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

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