Publications
Every paper, searchable by title, journal or co-author.
Showing 52 of 52 publications
2026
- Bladder mucosal afferents detect UTI and aid pathogen clearanceTay C, Sharma H, Ramsay S, …, Ryan FJ, …, Grundy LPNAS0cited
- OpusTaxa: A Unified Workflow for Taxonomic Profiling, Assembly, and Functional Analysis of Shotgun MetagenomesChen YK, Harker CM, Pham CM, Grundy L, Wardill HR, Roach MJ, Ryan FJbioRxivPreprint0cited
- 0cited
- Pre-treatment gut microbiome and salivary metabolome signatures associate with chemotherapy-induced cognitive decline in women with breast cancer: A prospective pilot studyCross CB, Bowen JM, Leifert WR, …, Ryan FJ, Wardill HRCancer Letters1cited
- The gut–heart axis in cardio-oncologyChan NSL, Cross C, Bowen J, …, Ryan FJ, …, Joyce PCardiovascular Research1cited
- Total RNA and MicroRNA Transcriptomic Responses of Human Retinal Müller Glial Cells to Infection with Toxoplasma gondii TachyzoitesRochet E, Ryan FJ, Ma Y, …, Smith JROphthalmology Science0cited
2025
- A study protocol for a double-blinded, randomised, placebo-controlled trial on the use of encapsulated FMT for reducing the side effects of HSCT: the HSCT-BIOME studyLi A, Costello SP, Bryant RV, …, Ryan FJ, …, Wardill HRBMC Cancer1cited
- Acute urinary tract infection elicits bladder afferent hypersensitivitySharma H, Manning SK, Stevens NE, …, Ryan FJ, …, Grundy LBrain, Behavior, and Immunity - Health3cited
- 46cited
- DNA hydroxy methylases Tet1 and Tet2 regulate bone aging and bone marrow stromal cell metabolism through the IGF-1/mTOR signaling axisSmith N, Cakouros D, Ryan FJ, Lynn DJ, Paton S, Arthur A, Gronthos SStem Cells3cited
- Enteral versus parenteral nutrition in auto-HCT: a randomized controlled trial on clinical outcomes and gut microbiome dynamicsWardill HR, van Groningen LFJ, Dorraki M, …, Ryan FJ, …, Blijlevens NMASupportive Care in Cancer2cited
- TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databasesPham CM, Rankin TJ, Stinear TP, Walsh CJ, Ryan FJBriefings in Bioinformatics4cited
- The role of the gut microbiota in regulating responses to vaccination: current knowledge and future directionsRossouw C, Ryan FJ, Lynn DJThe FEBS Journal18cited
2024
- Peroxisomal β-oxidation enzyme, DECR2, regulates lipid metabolism and promotes treatment resistance in advanced prostate cancerMah CY, Nguyen ADT, Niijima T, …, Ryan FJ, …, Butler LMBritish Journal of Cancer24cited
- Post-acute sequelae of SARS-CoV-2 cardiovascular symptoms are associated with trace-level cytokines that affect cardiomyocyte functionSinclair JE, Vedelago C, Ryan FJ, …, Short KRNature Microbiology21cited
- Spatial MS multiomics on clinical prostate cancer tissuesTruong JXM, Rao SR, Ryan FJ, Lynn DJ, Snel MF, Butler LM, Trim PJAnalytical and Bioanalytical Chemistry15cited
2023
- A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccinesRyan FJ, Norton TS, McCafferty C, …, Lynn DJCell Reports Medicine50cited
- Autologous Faecal Microbiota Transplantation to Improve Outcomes of Haematopoietic Stem Cell Transplantation: Results of a Single-Centre Feasibility StudyLi A, Bowen JM, Ball IA, …, Ryan FJ, Wardill HRBiomedicines3cited
- 92cited
- Interpersonal variability of the human gut virome confounds disease signal detection in IBDStockdale SR, Shkoporov AN, Khokhlova EV, …, Ryan FJ, …, Hill CCommunications Biology37cited
- No evidence of durable trained immunity after two doses of adenovirus-vectored or mRNA COVID-19 vaccinesStevens NE, Ryan FJ, Messina NL, …, Lynn DJJournal of Clinical Investigation20cited
- Selective Transcription Factor Blockade Reduces Human Retinal Endothelial Cell Expression of Intercellular Adhesion Molecule-1 and Leukocyte BindingMa Y, Ashander LM, Appukuttan B, Ryan FJ, …, Smith JRInternational Journal of Molecular Sciences6cited
2022
- Immunisation with the BCG and DTPw vaccines induces different programs of trained immunity in miceStevens NE, van Wolfswinkel M, Bao W, Ryan FJ, …, Lynn DJVaccine14cited
- Long-term perturbation of the peripheral immune system months after SARS-CoV-2 infectionRyan FJ, Hope CM, Masavuli MG, …, Lynn DJBMC Medicine283cited
- Protocol to assess the impact of early-life antibiotic exposure on murine longevityLynn MA, Ryan FJ, Tee YC, Benson SC, Lynn DJSTAR Protocols8cited
- Protocol to colonize gnotobiotic mice in early life and assess the impact on early life immune programmingLynn MA, Ryan FJ, Tee YC, Lynn DJSTAR Protocols5cited
- Transcriptomic Responses of Human Retinal Vascular Endothelial Cells to Inflammatory CytokinesRyan FJ, Ma Y, Ashander LM, Kvopka M, Appukuttan B, Lynn DJ, Smith JRTranslational Vision Science and Technology11cited
2021
- A Postbiotic Consisting of Heat-Treated Lactobacilli Has a Bifidogenic Effect in Pure Culture and in Human Fermented Fecal CommunitiesWarda AK, Clooney AG, Ryan F, de Almeida Bettio PH, Di Benedetto G, Ross RP, Hill CApplied and Environmental Microbiology44cited
- Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental studyClooney AG, Eckenberger J, Laserna-Mendieta E, …, Ryan FJ, …, Claesson MJGut252cited
- The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later lifeLynn MA, Eden G, Ryan FJ, …, Lynn DJCell Reports70cited
- The immunotoxicity, but not anti-tumor efficacy, of anti-CD40 and anti-CD137 immunotherapies is dependent on the gut microbiotaBlake SJ, James J, Ryan FJ, …, Lynn DJCell Reports Medicine39cited
- Zika Virus Infection of Human Iris Pigment Epithelial CellsRyan FJ, Carr JM, Furtado JM, …, Smith JRFrontiers in Immunology17cited
2020
- Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbationDraper LA, Ryan FJ, Dalmasso M, Casey PG, McCann A, Velayudhan V, Ross RP, Hill CBMC Biology93cited
- Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel diseaseRyan FJ, Ahern AM, Fitzgerald RS, …, Claesson MJNature Communications292cited
2019
- Application of machine learning techniques for creating urban microbial fingerprintsRyan FJBiology Direct47cited
- Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary DysplasiaRyan FJ, Drew DP, Douglas C, …, Lynn DJmSystems41cited
- Choice of assembly software has a critical impact on virome characterisationSutton TDS, Clooney AG, Ryan FJ, Ross RP, Hill CMicrobiome165cited
- Differential gene expression in the mesocorticolimbic system of innately high- and low-impulsive ratsMoloney GM, van Oeffelen WEPA, Ryan FJ, …, Cryan JFBehavioural Brain Research12cited
- Host Microbiota Regulates Central Nervous System Serotonin Receptor 2C Editing in Rodentsvan de Wouw M, Stilling RM, Peterson VL, Ryan FJ, …, Schellekens HACS Chemical Neuroscience15cited
- Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infectionLas Heras V, Clooney AG, Ryan FJ, …, Gahan CGMMicrobiome88cited
- The Human Gut Virome Is Highly Diverse, Stable, and Individual SpecificShkoporov AN, Clooney AG, Sutton TDS, Ryan FJ, …, Hill CCell Host & Microbe797cited
- Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel DiseaseClooney AG, Sutton TDS, Shkoporov AN, …, Ryan FJ, …, Hill CCell Host & Microbe494cited
2018
- Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human GutGuerin E, Shkoporov A, Stockdale SR, …, Ryan FJ, …, Hill CCell Host & Microbe342cited
- Long-term colonisation with donor bacteriophages following successful faecal microbial transplantationDraper LA, Ryan FJ, Smith MK, …, Hill CMicrobiome165cited
- Reproducible protocols for metagenomic analysis of human faecal phageomesShkoporov AN, Ryan FJ, Draper LA, …, Hill CMicrobiome218cited
- Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient miceStilling RM, Moloney GM, Ryan FJ, …, Cryan JFeLife107cited
- Viral Dark Matter in the Gut Virome of Elderly HumansStockdale SR, Ryan FJ, McCann A, Dalmasso M, Ross PR, Hill CPreprints.orgPreprint5cited
- Viromes of one year old infants reveal the impact of birth mode on microbiome diversityMcCann A, Ryan FJ, Stockdale SR, …, Hill CPeerJ136cited
2017
- Tumour-associated and non-tumour-associated microbiota in colorectal cancerFlemer B, Lynch DB, Brown JMR, …, Ryan FJ, …, O'Toole PWGut854cited
2016
- Regulation of prefrontal cortex myelination by the microbiotaHoban AE, Stilling RM, Ryan FJ, Shanahan F, Dinan TG, Claesson MJ, Clarke G, Cryan JFTranslational Psychiatry655cited
2015
- Microbes & neurodevelopment – Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdalaStilling RM, Ryan FJ, Hoban AE, Shanahan F, Clarke G, Claesson MJ, Dinan TG, Cryan JFBrain, Behavior, and Immunity235cited
- SPINGO: a rapid species-classifier for microbial amplicon sequencesAllard G, Ryan FJ, Jeffery IB, Claesson MJBMC Bioinformatics167cited
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Synced from ORCID on 16 September 2026, with author lists from Crossref and citation counts from OpenAlex. Counts differ slightly from Google Scholar.