    Nucleic Acids Res 45:D812-D818. 2017
    ..We expect this database to continue to serve as a valuable source for cancer investigation and potential clinical application related to miRNAs. dbDEMC 2.0 is freely available at http://www.picb.ac.cn/dbDEMC...
  58. pmc Epigenetic and genetic deregulation in cancer target distinct signaling pathway domains
    Yang Gao
    CAS Key Lab for Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, 320 Yue Yang Road, Shanghai 200031, China
    Nucleic Acids Res 45:583-596. 2017
    ....
  59. pmc JAK2-centered interactome hotspot identified by an integrative network algorithm in acute Stanford type A aortic dissection
    Sun Pan
    Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
    PLoS ONE 9:e89406. 2014
    ..Overall, the analytical strategy used in this study offered the possibility to identify functional relevant network modules and subsequently facilitated the biological interpretation in the complicated disease. ..
  60. doi request reprint A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control
    Yinming Jiao
    Computational Systems Genomics, CAS MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China, Department of Women s Cancer, UCL Elizabeth Garrett Anderson Institute for Women s Health and Statistical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, London WC1E 6BT, UK
    Bioinformatics 30:2360-6. 2014
    ..Such integrative tools are important for the discovery of epigenetically regulated gene modules or molecular pathways, which play key roles in cellular differentiation and disease...