Dr. Hai Fang Computational Genomics Group Department of Computer Science University of Bristol The Merchant Venturers Building Woodland Road Bristol BS8 1UB, United Kingdom Email: hfang@cs.bris.ac.uk

Career Summary

• Bioinformatics Research Associate (2012 - Now) in Computational Genomics Group, Department of Computer Science, University of Bristol
• Bioinformatics Research Assistant (2010 - 2011) in Intelligent Systems Laboratory, Department of Computer Science, University of Bristol
• Post-Doctoral Researcher (2009 - 2010) from Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
• M.S. - Ph.D. program in Genetics/Bioinformatics (2003 - 2009) from Institute of Health Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences
• B.S. in Biotechnology Engineering (1999 - 2003) from Jiangnan University

Research Interests

• The dcGO database of domain-centric ontologies
• An R package tailored to needs of analysing dcGO: dcGOR
• Function and phenotype prediction for genome sequences (dcGO Predictor) and domain sets (dcGO Enrichment)
• Structural phylogenomics to tree of (sequenced) life (sTOL)
• Function-selective evolution in eukaryotic genome evolution (Pevo)
• Network-oriented connections among diseases, drugs and phenotypes using Random Walk with Restart
• Developing software (R packages supraHex and dnet, Matlab toolbox TPSC) for analysing omics data (e.g. expression, mutation, replication timing)

Provisional Projects

• Predicting body-plan phenotype genes in humans and animals
• General phenotype-genotype causality understood via specific study of model hematological systems

Academic Publications (Google Scholar)

Publications on 'Domain Ontology Analysis'

• Linkeviciute V, Rackham OJ, Gough J, Oates ME, Fang H. (2015) Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. Biochimie (In Press)
• Oates ME, Stahlhacke J, Vavoulis DV, Smithers B, Rackham OJ, Sardar AJ, Zaucha J, Thurlby N, Fang H, Gough J. (2015) The SUPERFAMILY 1.75 database in 2014: a doubling of data. Nucleic Acids Res 43(Database issue):D227-33 PubMed ID:(25414345) PDF
• Fang H. (2014) dcGOR: an R package for analysing ontologies and protein domain annotations. PLoS Computational Biology 10(10):e1003929 PubMed ID:(25356683) PDF
• Sardar AJ, Oates ME, Fang H, Forrest ARR, Kawaji H, The FANTOM consortium, Gough J, Rackham O. (2014) The evolution of human cells in terms of protein innovation. Molecular Biology and Evolution 31(6):1364-74 PubMed ID:(24692656) PDF
• Fang H, Oates ME, Pethica RB, Greenwood JM, Sardar AJ, Rackham OJ, Donoghue PC, Stamatakis A, de Lima Morais DA, Gough J. (2013) A daily-updated tree of (sequenced) life as a reference for genome research. Scientific Reports 3:2015 PubMed ID:(23778980) PDF
• Fang H, Gough J. (2013) A disease-drug-phenotype matrix inferred by walking on a functional domain network. Molecular BioSystems 9(7):1686-96 PubMed ID:(23462907) PDF
• Fang H, Gough J. (2013) A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics 14(Suppl 3):S9 PubMed ID:(23514627) PDF
• Radivojac P, et al. (2013) A large-scale evaluation of computational protein function prediction. Nature Methods 10(3):221-7 PubMed ID:(23353650) PDF
• Fang H, Gough J. (2012) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res 41(Database issue):D536-44 PubMed ID:(23161684) PDF
• de Lima Morais DA, Fang H*, Rackham OJ, Wilson D, Pethica R, Chothia C, Gough J. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res 39 (Database issue), D427-34 PubMed ID:(21062816) PDF

Publications on 'Omics Data Analysis'

• Zaucha J, Stahlhacke J, Oates ME, Thurlby N, Rackham OJ, Fang H, Smithers B, Gough J. (2015) A proteome quality index. Environmental Microbiology 17(1):4-9 PubMed ID:(25339269) PDF
• Fang H, Gough J. (2014) The 'dnet' approach promotes emerging research on cancer patient survival. Genome Medicine 6(8):64 PubMed ID:(25246945) PDF
• Burton B, Britton G, Fang H, Verhagen J, Smithers B, Sabatos-Peyton C, Carney L, Gough J, Strobel S, Wraith D. (2014) Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy. Nature Communications 5:4741 PubMed ID:(25182274) PDF
• The FANTOM consortium. (2014) A promoter-level mammalian expression atlas. Nature 507(7493):462-70 PubMed ID:(24670764) PDF
• Fang H, Gough J. (2014) supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map. Biochemical and Biophysical Research Communications 443(1):285-289 PubMed ID:(24309102) PDF
• Zhang H, Mi JQ, Fang H*, Wang Z, Wang C, Wu L, Zhang B, Minden M, Yang WT, Wang HW, Li JM, Xi XD, Chen SJ, Zhang J, Chen Z, Wang KK. (2013) Preferential eradication of acute myelogenous leukemia stem cells by fenretinide. Proc Natl Acad Sci U S A, 110(14):5606-5611 PubMed ID:(23513221)
• Zhang J, Fang H. (2012) Using self-organizing maps to visualize, filter and cluster multidimensional bio-omics data. In: Developments and Applications of Self-Organizing Maps. Edited by Johnsson M: InTech.
• Fang H, Du Y, Xia L, Li J, Zhang J, Wang K. (2011) A topology-preserving approach for selection and clustering of multi-dimensional biological data. OMICS: A Journal of Integrative Biology 15 (7-8), 483-94 PubMed ID:(21699401) PDF
• Fang H, Jin W, Yang Y, Jin Y, Zhang J, Wang K. (2011) An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro. BMC System Biology 5(1):108 PubMed ID:(21733158)
• Fang H, Yang Y, Li CL, Fu S, Yang Z, Jin G, Wang K, Zhang J, Jin Y. (2010) Transcriptome Analysis of Early Organogenesis in Human Embryos. Developmental Cell 19 (1), 174-184 PubMed ID:(20643359) PDF. This work is highlighted by Genome Biology (Elucidating the molecular characteristics of organogenesis in human embryos)
• Liu R, Wang W, Ye L, Bi Y, Fang H, Cui B, Zhou W, Dai M, Zhang J, Li X, Ning G. (2010) p21-Activated kinase 3 is overexpressed in thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome and participates in cell migration. Endocrine 38 (1), 38-47 PubMed ID:(20960100) PDF
• Wang K, Wang P, Shi J, Zhu X, He M, Jia X, Yang X, Qiu F, Jin W, Qian M, Fang H, Mi J, Yang X, Xiao H, Minden M, Du Y, Chen Z, Zhang J. (2010) PML/RARalpha Targets Promoter Regions Containing PU.1 Consensus and RARE Half Sites in Acute Promyelocytic Leukemia. Cancer Cell 17 (2), 186-197 PubMed ID:(20159610) PDF
• Bi Y, Liu R, Ye L, Fang H, Li X, Wang W, Zhang J, Wang K, Jiang L, Su T, Chen Z, Ning G. (2009) Gene expression profiles of thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome reveal novel molecular mechanism. Endocrine-Related Cancer 16 (4), 1273-82 PubMed ID:(19625467) PDF
• Fang H, Zhang J and Wang K. (2009) Connecting biological themes using a single human network of gene associations. International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing 463 - 471 (IJCBS) PDF
• Wang K, Fang H*, Xiao D, Zhu X, He M, Pan X, Shi J, Zhang H, Jia X, Du Y, Zhang J. (2009) Converting Redox Signaling to Apoptotic Activities by Stress-Responsive Regulators HSF1 and NRF2 in Fenretinide Treated Cancer Cells. PLoS ONE 4 (10), e7538 PubMed ID:(19844581) PDF
• Fang H, Wang K, Zhang J. (2008) Transcriptome and proteome analyses of drug interactions with natural products. Current Drug Metabolism 9 (10), 1038-48 PubMed ID:(19075620) PDF
• Du Y, Wang K, Fang H, Li J, Xiao D, Zheng P, Chen Y, Fan H, Pan X, Zhao C, Zhang Q, Imbeaud S, Graudens E, Eveno E, Auffray C, Chen S, Chen Z, Zhang J. (2006) Coordination of intrinsic, extrinsic, and endoplasmic reticulum-mediated apoptosis by imatinib mesylate combined with arsenic trioxide in chronic myeloid leukemia. Blood 107 (4), 1582-90 PubMed ID:(16249384) PDF