Dr Fan Zhang

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I received PhD in Computer Science from Nanyang Technological University Singapore. I am now working as a Lecturer at the Microbiome Research Centre, St George and Sutherland Campuses, University of New South Wales in Sydney. My current research focuses on bioinformatics, computational biology, data science and statistical inference.

E-mail

fan.zhang7@unsw.edu.au

Book Chapters | 2023

Shu K; Liang Q; Guo H; Zhang F; Wang K; Yuan L, 2023, 'Finding Introverted Cores in Bipartite Graphs', in Web Information Systems and Applications, Springer Nature Singapore, pp. 162 - 170, http://dx.doi.org/10.1007/978-981-99-6222-8_14
Journal articles | 2024

Little RD; Jayawardana T; Koentgen S; Zhang F; Connor SJ; Boussioutas A; Ward MG; Gibson PR; Sparrow MP; Hold GL, 2024, 'Pathogenesis and precision medicine for predicting response in inflammatory bowel disease: Advances and future directions', eGastroenterology, 2, http://dx.doi.org/10.1136/egastro-2023-100006

Journal articles | 2024

Rimmer P; Scott G; Quraishi MN; Hazel K; Cooney R; Zhang F; Hold GL; Gordon M; Iqbal T; Hansen R, 2024, 'Sa1887 IS DIVERSITY IMPORTANT IN THE GUT MICROBIOME AT IBD ONSET? A SYSTEMATIC REVIEW OF THE LITERATURE AND META-ANALYSIS OF ALPHA-DIVERSITY DATA', Gastroenterology, 166, http://dx.doi.org/10.1016/s0016-5085(24)01772-4

Journal articles | 2023

Zhang F; Gia A; Chen G; Gong L; Behary J; Hold GL; Zekry A; Tang X; Sun Y; El-Omar E; Jiang XT, 2023, 'Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients', Viruses, 15, pp. 53, http://dx.doi.org/10.3390/v15010053

Journal articles | 2023

Zhang F; Guo H; Ouyang D; Yang S; Lin X; Tian Z, 2023, 'Size-constrained Community Search on Large Networks: An Effective and Efficient Solution', IEEE Transactions on Knowledge and Data Engineering, http://dx.doi.org/10.1109/TKDE.2023.3280483

Journal articles | 2022

Chen J; Zhao Y; Zhang F; Li J; Boland JA; Cheng NC; Liu K; Tiffen JC; Bertolino P; Bowen DG; Krueger A; Lisowski L; Alexander IE; Vadas MA; El-Omar E; Gamble JR; McCaughan GW, 2022, 'Liver-specific deletion of miR-181ab1 reduces liver tumour progression via upregulation of CBX7', Cellular and Molecular Life Sciences, 79, http://dx.doi.org/10.1007/s00018-022-04452-6

Journal articles | 2022

Gemikonakli G; Mach J; Zhang F; Bullock M; Tran T; El-Omar E; Hilmer SN, 2022, 'Polypharmacy with high Drug Burden Index (DBI) alters the gut microbiome overriding aging effects and is reversible with deprescribing.', The Journals of Gerontology Series A, 78, http://dx.doi.org/10.1093/gerona/glac195

Journal articles | 2022

Li Y; Zhang F; Zheng H; Kalasabail S; Hicks C; Fung KY; Preaudet A; Putoczki T; Beretov J; Millar EKA; El-Omar E; Jiang XT; Yim HCH, 2022, 'Fecal DNA Virome Is Associated with the Development of Colorectal Neoplasia in a Murine Model of Colorectal Cancer', Pathogens, 11, http://dx.doi.org/10.3390/pathogens11040457

Journal articles | 2022

Pandey D; Szczesniak M; Maclean J; Yim HCH; Zhang F; Graham P; El-Omar EM; Wu P, 2022, 'Dysbiosis in Head and Neck Cancer: Determining Optimal Sampling Site for Oral Microbiome Collection', Pathogens, 11, http://dx.doi.org/10.3390/pathogens11121550

Journal articles | 2021

Liang ZG; Zhang F; Li Y; Li L; Qu S; Su F; Yu BB; Guan Y; Han L; Li KG; Zhu XD, 2021, 'The Integration of the Pre-Treatment Neutrophil-to-Lymphocyte Ratio in the Eighth Edition of the AJCC Staging System for Nasopharynx Cancer', Frontiers in Oncology, 11, http://dx.doi.org/10.3389/fonc.2021.724467

Journal articles | 2021

Qiao C; Brown KN; Zhang F; Tian Z, 2021, 'Federated Adaptive Asynchronous Clustering Algorithm for Wireless Mesh Networks', IEEE Transactions on Knowledge and Data Engineering, pp. 1 - 1, http://dx.doi.org/10.1109/tkde.2021.3119550

Journal articles | 2020

Liang ZG; Zhang F; Yu BB; Li L; Qu S; Li Y; Guan Y; Liang RB; Han L; Zhu XD, 2020, 'The double-edge role of the addition of adjuvant chemotherapy to concurrent chemoradiotherapy in the treatment of nasopharyngeal carcinoma', Cancer Management and Research, 12, pp. 801 - 812, http://dx.doi.org/10.2147/CMAR.S236128

Journal articles | 2019

Liang ZG; Tan HQ; Zhang F; Tan LKR; Lin L; Lenkowicz J; Wang H; Ong EHW; Kusumawidjaja G; Phua JH; Gan SA; Sin SY; Ng YY; Tan TWK; Soong YL; Fong KW; Park SY; Soo KC; Wee JTS; Zhu XD; Valentini V; Boldrini L; Sun Y; Chua MLK, 2019, 'Comparison of radiomics tools for image analyses and clinical prediction in nasopharyngeal carcinoma', British Journal of Radiology, 92, http://dx.doi.org/10.1259/bjr.20190271

Journal articles | 2019

Liang ZG; Zhang F; Tan L; Lin L; Lenkowicz J; Wang HT; Ong EHW; Kusumawidjaja G; Phua JH; Tan TWK; Soong YL; Fong KW; Soo KC; Wee J; Zhu XD; Boldrini L; Sun Y; Chua MLK, 2019, 'Radio-Transcriptomic Phenotypes Predict Radioresistance in Nasopharyngeal Carcinoma', INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS, 105, pp. E388 - E389, http://dx.doi.org/10.1016/j.ijrobp.2019.06.1657

Journal articles | 2019

Lorenzini PA; Chew RSE; Tan CW; Yong JY; Zhang F; Zheng J; Roca X, 2019, 'Human PRPF40B regulates hundreds of alternative splicing targets and represses a hypoxia expression signature', RNA, 25, pp. 905 - 920, http://dx.doi.org/10.1261/rna.069534.118

Journal articles | 2018

Liu H; Lorenzini PA; Zhang F; Xu S; Wong MSM; Zheng J; Roca X, 2018, 'Alternative splicing analysis in human monocytes and macrophages reveals MBNL1 as major regulator', Nucleic Acids Research, 46, pp. 6069 - 6086, http://dx.doi.org/10.1093/nar/gky401

Journal articles | 2018

Shanmugam R; Zhang F; Srinivasan H; Richard JLC; Liu KI; Zhang X; Woo CWA; Chua ZHM; Buschdorf JP; Meaney MJ; Tan MH, 2018, 'SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates', Nucleic Acids Research, 46, pp. 7379 - 7395, http://dx.doi.org/10.1093/nar/gky615

Journal articles | 2018

Wang Y; Liu KI; Sutrisnoh NAB; Srinivasan H; Zhang J; Li J; Zhang F; Lalith CRJ; Xing H; Shanmugam R; Foo JN; Yeo HT; Ooi KH; Bleckwehl T; Par YYR; Lee SM; Ismail NNB; Sanwari NAB; Lee STV; Lew J; Tan MH, 2018, 'Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells', Genome Biology, 19, http://dx.doi.org/10.1186/s13059-018-1445-x

Journal articles | 2017

Pek M; Yatim SMJM; Chen Y; Li J; Gong M; Jiang X; Zhang F; Zheng J; Wu X; Yu Q, 2017, 'Oncogenic KRAS-associated gene signature defines co-targeting of CDK4/6 and MEK as a viable therapeutic strategy in colorectal cancer', Oncogene, 36, pp. 4975 - 4986, http://dx.doi.org/10.1038/onc.2017.120

Journal articles | 2016

Jiang L; Wu WF; Sun LY; Chen PP; Wang W; Benito-Vicente A; Zhang F; Pan XD; Cui W; Yang SW; Zhou YJ; Martin C; Wang LY, 2016, 'The use of targeted exome sequencing in genetic diagnosis of young patients with severe hypercholesterolemia', Scientific Reports, 6, http://dx.doi.org/10.1038/srep36823

Journal articles | 2016

Liu H; Zhang F; Mishra SK; Zhou S; Zheng J, 2016, 'Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data', Scientific Reports, 6, http://dx.doi.org/10.1038/srep35652

Journal articles | 2016

Zhang F; Chen H; Zhao LN; Liu H; Przytycka TM; Zheng J, 2016, 'Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways', BMC Systems Biology, 10, http://dx.doi.org/10.1186/s12918-015-0249-9

Journal articles | 2016

Zhang F; Liu R; Zheng J, 2016, 'Sig2GRN: A software tool linking signaling pathway with gene regulatory network for dynamic simulation', BMC Systems Biology, 10, http://dx.doi.org/10.1186/s12918-016-0365-1

Journal articles | 2016

Zhang F; Wu M; Kwoh CK; Zheng J, 2016, 'Power-law modeling of cancer cell fates driven by signaling data to reveal drug effects', Plos One, 11, http://dx.doi.org/10.1371/journal.pone.0165049

Journal articles | 2015

Mishra SK; Bhowmick SS; Chua HE; Zhang F; Zheng J, 2015, 'Computational cell fate modelling for discovery of rewiring in apoptotic network for enhanced cancer drug sensitivity', BMC Systems Biology, 9, http://dx.doi.org/10.1186/1752-0509-9-S1-S4

Journal articles | 2015

Zhang F; Wu M; Li XJ; Li XL; Kwoh CK; Zheng J, 2015, 'Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates', Journal of Bioinformatics and Computational Biology, 13, http://dx.doi.org/10.1142/S0219720015410024

Journal articles | 2014

Li XJ; Mishra SK; Wu M; Zhang F; Zheng J, 2014, 'Syn-lethality: An integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies', Biomed Research International, 2014, http://dx.doi.org/10.1155/2014/196034

Journal articles | 2014

Wu M; Li X; Zhang F; Li X; Kwoh CK; Zheng J, 2014, 'In silico prediction of synthetic lethality by meta-analysis of genetic interactions, functions, and pathways in yeast and human cancer', Cancer Informatics, 13, pp. 71 - 80, http://dx.doi.org/10.4137/CIN.S14026
Conference Abstracts | 2024

Jayawardana T; Little R; Zhang F; Koentgen S; Wu N; Tavakoli P; Chung A; Ho A; Boussioutas A; Ward M; Sparrow MP; Gibson P; Ghaly S; Corte C; Talley NJ; Leach S; Dutt S; Lemberg A; Paramsothy S; Leong R; Connor SJ; Hold G, 2024, 'Microbial signatures associated with inflammatory bowel disease in Australia: baseline sequencing from the Australian IBD Microbiome study', in JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, WILEY, Vol. 39, pp. 216 - 217

Conference Papers | 2024

Rimmer P; Scott G; Quraishi MN; Hazel K; Cooney R; Hold G; Zhang F; Gordon M; Iqbal T; Hansen R, 2024, 'P107 Is gut microbiome diversity important at IBD onset? A systematic review of the literature and meta-analysis of alpha diversity data', in Poster Presentations, BMJ Publishing Group Ltd and British Society of Gastroenterology, pp. A114 - A115, presented at BSG LIVE’24, 17-20 June 2024, ICC Birmingham, http://dx.doi.org/10.1136/gutjnl-2024-bsg.189

Conference Papers | 2023

Huang Y; Wang L; Zhang F; Lin X, 2023, 'Unsupervised Graph Outlier Detection: Problem Revisit, New Insight, and Superior Method', in Proceedings - International Conference on Data Engineering, pp. 2565 - 2578, http://dx.doi.org/10.1109/ICDE55515.2023.00197

Conference Papers | 2023

Pandey D; Szcczesniak M; Maclean J; Zhang F; Yim H; El-Omar E; Graham P; Wu P, 2023, 'IMPLICATIONS OF ORO-PHARYNGEAL DYSBIOSIS IN HEAD AND NECK CANCER: ORAL MICROBIOME AND CHEMORADIATION-RELATED COMPLICATIONS', in GUT, BMJ PUBLISHING GROUP, PEOPLES R CHINA, Hong Kong, pp. A114 - A116, presented at International Digestive Disease Forum (IDDF), PEOPLES R CHINA, Hong Kong, 10 June 2023 - 11 June 2023, http://dx.doi.org/10.1136/gutjnl-2023-IDDF.101

Conference Papers | 2023

Teng S; Xie J; Zhang M; Wang K; Zhang F, 2023, 'IMinimize: A System for Negative Influence Minimization via Vertex Blocking', in Proceedings of the 32nd ACM International Conference on Information and Knowledge Management, ACM, presented at CIKM '23: The 32nd ACM International Conference on Information and Knowledge Management, http://dx.doi.org/10.1145/3583780.3614743

Conference Papers | 2023

Xie J; Zhang F; Wang K; Lin X; Zhang W, 2023, 'Minimizing the Influence of Misinformation via Vertex Blocking', in Proceedings - International Conference on Data Engineering, pp. 789 - 801, http://dx.doi.org/10.1109/ICDE55515.2023.00066

Conference Papers | 2023

Zhang F; Linghu Q; Xie J; Wang K; Lin X; Zhang W, 2023, 'Quantifying Node Importance over Network Structural Stability', in Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 3217 - 3228, http://dx.doi.org/10.1145/3580305.3599480

Conference Papers | 2023

Zhang J; Yang S; Ouyang D; Zhang F; Lin X; Yuan L, 2023, 'Hop-Constrained s-t Simple Path Enumeration on Large Dynamic Graphs', in Proceedings - International Conference on Data Engineering, pp. 762 - 775, http://dx.doi.org/10.1109/ICDE55515.2023.00064

Conference Papers | 2022

Pandey D; Szczesniak M; Maclean J; Yim HCH; Zhang F; Graham P; El-Omar EM; Wu P, 2022, 'Dysbiosis in Head and Neck Cancer: Determining Optimal Sampling Site for Oral Microbiome Collection', in Pathogens, WILEY, pp. 27 - 28, http://dx.doi.org/10.3390/pathogens11121550

Conference Papers | 2014

Zhang F; Kwoh CK; Wu M; Zheng J, 2014, 'Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways', in ACM Bcb 2014 5th ACM Conference on Bioinformatics Computational Biology and Health Informatics, pp. 436 - 444, http://dx.doi.org/10.1145/2649387.2649425

Conference Papers | 2013

Li X-J; Mishra SK; Wu M; Zhang F; Zheng J, 2013, 'Syn-Lethality: An integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies', in 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE, pp. 4 - 4, presented at 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 18 December 2013 - 21 December 2013, http://dx.doi.org/10.1109/bibm.2013.6732609

Conference Papers | 2013

Wu M; Li X; Zhang F; Li X; Kwoh CK; Zheng J, 2013, 'Meta-analysis of genomic and proteomic features to predict synthetic lethality of yeast and human cancer', in 2013 ACM Conference on Bioinformatics Computational Biology and Biomedical Informatics ACM Bcb 2013, pp. 384 - 391, http://dx.doi.org/10.1145/2506583.2506653

Harnessing microbial immunomodulatory function to improve treatment of inflammatory bowel diseases. National Health and Medical Research Council (NHMRC) Ideas Grants. CI. 2024-2027.

My Research Supervision

Currently 3 PhD students in areas relating to the microbiome and Inflammatory bowel disease

Have supervised 1 PhD student to finish

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