Dr. Hai Fang - Post-Doctoral Researcher

University of Bristol
81/83 Woodland Road
Bristol BS8 1UB, United Kingdom

Phone: +44 (0)792 9104281
Email: hfang@cs.bris.ac.uk

Background


Research interests


Publications

Publications on 'Domain Ontology Analysis'

  • Fang H. (2014) dcGOR: an R package for analysing ontologies and protein domain annotations. PLoS Computational Biology 10(10):e1003929 PubMed ID:(25356683)
  • 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)
  • 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)
  • Fang H, Gough J. (2013) A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics 14(Suppl 3):S9 PubMed ID:(23514627)
  • Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Toronen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Honigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Bjorne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Skunca N, Supek F, Bosnjak M, Panov P, Dzeroski S, Smuc T, Kourmpetis YA, van Dijk AD, Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. (2013) A large-scale evaluation of computational protein function prediction. Nature Methods 10(3):221-7 PubMed ID:(23353650)
  • Fang H, Gough J. (2012) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res PubMed ID:(23161684)
  • 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)

Publications on 'Omics Data Analysis'

  • Zaucha J, Stahlhacke J, Oates ME, Thurlby N, Rackham OJ, Fang H, Smithers B, Gough J. (2014) A proteome quality index. Environmental Microbiology PubMed ID:(25339269)
  • Fang H, Gough J. (2014) The 'dnet' approach promotes emerging research on cancer patient survival. Genome Medicine, 6(8):64 PubMed ID:(25246945)
  • 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)
  • The FANTOM consortium. (2014) A promoter-level mammalian expression atlas. Nature, 507(7493):462-70 PubMed ID:(24670764)
  • 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)
  • 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)
  • 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). This work is highlighted in Genome Biology and extended in BMC System Biology.
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)

Publications on 'network biology'

  • 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)
  • Fang H, Gough J. (2010) The evolutionary dynamics of protein networks. Genome Biology 11(Suppl 1), 12
  • 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)

Other publications

  • 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)
  • 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)
  • Fang H. Systems for In-depth Mining of BioX-omic data (SimBioX). PhD Thesis (Supervised by Prof. Ji Zhang), Spring 2009
  • Zhang J, Fang H: 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; 2012.