By Dr Fan Zhang

Journal articles

Li P; Xie L; Zheng H; Feng Y; Mai F; Tang W; Wang J; Lan Z; Lv S; Jayawardana T; Koentgen S; Xu S; Wan Z; Chen Y; Xu H; Shen S; Zhang F; Yang Y; Hold G; He F; El-Omar EM; Yu G; Chen X, 2025, 'Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome', Imeta, 4, http://dx.doi.org/10.1002/imt2.70065

Little RD; Jayawardana TC; Zhang F; Houshyar Y; Koentgen S; Wu N; Ellepola A; Tavakoli P; Read S; Ho A; Chung A; Boussioutas A; Ward MG; Sparrow MP; Gibson PR; Ghaly S; Corte C; Talley NJ; Leach S; Lemberg DA; Dutt S; Paramsothy S; Leong R; Connor SJ; Hold GL; AIM Study consortium , 2025, 'Gut Microbiota Are More Strongly Associated With Impairments in Health-Related Quality of Life Than Disease Activity in Inflammatory Bowel Disease.', Am J Gastroenterol, http://dx.doi.org/10.14309/ajg.0000000000003773

Barnet MB; Jackson KJL; Masle-Farquhar E; Russell A; Burnett DL; Chye A; Jara CJ; Faulks M; Mawson A; Peters TJ; Brink R; Wright K; Allen I; Junankar S; Davis ID; Heller G; Khan Z; Bruce J; Yang C; Prokopec S; Pugh T; Behren A; Hold GL; Zhang F; Cooper WA; Gao B; Nagrial A; Joshua AM; John T; Peters G; Hui R; Boyer M; Blinman PL; Kao SC; Cebon J; Goodnow CC, 2025, 'Common inherited loss-of-function mutations in the innate sensor NOD2 contribute to exceptional immune response to cancer immunotherapy', Proceedings of the National Academy of Sciences of the United States of America, 122, http://dx.doi.org/10.1073/pnas.2314258122

Little R; Jayawardana T; Zhang F; Houshyar Y; Koentgen S; Wu N; Ellepola A; Tavakoli P; Chung A; Ho A; Read S; Boussioutas A; Ward M; Sparrow M; Gibson P; Ghaly S; Corte C; Talley N; Leach S; Lemberg D; Dutt S; Paramsothy S; Leong R; Connor S; Hold G, 2025, 'Association of gut microbiota changes and disease activity in patients with Crohn's disease and ulcerative colitis: baseline data from the Australian IBD Microbiome study', JOURNAL OF CROHNS & COLITIS, 19, pp. i2425 - i2426, http://dx.doi.org/10.1093/ecco-jcc/jjae190.1519

Little R; Jayawardana T; Zhang F; Koentgen S; Wu N; Tavakoli P; Chung A; Ho A; Read S; Boussioutas A; Ward M; Sparrow M; Gibson P; Ghaly S; Corte C; Talley N; Leach S; Lemberg D; Dutt S; Paramsothy S; Leong R; Connor S; Hold G, 2025, 'Gut microbiota changes are associated with type of advanced therapy in patients with Inflammatory Bowel Disease: baseline data from the Australian IBD Microbiome study', JOURNAL OF CROHNS & COLITIS, 19, pp. i2413 - i2415, http://dx.doi.org/10.1093/ecco-jcc/jjae190.1514

Koentgen S; Zhang F; Khadka S; O'Brien C; Grimm M; Allen-Vercoe E; Hold GL, 2025, 'High fat diet drives increased dysbiosis in IBD compared to healthy controls', JOURNAL OF CROHNS & COLITIS, 19, pp. i2409 - i2409, http://dx.doi.org/10.1093/ecco-jcc/jjae190.1511

Jayawardana T; Little RD; Zhang F; Koentgen S; Wu N; Houshyar Y; Tavakoli P; Boussioutas A; Ward MG; Sparrow MP; Gibson PR; Ghaly S; Corte C; Talley NJ; Leach S; Lemberg D; Dutt S; Paramsothy S; Leong R; Connor SJ; Hold G; Australia IBDMAIMS, 2025, 'Impaired health-related quality of life is associated with alterations in gut microbiota signatures in patients with Inflammatory Bowel Disease: baseline data from the Australian IBD Microbiome study', JOURNAL OF CROHNS & COLITIS, 19, pp. i2422 - i2424, http://dx.doi.org/10.1093/ecco-jcc/jjae190.1518

Jayawardana T; Little RD; Zhang F; Koentgen S; Wu N; Tavakoli P; Sidhu S; Le A; Boussioutas A; Ward MG; Miles S; Gibson PR; Ghaly S; Corte C; Talley NJ; Leach S; Lemberg D; Dutt S; Paramsothy S; Leong R; Connor SJ; Hold G; Australia IBDMAIMS, 2025, 'Microbial signatures associated with Inflammatory Bowel Disease in Australia: baseline data from the Australian IBD Microbiome study', JOURNAL OF CROHNS & COLITIS, 19, pp. i2391 - i2392, http://dx.doi.org/10.1093/ecco-jcc/jjae190.1501

Koentgen S; Zhang F; O'Brien C; Grimm M; Allen-Vercoe E; Hold GL, 2025, 'Multi-omic modelling of antibiotic perturbed faecal microbial communities demonstrates reduced microbial resilience in IBD', JOURNAL OF CROHNS & COLITIS, 19, pp. I2377 - I2377, http://dx.doi.org/10.1093/ecco-jcc/jjae190.1493

Rimmer P; Zhang F; Scott G; Hold G; Gordon M; Iqbal T; Hansen R, 2025, 'P1330 The gut microbiome at the onset of inflammatory bowel disease: A systematic review of the literature and unified bioinformatic synthesis of sequencing data from >1000 treatment naïve patients', Journal of Crohn's and Colitis, 19, pp. i2394 - i2395, http://dx.doi.org/10.1093/ecco-jcc/jjae190.1504

Tearle J; Zhang F; Jackson K; Malhotra P; Tavakoli P; Koentgen S; Warren J; Williams C; Haque A; Arzivian A; Tedla N; Kim A; King H; Hold G; Ghaly S; James K, 2025, 'The primary sclerosing cholangitis and ulcerative colitis colonic mucosa defined through paired microbial and single-cell RNA sequencing', JOURNAL OF CROHNS & COLITIS, 19, pp. I557 - I557, http://dx.doi.org/10.1093/ecco-jcc/jjae190.0335

Koentgen S; Zhang F; Wu N; Jayawardana T; Little R; Tavakoli P; Ghaly S; Connor SJ; Hold GL, 2025, 'Unique faecal & oral microbiota signatures in first degree relatives of inflammatory bowel disease patients', JOURNAL OF CROHNS & COLITIS, 19, pp. i606 - i606, http://dx.doi.org/10.1093/ecco-jcc/jjae190.0377

Jayawardana TC; Little RD; Zhang F; Koentgen S; Wu N; Houshyar Y; Tavakoli P; Boussioutas A; Ward M; Sparrow M; Gibson PR; Ghaly S; Corte C; Talley NJ; Leach ST; Lemberg DA; Dutt S; Paramsothy S; Leong RW; Connor SJ; Hold GL, 2025, 'Mo1960: IMPAIRED HEALTH-RELATED QUALITY OF LIFE IS ASSOCIATED WITH ALTERATIONS IN GUT MICROBIOTA SIGNATURES IN PATIENTS WITH INFLAMMATORY BOWEL DISEASE: BASELINE DATA FROM THE AUSTRALIAN IBD MICROBIOME STUDY.', Gastroenterology, 169, pp. S - 1243, http://dx.doi.org/10.1016/s0016-5085(25)03747-3

Little RD; Jayawardana TC; Zhang F; Koentgen S; Wu N; Tavakoli P; Chung A; Ho A; Read S; Boussioutas A; Ward M; Sparrow M; Gibson PR; Ghaly S; Corte C; Talley NJ; Leach ST; Lemberg DA; Dutt S; Paramsothy S; Leong R; Connor SJ; Hold GL, 2025, 'Sa1795: GUT MICROBIOTA CHANGES ARE ASSOCIATED WITH TYPE OF ADVANCED THERAPY IN PATIENTS WITH IBD: BASELINE DATA FROM THE AUSTRALIAN IBD MICROBIOME STUDY', Gastroenterology, 169, pp. S - 532, http://dx.doi.org/10.1016/s0016-5085(25)02163-8

Fitzpatrick J; Little RD; Zhang F; Koentgen S; Gibson PR; Taylor KM; Hold GL; Halmos EP, 2025, 'Sa1921: IMPACT OF HIGH- AND LOW-EMULSIFIER DIETS ON GUT MICROBIOTA IN HEALTHY ADULTS', Gastroenterology, 169, http://dx.doi.org/10.1016/s0016-5085(25)02283-8

Little RD; Jayawardana TC; Zhang F; Houshyar Y; Koentgen S; Dutt S; Leach ST; Lemberg DA; Hold GL, 2025, 'Tu2093: DISTINCT MICROBIAL SIGNATURES ARE ASSOCIATED WITH PEDIATRIC INFLAMMATORY BOWEL DISEASE - BASELINE DATA FROM THE AUSTRALIAN IBD MICROBIOME STUDY', Gastroenterology, 169, http://dx.doi.org/10.1016/s0016-5085(25)04560-3

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Conference Papers

Rimmer P; Scott G; Quraishi MN; Hazel K; Cooney R; Hold G; Zhang F; Gordon M; Iqbal T; Hansen R, 2024, 'Is gut microbiome diversity important at IBD onset? A systematic review of the literature and meta-analysis of alpha diversity data', in GUT, BMJ PUBLISHING GROUP, pp. A114 - A115, http://dx.doi.org/10.1136/gutjnl-2024-BSG.189

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

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

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

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

Conference Abstracts

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

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