Hai Fang

Summary

Affiliation: University of Bristol
Location: Bristol, UK
URL: http://www.cs.bris.ac.uk/~hfang/
Summary:
I have a great interest in genome-scale data mining: I developed the database of domain-centric ontologies to aid in functional genomics and phenotype prediction; applied network techniques to identify the possible connections among drugs, diseases and phenotypes; used the tree of life to study network evolution. I have also published several papers about transcriptome data mining which is unique in topology-preserving selection and clustering.
Grants:
Bachelors Degree in Biotechnology Engineering (1999 - 2003) from Jiangnan University
M.S. - Ph.D. Degree in Genetics/Bioinformatics (2003 - 2009) from Institute of Health Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences
Research post-Doc on Network Biology (2009 - 2010) from Sino-French Laboratory of Genomics and Life Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
Post-Doctoral Research Associate (2010 - Now) in Intelligent Systems Laboratory, Department of Computer Science, University of Bristol

Publications

  1. ncbi Coordination of intrinsic, extrinsic, and endoplasmic reticulum-mediated apoptosis by imatinib mesylate combined with arsenic trioxide in chronic myeloid leukemia
    Yanzhi Du
    State Key Laboratory of Medical Genomics and Shanghai Institute of Ruijin Hospital, School of Medicine of Shanghai Jiao Tong University, Shanghai 200025, China
    Blood 107:1582-90. 2006
  2. ncbi Transcriptome and proteome analyses of drug interactions with natural products
    Hai Fang
    Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai Jiao Tong University School of Medicine SJTUSM, and Ruijin Hospital, Shanghai, China
    Curr Drug Metab 9:1038-48. 2008
  3. doi Gene expression profiles of thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome reveal novel molecular mechanism
    Yu fang Bi
    Department of Endocrinology and Metabolism, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, People s Republic of China
    Endocr Relat Cancer 16:1273-82. 2009
  4. pmc Converting redox signaling to apoptotic activities by stress-responsive regulators HSF1 and NRF2 in fenretinide treated cancer cells
    Kankan Wang
    State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
    PLoS ONE 4:e7538. 2009
  5. doi PML/RARalpha targets promoter regions containing PU.1 consensus and RARE half sites in acute promyelocytic leukemia
    Kankan Wang
    Sino French Research Center for Life Sciences and Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
    Cancer Cell 17:186-97. 2010
  6. doi Transcriptome analysis of early organogenesis in human embryos
    Hai Fang
    Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine SJTU SM, Shanghai 200025, China
    Dev Cell 19:174-84. 2010
  7. doi p21-activated kinase 3 is overexpressed in thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome and participates in cell migration
    Rui xin Liu
    Shanghai Key Laboratory for Endocrine Tumors, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People s Republic of China
    Endocrine 38:38-47. 2010
  8. pmc SUPERFAMILY 1.75 including a domain-centric gene ontology method
    David A de Lima Morais
    Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK
    Nucleic Acids Res 39:D427-34. 2011
  9. doi A topology-preserving selection and clustering approach to multidimensional biological data
    Hai Fang
    State Key Laboratory of Medical Genomics, Sino French Research Center for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine SJTU SM, People s Republic of China
    OMICS 15:483-94. 2011
  10. pmc DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more
    Hai Fang
    Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK
    Nucleic Acids Res 41:D536-44. 2013

Collaborators

Detail Information

Publications15

  1. ncbi Coordination of intrinsic, extrinsic, and endoplasmic reticulum-mediated apoptosis by imatinib mesylate combined with arsenic trioxide in chronic myeloid leukemia
    Yanzhi Du
    State Key Laboratory of Medical Genomics and Shanghai Institute of Ruijin Hospital, School of Medicine of Shanghai Jiao Tong University, Shanghai 200025, China
    Blood 107:1582-90. 2006
    ..This finding appears to be supported also by data derived from bone marrow cells of 2 patients with CML, one in chronic phase and the other in blast-crisis phase of the disease...
  2. ncbi Transcriptome and proteome analyses of drug interactions with natural products
    Hai Fang
    Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai Jiao Tong University School of Medicine SJTUSM, and Ruijin Hospital, Shanghai, China
    Curr Drug Metab 9:1038-48. 2008
    ..Here, these recent advancements will be discussed in detail, along with perspectives in the field of drug synergism...
  3. doi Gene expression profiles of thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome reveal novel molecular mechanism
    Yu fang Bi
    Department of Endocrinology and Metabolism, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, People s Republic of China
    Endocr Relat Cancer 16:1273-82. 2009
    ..Hence, this study has provided not only a detailed comprehension of the molecular pathogenesis of thymic carcinoids with ectopic ACTH syndrome, but also a road map to approach thymic NETs at the system level...
  4. pmc Converting redox signaling to apoptotic activities by stress-responsive regulators HSF1 and NRF2 in fenretinide treated cancer cells
    Kankan Wang
    State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
    PLoS ONE 4:e7538. 2009
    ..However, little is known about mechanisms underlying the conversion from oxidative signaling to downstream activities leading cells to death...
  5. doi PML/RARalpha targets promoter regions containing PU.1 consensus and RARE half sites in acute promyelocytic leukemia
    Kankan Wang
    Sino French Research Center for Life Sciences and Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, China
    Cancer Cell 17:186-97. 2010
    ..Thus, selective targeting of PU.1-regulated genes by PML/RARalpha is a critical mechanism for the pathogenesis of APL...
  6. doi Transcriptome analysis of early organogenesis in human embryos
    Hai Fang
    Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine SJTU SM, Shanghai 200025, China
    Dev Cell 19:174-84. 2010
    ..Our results represent a significant step in characterization of early human embryogenesis and provide a resource for understanding human development and for stem cell engineering...
  7. doi p21-activated kinase 3 is overexpressed in thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome and participates in cell migration
    Rui xin Liu
    Shanghai Key Laboratory for Endocrine Tumors, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People s Republic of China
    Endocrine 38:38-47. 2010
    ..Activation of JNK pathway was also detected in thymic carcinoid with high level of PAK3 expression. Our findings suggested a potential role of PAK3 in the progression of ACTH-producing thymic carcinoid...
  8. pmc SUPERFAMILY 1.75 including a domain-centric gene ontology method
    David A de Lima Morais
    Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK
    Nucleic Acids Res 39:D427-34. 2011
    ..A new methodology was developed to ensure a high quality GO annotation. The new methodology is general purpose and has been used to produce domain-based phenotypic ontologies in addition to GO...
  9. doi A topology-preserving selection and clustering approach to multidimensional biological data
    Hai Fang
    State Key Laboratory of Medical Genomics, Sino French Research Center for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine SJTU SM, People s Republic of China
    OMICS 15:483-94. 2011
    ..A Web server ( http://www.cs.bris.ac.uk/∼hfang/TPSC ) hosting a MATLAB package that implements the methodology is freely available to both academic and nonacademic users. These advances will expand the scope of omics applications...
  10. pmc DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more
    Hai Fang
    Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK
    Nucleic Acids Res 41:D536-44. 2013
    ..The dcGO database is updated fortnightly, and its website provides downloads, search, browse, phylogenetic context and other data-mining facilities...
  11. pmc Function-selective domain architecture plasticity potentials in eukaryotic genome evolution
    Viktorija Linkeviciute
    Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK School of Biological Sciences, University of Edinburgh, Darwin Building, The King s Buildings, Edinburgh EH9 3BF, UK
    Biochimie 119:269-77. 2015
    ..A web search tool, available at http://supfam.org/Pevo, offers a wide spectrum of options for exploring functional importance in eukaryotic genome evolution. ..
  12. pmc supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map
    Hai Fang
    Computational Genomics Group, Department of Computer Science, University of Bristol, Merchant Venturers Building, Bristol BS8 1UB, UK Electronic address
    Biochem Biophys Res Commun 443:285-9. 2014
    ..This package can run on Windows, Mac and Linux, and is freely available together with many tutorials on featuring real examples at http://supfam.org/supraHex. ..
  13. pmc An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro
    Hai Fang
    State Key Laboratory of Medical Genomics, Sino French Research Center for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Ruijin Rd, II, Shanghai 200025, China
    BMC Syst Biol 5:108. 2011
    ..However, owing to its hypothetical nature, it remains unclear whether this network allows for comparative transcriptome analysis to advance our understanding of early human development, both in vivo and in vitro...
  14. pmc A domain-centric solution to functional genomics via dcGO Predictor
    Hai Fang
    Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK
    BMC Bioinformatics 14:S9. 2013
    ..We expect, however, to some extent functional signals can be carried by protein domains and supra-domains, and consequently used in function prediction and functional genomics...
  15. doi A disease-drug-phenotype matrix inferred by walking on a functional domain network
    Hai Fang
    Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK
    Mol Biosyst 9:1686-96. 2013
    ..All three can be found at ...