Water & Environment

Keating, C., Trego, A., O'Flaherty, V., Ijaz, U. Z. (2025) Microbiomes of high-rate anaerobic digestors reveal ‘study’-specific factors and limitations of synthetic wastewater. Water Research, 282, (doi: 10.1016/j.watres.2025.123931)

Ogundero, A., Connelly, S., Sloan, W. T. (2025) Developing Lotka-Volterra based models to describe Bdellovibrio predation in a batch and chemostat experimental system. Environmental Microbiology Reports, 17, (doi: 10.1111/1758-2229.70141)

Badar, A., Aqueel, R., Malik, K., Saleem, N., Ijaz, U. Z. (2025) Leveraging cell-free supernatants of phyllospheric bacteria to combat wheat pathogens and boost growth. Plant-Environment Interactions, 6, (doi: 10.1002/pei3.70063)

Cholet, F., Vignola, M., Quinn, D., Ijaz, U. Z., Sloan, W. T., Smith, C. J. (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281, (doi: 10.1016/j.watres.2025.123684)

Comadran-Casas, C., Unluer, C., Bass, A. M., Macdonald, J., Khaksar Najafi, E., Spruzeniece, L., Gauchotte-Lindsay, C. (2025) Bioremediation of multiple heavy metals through biostimulation of Microbial-Induced Calcite Precipitation at varying calcium-to-urea concentrations. Journal of Hazardous Materials, 491, (doi: 10.1016/j.jhazmat.2025.137691)

Thom, C., Ijaz, U., Moore, G., Weir, P., Smith, C. J. (2025) Evaluation of existing lacZ primers and de novo design of an optimised qPCR assay to quantify coliform bacteria in drinking water. Journal of Applied Microbiology, (doi: 10.1093/jambio/lxaf156)

Yusuf, L. A., McHugh, P. J., Cioncoloni, G., Song, J., Morrison, C. A., Palmer, E., Franco, F. F., Amini Boroujeni, F., Gauchotte-Lindsay, C., Prentice, P., Symes, M. D. (2025) Toward decentralized nitrogen fixation using pulsed ultrasound. Cell Reports Physical Science, (doi: 10.1016/j.xcrp.2025.102662)

Mellya, R. V.K., Hopcraft, J. G. C., Mwakilema, W., Eblate, E. M., Mduma, S., Mnaya, B., Chuma, I. S., Macha, E. S., Wambura, D., Fyumagwa, R. D., Kilbride, E., Ijaz, U. Z., Mable, B. K., Khan, A. (2025) Natural dispersal is better than translocation for reducing risks of inbreeding depression in eastern black rhinoceros (Diceros bicornis michaeli) Proceedings of the National Academy of Sciences of the United States of America, 122, (doi: 10.1073/pnas.2414412122)

Li, J., Boxall, A. B.A., Swan, C., Wilkinson, J., McGimpsey, N., Evans, H., Kirton, M., Stanforth, R., Gunby, C., Niemi, L., Taggart, M., Robison-Smith, C., Tarring, E., Bloor, M., Gauchotte-Lindsay, C. (2025) Concentrations of Trifluoroacetic Acid (TFA) in UK Surface Waters.

Gupta, R., Murray, C., Sloan, W. T., You, S. (2025) Predicting the methane production of microwave-pretreated anaerobic digestion of food waste: a machine learning approach. Energy, (doi: 10.1016/j.energy.2025.136613)

Trego, A., Morabito, C., Bourven, I., Guibaud, G., O’Flaherty, V., Collins, G., Ijaz, U. Z. (2025) Size matters: anaerobic granules exhibit distinct ecological and physico-chemical gradients across biofilm size. Environmental Science and Ecotechnology, 25, (doi: 10.1016/j.ese.2025.100561)

Saleem, F., Ameer, A., Afzal, F., Usman, M., Irshad, H., Sattar, S., Ijaz, U. Z., Javed, S. (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18, (doi: 10.1186/s13104-025-07220-4)

Badar, A., Aqueel, R., Nawaz, A., Ijaz, U. Z., Malik, K. A. (2025) Microbiota transplantation for Cotton Leaf Curl Disease suppression - core microbiome and transcriptome dynamics. Communications Biology, 8, (doi: 10.1038/s42003-025-07812-7)

Zainy, Z., Hyder, M. Z., Uzma, U., Fayyaz, M., Ijaz, U. Z., Farrakh, S. (2025) Comparative transcriptome analysis of resistant, moderately resistant and susceptible wheat near isogenic lines in response to Puccinia striiformis tritici. Journal of Plant Interactions, 20, (doi: 10.1080/17429145.2025.2481853)

Li, X., Song, Y., Glidle, A., Smith, C., Sloan, W., Cusack, M., Yin, H. (2025) A simple three-dimensional microfluidic platform for studying chemotaxis and cell sorting. Lab on a Chip, 25, pp. 343-353. (doi: 10.1039/D4LC00892H)

Alghafli, K., Shi, X., Sloan, W., Ali, A. M. (2025) Investigating the role of ENSO in groundwater temporal variability across Abu Dhabi Emirate, United Arab Emirates using machine learning algorithms. Groundwater for Sustainable Development, 28, (doi: 10.1016/j.gsd.2024.101389)

Pangga, G. M., Star-Shirko, B., Psifidi, A., Xia, D., Corcionivoschi, N., Kelly, C., Hughes, C., Lavery, U., Richmond, A., Ijaz, U. Z., Gundogdu, O. (2025) Impact of commercial gut health interventions on caecal metagenomic and broiler performance. Microbiome, 13, (doi: 10.1186/s40168-024-02012-7)

Khan, A., Carter, R., Mpamhanga, C. D., Masiga, D., Channumsin, M., Ciosi, M., Manangwa, O., Mramba, F., Ijaz, U. Z., Auty, H., Mable, B. K. (2025) Swatting flies: Biting insects as non-invasive samplers for mammalian population genomics. Molecular Ecology, (doi: 10.1111/mec.17661)

Milling, S., Ijaz, U. Z., Venieri, D., Christidis, G. E., Rattray, N. J. W., Gounaki, I., Andrusaite, A., Hareendran, A., Knapp, C. W., Jones, A. X., Photos-Jones, E. (2024) Beneficial modulation of the gut microbiome by leachates of Penicillium purpurogenum in the presence of clays: A model for the preparation and efficacy of historical Lemnian Earth. PLoS ONE, 19, (doi: 10.1371/journal.pone.0313090)

Su, Q., Domingo-Felez, C., Zhi, M., Jensen, M. M., Xu, B., Ng, H. Y., Smets, B. F. (2024) Formation and fate of reactive nitrogen during biological nitrogen removal from water: important yet often ignored chemical aspects of the nitrogen cycle. Environmental Science and Technology, (doi: 10.1021/acs.est.4c03086)

Lui, J., Lee, S., Sloan, W. T., You, S. (2024) Life cycle assessment of drinking water and wastewater treatment works in mainland Scotland. Science of the Total Environment,

Ameer, A., Saleem, F., Keating, C., Gundogdu, O., Ijaz, U., Javed, S. (2024) Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan. Data In Brief, 57, (doi: 10.1016/j.dib.2024.110957)

Fantinelli Franco, F., Malik, M., Manjakkal, L., Roshanghias, A., Smith, C., Gauchotte-Lindsay, C. (2024) Optimising carbon structures in laser-induced graphene electrodes using design of experiments for enhanced electrochemical sensing characteristics. ACS Applied Materials and Interfaces, 16, pp. 65489-65502. (doi: 10.1021/acsami.4c13124)

Fantinelli Franco, F., Malik, M. H., Manjakkal, L., Roshanghias, A., Smith, C. J., Gauchotte-Lindsay, C. (2024) Optimizing carbon structures in laser-induced graphene electrodes using design of experiments for enhanced electrochemical sensing characteristics. ACS Applied Materials and Interfaces, 16, pp. 65489-65502. (doi: 10.1021/acsami.4c13124)

Stewart, K., Boerlage, A. S., Barr, W., Ijaz, U. Z., Smith, C. (2024) Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea. Animal Microbiome, 6, (doi: 10.1186/s42523-024-00347-y)

Keating, C., Kilbride, E., Stalham, M. A., Nellist, C., Milner, J., Humphris, S., Toth, I., Mable, B. K., Ijaz, U. Z. (2024) Balancing the scales: assessing the impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities. Microbiome, 12, (doi: 10.1186/s40168-024-01918-6)

Nichols, B., Russell, R. K., Short, B., Papadopoulou, R., Focht, G., Ijaz, U. Z., Walters, T. D., Sladek, M., Hansen, R., Mack, D. R., Wine, E., Griffiths, A. M., Turner, D., Gerasimidis, K. (2024) Gut microbial signatures in pediatric Crohn's disease vary according to disease activity measures and are influenced by proxies of gastrointestinal transit time: an ImageKids study. Inflammatory Bowel Diseases, (doi: 10.1093/ibd/izae199)

Ye, J., Mark Jensen, M., Goonesekera, E. M., Yu, R., Smets, B. F., Valverde-Pérez, B., Domingo-Felez, C. (2024) Denitrifying communities enriched with mixed nitrogen oxides preferentially reduce N₂O under conditions of electron competition in wastewater. Chemical Engineering Journal, 498, (doi: 10.1016/j.cej.2024.155292)

Ashraf, H., Dikarlo, P., Masia, A., Zarbo, I. R., Solla, P., Ijaz, U. Z., Sechi, L. A. (2024) Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with Multiple Sclerosis. Scientific Reports, 14, (doi: 10.1038/s41598-024-74975-4)

Cholet, F., Agogué, H., Ijaz, U. Z., Lachaussée, N., Pineau, P., Smith, C. J. (2024) Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France. Science of the Total Environment, 946, (doi: 10.1016/j.scitotenv.2024.174312)

Bibi, S., Kerbiriou, C., Uzma, , Mckirdy, S., Kostrytsia, A., Rasheed, H., Eqani, S. A. M. A. S., Gerasimidis, K., Nurulain, S. M., Ijaz, U. Z. (2024) Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan. Ecotoxicology and Environmental Safety, 284, (doi: 10.1016/j.ecoenv.2024.116959)

Thapa, S., Sinclair, H. D., Creed, M. J., Borthwick, A., Watson, C. S., Muthusamy, M. (2024) Sediment transport and flood risk: impact of newly constructed embankments on river morphology and flood dynamics in Kathmandu, Nepal. Water Resources Research, 60, (doi: 10.1029/2024wr037742)

Martin, S., Smith, C., Stewart, K., Barr, W., Cheslett, D., O'Connor, I., Swords, F., Ijaz, U. Z., O'Dwyer, K. (2024) The hepatopancreas microbiome of velvet crab, Necora puber. Environmental Microbiology Reports, 16, (doi: 10.1111/1758-2229.70014)

Quinn, D., Tsagkari, E., Bhandari, D. S., Fish, K., You, S., Sloan, W. T., Boxall, J., Smith, C. J. (2024) Pseudomonas aeruginosa interactions with drinking water biofilm after an acute spike in annular bioreactors—attachment, persistence, release, and reattachment. (doi: 10.3390/engproc2024069148)

Shi, X., Pereira, R., Uzma, , Savage, L., Poursat, B., Quinn, D., Kostrytsia, A., Cholet, F., Smith, C. J., Gauchotte-Lindsay, C., Sloan, W. T., Ijaz, U., Vignola, M. (2024) Microbial stratification and DOM removal in drinking water biofilters: implications for enhanced performance. Water Research, 262, (doi: 10.1016/j.watres.2024.122053)

Singh Bhandari, D., Quinn, D., Tsagkari, E., Fish, K., Pick, F., Boxall, J., Smith, C., You, S., Sloan, W. (2024) Modelling the Dynamics of P. aeruginosa in the Formation of Biofilms. (doi: 10.3390/engproc2024069141)

Trego, A., O'Sullivan, S., O'Flaherty, V., Collins, G., Ijaz, U. Z. (2024) Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues. Environmental Microbiome, 19, (doi: 10.1186/s40793-024-00615-z)

Cossu, L. O., De Aquino, S. F., Filho, C. R. M., Smith, C. J., Vignola, M. (2024) Review on pesticide contamination and drinking water treatment in Brazil: the need for improved treatment methods. ACS ES&T Water, 4, pp. 3629-3644. (doi: 10.1021/acsestwater.4c00063)

Trego, A., Palmeiro-Sánchez, T., Graham, A., Ijaz, U. Z., O'Flaherty, V. (2024) First evidence for temperature influencing the enrichment, assembly and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities. Frontiers in Systems Biology, 4, (doi: 10.3389/fsysb.2024.1375472)

Aqueel, R., Badar, A., Roy, N., Ijaz, U. Z., Malik, K. A. (2024) Disease resistance correlates with core microbiome diversity in cotton. Current Microbiology, 81, (doi: 10.1007/s00284-024-03827-1)

Ashraf, H., Dikarlo, P., Masia, A., Zarbo, I. R., Solla, P., Ijaz, U. Z., Sechi, L. A. (2024) Network analysis of gut microbial communities reveal key genera for a multiple sclerosis cohort with Mycobacterium avium subspecies paratuberculosis infection. Gut Pathogens, 16, (doi: 10.1186/s13099-024-00627-7)

Corbett, E., Ijaz, U. Z., Jackson, I., Phoenix, V. R. (2024) Stormwater quality and microbial ecology in an urban rain garden system. Frontiers in Water, 6, (doi: 10.3389/frwa.2024.1383382)

Koci, O., Russell, R. K., Shaikh, M. G., Edwards, C., Gerasimidis, K., Ijaz, U. Z. (2024) CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets. Microbiome, 12, (doi: 10.1186/s40168-024-01834-9)

Hassard, F., Curtis, T. P., Dotro, G. C., Golyshin, P., Gutierrez, T., Heaven, S., Horsfall, L., Jefferson, B., Jones, D. L., Krasnogor, N., Kumar, V., Lea-Smith, D. J., Le Corre Pidou, K., Liu, Y., Lyu, T., McCarthy, R. R., McKew, B., Smith, C., Yakunin, A., Yang, Z., Zhang, Y., Coulon, F. (2024) Scaling-up engineering biology for enhanced environmental solutions. ACS Synthetic Biology, 13, pp. 1586-1588. (doi: 10.1021/acssynbio.4c00292)

Jankowska, K., Domingo-Félez, C., Andres Prado-Rubio, O., Skiadas, I. V., Woodley, J. M., Pinelo, M. (2024) Effect of backwash as a strategy for biofouling control in the submerged ceramic membrane bioreactor for high-density cultivations: Process optimization and fouling mechanism at pilot scale. Separation and Purification Technology, 338, (doi: 10.1016/j.seppur.2024.126428)

Ameer, A., Saleem, F., Keating, C., Gundogdu, O., Ijaz, U. Z., Javed, S. (2024) Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data In Brief, 54, (doi: 10.1016/j.dib.2024.110487)

Saleem, F., Ameer, A., Star-Shirko, B., Keating, C., Gundogdu, O., Ijaz, U. Z., Javed, S. (2024) Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data In Brief, 54, (doi: 10.1016/j.dib.2024.110552)

Domingo-Felez, C., Jensen, M. M., Bang, A., Smets, B. F. (2024) Variability and uncertainty analysis of N2O emissions from WWTP to improve the accuracy of emission factors and the design of monitoring strategies. ACS ES&T Water, (doi: 10.1021/acsestwater.4c00048)

Qiu, Y., Ekström, S., Valverde-Pérez, B., Smets, B. F., Climent, J., Domingo-Félez, C., Martínez Cuenca, R., Plósz, B. G. (2024) Numerical modelling of surface aeration and N2O emission in biological water resource recovery. Water Research, 255, (doi: 10.1016/j.watres.2024.121398)

Gupta, R., Lee, S., Lui, J., Sloan, W., You, S. (2024) Carbon footprint assessment of water and wastewater treatment works in Scottish islands. Journal of Cleaner Production, 450, (doi: 10.1016/j.jclepro.2024.141650)

Gupta, R., Hajabdollahi Ouderji, Z., Uzma, , Yu, Z., Sloan, W. T., You, S. (2024) Machine learning for sustainable organic waste treatment: a critical review. npj Materials Sustainability, 2, (doi: 10.1038/s44296-024-00009-9)

Nichols, B., Briola, A., Logan, M., Havlik, J., Mascellani, A., Gkikas, K., Milling, S., Ijaz, U. Z., Quince, C., Svolos, V., Russell, R. K., Hansen, R., Gerasimidis, K. (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119, pp. 885-895. (doi: 10.1016/j.ajcnut.2023.12.027)

Aqueel, R., Badar, A., Ijaz, U., Malik, A. K. (2024) Microbial influencers and Cotton Leaf Curl Disease (CLCuD) susceptibility: a network perspective. Frontiers in Microbiology, 15, (doi: 10.3389/fmicb.2024.1381883)

Thapa, S., Sinclair, H. D., Creed, M. J., Mudd, S. M., Attal, M., Borthwick, A., Ghimire, B. N., Scott Watson, C. (2024) The impact of sediment flux and calibre on flood risk in the Kathmandu Valley, Nepal. Earth Surface Processes and Landforms, 49, pp. 706-727. (doi: 10.1002/esp.5731)

Gul, F., Herrema, H., Davids, M., Keating, C., Nasir, A., Ijaz, U. Z., Javed, S. (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16, (doi: 10.1186/s13099-024-00596-x)

Uri-Carreño, N., Nielsen, P. H., Gernaey, K. V., Domingo-Félez, C., Flores-Alsina, X. (2024) Nitrous oxide emissions from two full-scale membrane-aerated biofilm reactors. Science of the Total Environment, 908, (doi: 10.1016/j.scitotenv.2023.168030)

Scott Watson, C., Gyawali, J., Creed, M., Elliott, J. R. (2024) City-scale high-resolution flood models and the role of topographic data: a case study of Kathmandu, Nepal. Geocarto International, 39, (doi: 10.1080/10106049.2024.2387073)

Aqueel, R., Badar, A., Roy, N., Mushtaq, Q., Ali, A. F., Bashir, A., Ijaz, U. Z., Malik, K. A. (2023) Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated. npj Biofilms and Microbiomes, 9, (doi: 10.1038/s41522-023-00470-9)

Sperling, J. R., Poursat, B. A.J., Savage, L., Christie, I., Cuthill, C., Aekbote, B., McGuire, K., Karimullah, A. S., Robbie, J., Sloan, W. T., Gauchotte-Lindsay, C., Peveler, W. J., Clark, A. W. (2023) A cross-reactive plasmonic sensing array for drinking water assessment. Environmental Science: Nano, 10, pp. 3500-3508. (doi: 10.1039/D3EN00565H)

Alghafli, K., Ali, A. M., Shi, X., Sloan, W., Obeid, A. A.A., Shamsudduha, M. (2023) Evaluation of runoff estimation from GRACE coupled with different meteorological gridded products over the Upper Blue Nile Basin. Journal of Hydrology: Regional Studies, 50, (doi: 10.1016/j.ejrh.2023.101545)

Tsagkari, E., Sloan, W. (2023) The role of chlorine in the formation and development of tap water biofilms under different flow regimes. Microorganisms, 11, (doi: 10.3390/microorganisms11112680)

Okonkwo, V., Cholet, F., Ijaz, U. Z., Koottatep, T., Pussayanavin, T., Polpraset, C., Sloan, W. T., Connelly, S., Smith, C. J. (2023) intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Applied and Environmental Microbiology, 89, (doi: 10.1128/aem.01071-23)

Craven, H., Erlandsson, H., McGuinness, D., McGuinness, D., Mafra, D., Ijaz, U. Z., Bergman, P., Shiels, P. G., Stenvinkel, P. (2023) A normative microbiome is not restored following kidney transplantation. Clinical Science, 137, pp. 1563-1575. (doi: 10.1042/CS20230779)

Shrestha, D., Basnyat, D. B., Gyawali, J., Creed, M. J., Sinclair, H. D., Golding, B., Muthusamy, M., Shrestha, S., Scott Watson, C., Subedi, D. L., Haiju, R. (2023) Rainfall extremes under future climate change with implications for urban flood risk in Kathmandu, Nepal. International Journal of Disaster Risk Reduction, 97, (doi: 10.1016/j.ijdrr.2023.103997)

Vignola, M., Lenselink, J., Quinn, D., Ijaz, U. Z., Pereira, R., Sloan, W. T., Connelly, S., Moore, G., Gauchotte-Lindsay, C., Smith, C. J. (2023) Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities. AQUA: Water Infrastructure, Ecosystems and Society, 72, pp. 1837-1851. (doi: 10.2166/aqua.2023.036)

Dessì, P., Buenaño, C., Martínez-Sosa, S., Mills, S., Trego, A., Ijaz, U. Z., Pant, D., Puig, S., O'Flaherty, V., Farràs, P. (2023) Microbial electrosynthesis of acetate from CO2 in three-chamber cells with gas diffusion biocathode under moderate saline conditions. Environmental Science and Ecotechnology, 16, (doi: 10.1016/j.ese.2023.100261)

Elad, T., Philipsen Hally, M., Domingo-Félez, C., Knoop, O., E. Drewes, J., Valverde-Pérez, B., Smets, B. F. (2023) Exploring the effects of intermittent aeration on the performance of nitrifying membrane-aerated biofilm reactors. Science of the Total Environment, 891, pp. 164329. (doi: 10.1016/j.scitotenv.2023.164329)

Ameer, A., Cheng, Y., Saleem, F., Uzma, , McKenna, A., Richmond, A., Gundogdu, O., Sloan, W. T., Javed, S., Ijaz, U. Z. (2023) Temporal stability and community assembly mechanisms in healthy broiler cecum. Frontiers in Microbiology, 14, (doi: 10.3389/fmicb.2023.1197838)

Quick, L., Creed, M. J., Sinclair, H. D., Attal, M., Borthwick, A. G. L., Sinha, R. (2023) Hyperconcentrated floods cause extreme gravel transport through the sandy rivers of the Gangetic Plains. Communications Earth and Environment, 4, (doi: 10.1038/s43247-023-00953-9)

Sloan, W. T., Gómez-Borraz, T. L. (2023) Engineering biology in the face of uncertainty. Interface Focus, 13, (doi: 10.1098/rsfs.2023.0001)

Domingo-Félez, C., Jankowska, K., Skiadas, I. V., Woodley, J. M., Pinelo, M. (2023) Continuous ethanol production via ultrasound-enhanced yeast sedimentation. Food and Bioproducts Processing, 140, pp. 181-188. (doi: 10.1016/j.fbp.2023.06.002)

Li, W., Gupta, R., Zhang, Z., Cao, L., Li, Y., Show, P. L., Gupta, V. K., Kumar, S., Lin, K.-Y. A., Varjani, S., Connelly, S., You, S. (2023) A review of high-solid anaerobic digestion (HSAD): from transport phenomena to process design. Renewable and Sustainable Energy Reviews, 180, (doi: 10.1016/j.rser.2023.113305)

Singh, S., Keating, C., Ijaz, U. Z., Hassard, F. (2023) Molecular insights informing factors affecting low temperature anaerobic applications: diversity, collated core microbiomes and complexity stability relationships in LCFA-fed systems. Science of the Total Environment, 874, (doi: 10.1016/j.scitotenv.2023.162420)

Chrysochoidis, V., Andersen, M. H., Remigi, E. U., Faragó, M., Smets, B. F., Domingo-Félez, C., Valverde-Pérez, B. (2023) Critical evaluation of different mass transfer equations to model N2O emissions from Water Resource Recovery Facilities with diffuse aeration. Environmental Technology, (doi: 10.1080/09593330.2023.2215454)

Aziz, I., Noreen, Z., Ijaz, U. Z., Gundogdu, O., Hamid, M. H., Muhammad, N., Khan, A., Bokhari, H. (2023) A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome. Scientific Reports, 13, (doi: 10.1038/s41598-023-32491-x)

Alghafli, K., Shi, X., Sloan, W., Shamsudduha, M., Tang, Q., Sefelnasr, A., Ebraheem, A. A. (2023) Groundwater recharge estimation using in-situ and GRACE observations in the eastern region of the United Arab Emirates. Science of the Total Environment, 867, (doi: 10.1016/j.scitotenv.2023.161489)

Bach, L., Ram, A., Ijaz, U. Z., Evans, T. J., Haydon, D. T., Lindström, J. (2023) The effects of smoking on human pharynx microbiota composition and stability. Microbiology Spectrum, 11, (doi: 10.1128/spectrum.02166-21)

Sperling, J. R., Savage, L., Wilson, L. T., Cuthill, C., Mcguire, K., Robbie, J., Sloan, W. D., Gauchotte-Lindsay, C., Peveler, W. J., Clark, A. W. (2023) Optical Tastebuds for Water Quality Testing. (doi: 10.1117/12.2647396)

Woolfendon, C., Fowler, E., Gill, A., Kaplan, A., Curley, E., Lacsny, A., Naylor, L.A., McGregor, A., Bailey, D., Bass, A., Gauchotte-Lindsay, C., Li, Y., Moreau, J., Nager, R.G., White, S., Olive, V., Palmer, E., Prentice, T., Roberts, K., Slaymark, C., Wang, Y. (2023) Glasgow’s Floating Estuarine Wetlands Baseline Monitoring Report. (doi: 10.36399/gla.pubs.295312)

Cremen, G., Galasso, C., McCloskey, J., Barcena, A., Creed, M., Filippi, M. E., Gentile, R., Jenkins, L., Kalaycioglu, M., Mentese, E. Y., Muthusamy, M., Tarbali, K., Trogrlic, R. S. (2023) A state-of-the-art decision-support environment for risk-sensitive and pro-poor urban planning and design in Tomorrow's cities. International Journal of Disaster Risk Reduction, 85, (doi: 10.1016/j.ijdrr.2022.103400)

Evangelina Filippi, M., Barcena, A., Šakić Trogrlić, R., Cremen, G., Menteşe, E. Y., Gentile, R., Creed, M. J., Jenkins, L. T., Kalaycioglu, M., Poudel, D. P., Muthusamy, M., Manandhar, V., Adhikari, S., Rai, M., Dhakal, A., Barake, B., Tarbali, K., Galasso, C., McCloskey, J. (2023) Interdisciplinarity in practice: reflections from early-career researchers developing a risk-informed decision support environment for Tomorrow's cities. International Journal of Disaster Risk Reduction, 85, (doi: 10.1016/j.ijdrr.2022.103481)

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Cholet, F., Ijaz, U. Z., Smith, C. J. (2020) Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts. Environmental Microbiology, 22, pp. 2383-2402. (doi: 10.1111/1462-2920.15017)

Dingle, E. H., Sinclair, H. D., Venditti, J. G., Attal, M., Kinnaird, T. C., Creed, M., Quick, L., Nittrouer, J. A., Gautam, D. (2020) Sediment dynamics across gravel-sand transitions: implications for river stability and floodplain recycling. Geology, 48, pp. 468-472. (doi: 10.1130/g46909.1)

Logan, M., Gkikas, K., Svolos, V., Nichols, B., Milling, S., Gaya, D. R., Seenan, J., Macdonald, J., Hansen, R., Ijaz, U. Z., Russell, R. K., Gerasimidis, K. (2020) Analysis of 61 exclusive enteral nutrition formulas used in management of active Crohn's disease - new insights into dietary disease triggers. Alimentary Pharmacology and Therapeutics, 51, pp. 935-947. (doi: 10.1111/apt.15695)

Creed, M. J., Dingle, E. H., Sinclair, H. D., Gautam, D., Gourmelen, N., Borthwick, A. G. L., Attal, M. (2020) Numerical Modelling of Dynamic Flood Topographies in the Terai Region, Nepal. (doi: 10.5194/egusphere-egu2020-5533)

Dingle, E., Sinclair, H., Venditti, J., Attal, M., Kinnaird, T., Creed, M., Quick, L., Nittrouer, J., Gautam, D. (2020) Sediment Dynamics Across Gravel-Sand Transitions: Implications for River Stability and Floodplain Recycling. (doi: 10.5194/egusphere-egu2020-573)

Heys, C., Cheaib, B., Busetti, A., Kazlauskaite, R., Maier, L., Sloan, W.T., Ijaz, U.Z., Kaufmann, J., McGinnity, P., Llewellyn, M.S. (2020) Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar. Applied and Environmental Microbiology, 86, (doi: 10.1128/AEM.02283-19)

Cheaib, B., Seghouani, H., Ijaz, U., Derome, N. (2020) Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations. Microbiome, 8, (doi: 10.1186/s40168-020-0789-0)

Domingo-Felez, C., Smets, B. F. (2020) Modelling N2O dynamics of activated sludge biomass: Uncertainty analysis and pathway contributions. Chemical Engineering Journal, 379, (doi: 10.1016/j.cej.2019.122311)

Bain, K.A., McDonald, E., Moffat, F., Tutino, M., Castelino, M., Barton, A., Cavanagh, J., Ijaz, U.Z., Siebert, S., McInnes, I.B., Astrand, A., Holmes, S., Milling, S.W.F. (2020) Alopecia areata is characterized by dysregulation in systemic type 17 and type 2 cytokines, which may contribute to disease‐associated psychological morbidity. British Journal of Dermatology, 182, pp. 130-137. (doi: 10.1111/bjd.18008)

Stratakos, A. C., Ijaz, U. Z., Ward, P., Linton, M., Kelly, C., Pinkerton, L., Scates, P., McBride, J., Pet, I., Criste, A., Stef, D., Couto, J. M., Sloan, W. T., Dorrell, N., Wren, B. W., Stef, L., Gundogdu, O., Corcionivoschi, N. (2020) In vitro and in vivo characterisation of Listeria monocytogenes outbreak isolates. Food Control, 107, (doi: 10.1016/j.foodcont.2019.106784)

Jebsen, J. M., Abbott, C., Oliver, R., Ochu, E., Jayasinghe, I., Gauchotte-Lindsay, C. (2020) A review of barriers women face in research funding processes in the UK. Psychology of Women and Equalities Review, 3,

Jukes, C., Ijaz, U. Z., Buckley, A., Spencer, J., Irvine, J., Li, J. V., Marchesi, J. R., Candlish, D., Douce, G. (2020) Bile salt metabolism is not the only factor contributing to Clostridioides (Clostridium) difficile disease severity in the murine model of disease. Gut Microbes, 11, pp. 481-496. (doi: 10.1080/19490976.2019.1678996)

Connelly, S., Pussayanavin, T., Randle-Boggis, R., Wicheansan, A., Jampathong, S., Keating, C., Ijaz, U. Z., Sloan, W., Koottatep, T. (2019) Solar Septic Tank: next generation sequencing reveals effluent microbial community composition as a useful index of system performance. Water, 11, (doi: 10.3390/w11122660)

Nakaew, N., Lumyong, S., Sloan, W. T., Sungthong, R. (2019) Bioactivities and genome insights of a thermotolerant antibiotics-producing Streptomyces sp. TM32 reveal its potentials for novel drug discovery. MicrobiologyOpen, 8, (doi: 10.1002/mbo3.842)

Song, Y., Glidle, A., Quince, C., Collins, G., Sloan, W., Yin, H. (2019) Single-Cell Microfluidic Platform to Study Anaerobic Bacteria.

Blair, R. M., Waldron, S., Gauchotte-Lindsay, C. (2019) Average daily flow of microplastics through a tertiary wastewater treatment plant over a ten-month period. Water Research, 163, (doi: 10.1016/j.watres.2019.114909)

Gerasimidis, K., Svolos, V., Nichols, B., Papadopoulou, R., Quince, C., Ijaz, U. Z., Milling, S., Gaya, D. R., Russell, R. K., Hansen, R. (2019) Reply. Gastroenterology, 157, pp. 1161-1162. (doi: 10.1053/j.gastro.2019.08.015)

Mohamad Ali Nasri, I. F., Mbomson, I., Sharp, G.J., De La Rue, R.M., Johnson, N.P., Sorel, M., Gauchotte-Lindsay, C. (2019) Biomedical optical sensing using nano-/micro-structured metamaterials. (doi: 10.1109/ICTON.2019.8840143)

Tsagkari, E., Connelly, S., Liu, Z., McBride, A., Sloan, W. T. (2019) A Novel Rapid Prototyping Tool for Suspended Biofilm Growth Media.

Logan, M., Clark, C. M., Ijaz, U. Z., Gervais, L., Duncan, H., Garrick, V., Curtis, L., Buchanan, E., Cardigan, T., Armstrong, L., Delahunty, C., Flynn, D. M., Barclay, A., Tayler, R., McDonald, E., Milling, S., Hansen, R., Gerasimidis, K., Russell, R. K. (2019) The reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food re-introduction. Alimentary Pharmacology and Therapeutics, 50, pp. 664-674. (doi: 10.1111/apt.15425)

Afonso, C. et al. (2019) Data mining and visualisation: general discussion. Faraday Discussions, 218, pp. 354-371. (doi: 10.1039/c9fd90044f)

Gauchotte-Lindsay, C., Aspray, T. J., Knapp, M., Ijaz, U. Z. (2019) Systems biology approach to elucidation of contaminants biodegradation in complex samples- integration of high-resolution analytical and molecular tools. Faraday Discussions, 218, pp. 481-504. (doi: 10.1039/C9FD00020H)

Keating, C., Song, Y., Ogundero, A., Mathur, N., Gonzalez-Cabaleiro, R., Quince, C., Collins, G., Yin, H., Sloan, W. (2019) Development of a Novel Anaerobic Incubation and Monitoring Platform Embedded with Microfluidics for Real-Time Growth Analysis of Anaerobic Cells.

Tsagkari, E., Connelly, S., Liu, Z., McBride, A., Sloan, W.T. (2019) How the Design of Filter Media Affects Hydrodynamics and Biofilms in Drinking Water.

Wu, L. et al. (2019) Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology, 4, pp. 1183-1195. (doi: 10.1038/s41564-019-0426-5)

Tsagkari, E., Sloan, W. T. (2019) Impact of Methylobacterium in the drinking water microbiome on removal of trihalomethanes. International Biodeterioration and Biodegradation, 141, pp. 10-16. (doi: 10.1016/j.ibiod.2018.07.015)

Plancq, J., Couto, J., Ijaz, U. Z., Leavitt, P. R., Toney, J. (2019) Next generation sequencing to identify lacustrine haptophytes in the Canadian Prairies: significance for temperature proxy applications. Journal of Geophysical Research: Biogeosciences, 124, pp. 2144-2158. (doi: 10.1029/2018JG004954)

Frau, A., Kenny, J. G., Lenzi, L., Campbell, B. J., Ijaz, U. Z., Duckworth, C. A., Burkitt, M. D., Hall, N., Anson, J., Darby, A. C., Probert, C. S.J. (2019) DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies. Scientific Reports, 9, (doi: 10.1038/s41598-019-44974-x)

Mohamad Ali Nasri, I. F., Sharp, G. J., De La Rue, R., Johnson, N.P., Sorel, M., Gauchotte-Lindsay, C. (2019) Array Metasurfaces Based on Asymmetric Split-H Resonator for Environment Monitoring System.

Trego, A. C., Galvin, E., Sweeney, C., Dunning, S., Murphy, C., Mills, S., Nzeteu, C., Quince, C., Connelly, S., Ijaz, U. Z., Collins, G. (2019) De novo growth of methanogenic granules indicates a biofilm life-cycle with complex ecology. bioRxiv, (doi: 10.1101/667386)

Su, Q., Domingo-Felez, C., Zhang, Z., Blum, J.-M., Mark Jensen, M., Smets, B. F. (2019) The effect of pH on N2O production in intermittently-fed nitritation reactors. Water Research, 156, pp. 223-231. (doi: 10.1016/j.watres.2019.03.015)

Domingo-Felez, C., Smets, B. F. (2019) Regulation of key N2O production mechanisms during biological water treatment. Current Opinion in Biotechnology, 57, pp. 119-126. (doi: 10.1016/j.copbio.2019.03.006)

Ormsby, M. J., Logan, M., Johnson, S. A., McIntosh, A., Fallata, G., Papadopoulou, R., Papachristou, E., Hold, G. L., Hansen, R., Ijaz, U. Z., Russell, R. K., Gerasimidis, K., Wall, D. M. (2019) Inflammation associated ethanolamine facilitates infection by Crohn's disease-linked adherent-invasive Escherichia coli. EBioMedicine, 43, pp. 325-332. (doi: 10.1016/j.ebiom.2019.03.071)

Mohamad Ali Nasri, I. F., Sharp, G. J., De La Rue, R., Johnson, N.P., Sorel, M., Gauchotte-Lindsay, C. (2019) Asymmetric Split H Resonators for Estrogenic Hormone Detection.

Su, Q., Domingo-Felez, C., Mark Jensen, M., Smets, B. F. (2019) Abiotic nitrous oxide (N2O) production is strongly pH dependent, but contributes little to overall N2O emissions in biological nitrogen removal systems. Environmental Science and Technology, (doi: 10.1021/acs.est.8b06193)

Brown, M.R., Baptista, J.C., Lunn, M., Swan, D.L., Smith, S.J., Davenport, R.J., Allen, B.D., Sloan, W.T., Curtis, T.P. (2019) Coupled virus - bacteria interactions and ecosystem function in an engineered microbial system. Water Research, 152, pp. 264-273. (doi: 10.1016/j.watres.2019.01.003)

Blair, R. M., Waldron, S., Phoenix, V., Gauchotte-Lindsay, C. (2019) Microscopy and elemental analysis characterisation of microplastics in sediment of a freshwater urban river in Scotland, UK. Environmental Science and Pollution Research, 26, pp. 12491-12504. (doi: 10.1007/s11356-019-04678-1)

Svolos, V., Hansen, R., Nichols, B., Quince, C., Ijaz, U.Z., Papadopoulou, R.T., Edwards, C.A., Watson, D., Alghamdi, A., Brejnrod, A., Ansalone, C., Duncan, H., Gervais, L., Tayler, R., Salmond, J., Bolognini, D., Klopfleisch, R., Gaya, D.R., Milling, S., Russell, R.K., Gerasimidis, K. (2019) Treatment of active Crohn’s disease with an ordinary food-based diet that replicates exclusive enteral nutrition. Gastroenterology, 156, pp. 1354-1367.e6. (doi: 10.1053/j.gastro.2018.12.002)

Dingle, K. E., Didelot, X., Quan, T. P., Eyre, D. W., Stoesser, N., Marwick, C. A., Coia, J., Brown, D., Buchanan, S., Ijaz, U. Z., Goswami, C., Douce, G., Fawley, W. N., Wilcox, M. H., Peto, T. E.A., Walker, A. S., Crook, D. W. (2019) A role for tetracycline selection in recent evolution of agriculture-associated Clostridium difficile PCR ribotype 078. mBio, 10, (doi: 10.1128/mBio.02790-18)

Knox, G.W., McInnes, C.R., Younger, P.L., Sloan, W.T. (2019) Engineering artificial thermal mountains for large-scale water management and carbon drawdown. Environmental Science: Water Research and Technology, 5, pp. 296-314. (doi: 10.1039/c8ew00571k)

Cholet, F., Ijaz, U. Z., Smith, C. J. (2019) Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples. Environmental Microbiology, 21, pp. 827-844. (doi: 10.1111/1462-2920.14516)

Liu, Z., Cichocki, N., Hübschmann, T., Süring, C., Ofiţeru, I. D., Sloan, W. T., Grimm, V., Müller, S. (2019) Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis. Environmental Microbiology, 21, pp. 164-181. (doi: 10.1111/1462-2920.14437)

Mohamad Ali Nasri, I. F., Sharp, G. J., De La Rue, R. M., Johnson, N.P., Sorel, M., Gauchotte-Lindsay, C. (2019) Detection of Organic Molecules using Asymmetric Plasmonic Nanostructures.

Keating, C., Hinchcliff, J., Davies, R., Wan, A., Davies, S., Fitzgerald, R., Ijaz, U., Smith, C., Bolton, M. (2019) Effects of Supplementing a Fishmeal Diet with Algae on the Hindgut Microbiome of Farmed Atlantic Cod (Gadus Morhua) [Poster]

Rangjaroen, C., Lumyong, S., Sloan, W. T., Sungthong, R. (2019) Herbicide-tolerant endophytic bacteria of rice plants as the biopriming agents for fertility recovery and disease suppression of unhealthy rice seeds. BMC Plant Biology, 19, (doi: 10.1186/s12870-019-2206-z)

Keating, C., Song, Y., Ogundero, A., Mathur, N., Gonzalez-Cabaleiro, R., Quince, C., Collins, G., Yin, H., Sloan, W. (2019) Single-Cell Real Time Analysis of the Anaerobic Bacteria Desulfovibrio Vulgaris Demonstrates Population Heterogeneity That Decreases with Increasing pH Stress [Poster]

Trego, A. C., Morabito, C., Mills, S., Connelly, S., Bourven, I., Guibaud, G., Quince, C., Ijaz, U. Z., Collins, G. (2018) Diversity converges during community assembly in methanogenic granules, suggesting a biofilm life-cycle. bioRxiv, (doi: 10.1101/484642)

Calus, S. T., Ijaz, U. Z., Pinto, A. (2018) NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform. GigaScience, 7, (doi: 10.1093/gigascience/giy140)

Kostrytsia, A., Papirio, S., Morrison, L., Ijaz, U. Z., Collins, G., Lens, P. N.L., Esposito, G. (2018) Biokinetics Of microbial consortia using biogenic sulfur as a novel electron donor for sustainable denitrification. Bioresource Technology, 270, pp. 359-367. (doi: 10.1016/j.biortech.2018.09.044)

De Vrieze, J., Ijaz, U. Z., Saunders, A. M., Theuerl, S. (2018) Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion. Scientific Reports, 8, (doi: 10.1038/s41598-018-34921-7)

Mohamad Ali Nasri, I. F., Sharp, G. J., De La Rue, R., Johnson, N.P., Sorel, M., Gauchotte-Lindsay, C. (2018) Optical Sensing of Estrogenic Hormones Using Nanostructured Metamaterials.

Ijaz, U. Z., Sivaloganathan, L., McKenna, A., Richmond, A., Kelly, C., Linton, M., Stratakos, A. C., Lavery, U., Elmi, A., Wren, B. W., Dorrell, N., Corcionivoschi, N., Gundogdu, O. (2018) Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter. Frontiers in Microbiology, 9, (doi: 10.3389/fmicb.2018.02452)

Vignola, M., Werner, D., Hammes, F., King, L. C., Davenport, R. J. (2018) Flow-cytometric quantification of microbial cells on sand from water biofilters. Water Research, 143, pp. 66-76. (doi: 10.1016/j.watres.2018.05.053)

Tsagkari, E., Sloan, W. T. (2018) The role of the motility of Methylobacterium in bacterial interactions in drinking water. Water, 10, (doi: 10.3390/w10101386)

Gerasimidis, K., Zafeiropoulou, K., Mackinder-Jonas, M., Ijaz, U. Z., Duncan, H., Buchanan, E., Cardigan, T., Edwards, C. A., McGrogan, P., Russell, R. K. (2018) Comparison of clinical methods with the faecal gluten immunogenic peptide to assess gluten intake in coeliac disease. Journal of Pediatric Gastroenterology and Nutrition, 67, pp. 356-360. (doi: 10.1097/MPG.0000000000002062)

Huang, W., Creed, M., Chen, F., Liu, H., Ma, A. (2018) Scour around submerged spur dikes with flexible mattress protection. Journal of Waterway, Port, Coastal, and Ocean Engineering, 144, (doi: 10.1061/(ASCE)WW.1943-5460.0000466)

Zhang, L., Duff, A., Smith, C. J. (2018) Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems. Environmental Microbiology, 20, pp. 2834-2853. (doi: 10.1111/1462-2920.14238)

Reich, I., Ijaz, U. Z., Gormally, M., Smith, C. J. (2018) 16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus. Scientific Reports, 8, (doi: 10.1038/s41598-018-28720-3)

Tsagkari, E., Sloan, W.T. (2018) Biofilm Growth in Drinking Water Systems under Stagnant Conditions.

Keating, C., Hughes, D., Mahony, T., Cysneiros, D., Ijaz, U.Z., Smith, C.J., O‘Flaherty, V. (2018) Cold adaptation and replicable microbial community development during long-term low temperature anaerobic digestion treatment of synthetic sewage. FEMS Microbiology Ecology, 94, (doi: 10.1093/femsec/fiy095)

Tsagkari, E., Sloan, W.T. (2018) Turbulence accelerates the growth of drinking water biofilms. Bioprocess and Biosystems Engineering, 41, pp. 757-770. (doi: 10.1007/s00449-018-1909-0)

Sampsonidis, I., Gauchotte-Lindsay, C. (2018) Characterisation of Semi-volatile Organic Compounds in Wastewater Produced During Underground Coal Gasification Using GCxGC-TOFMS.

Blum, J.-M., Su, Q., Ma, Y., Valverde-Pérez, B., Domingo-Félez,, C., Mark Jensen, M., Smets, B. F. (2018) The pH dependency of N-converting enzymatic processes, pathways and microbes: Effect on net N2O production. Environmental Microbiology, 20, pp. 1623-1640. (doi: 10.1111/1462-2920.14063)

Yuan, X., Song, Y., Song, Y., Xu, J., Wu, Y., Glidle, A., Cusack, M., Ijaz, U. Z., Cooper, J. M., Huang, W. E., Yin, H. (2018) Effect of laser irradiation on cell function and its implications in Raman spectroscopy. Applied and Environmental Microbiology, 84, (doi: 10.1128/AEM.02508-17)

Pedersen, C., Ijaz, U. Z., Gallagher, E., Horton, F., Ellis, R. J., Jaiyeola, E., Duparc, T., Russell-Jones, D., Hinton, P., Cani, P. D., La Ragione, R. M., Robertson, M. D. (2018) Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans. Physiological Reports, 6, (doi: 10.14814/phy2.13649)

Pinto, A. J., de Vrieze, J., Sloan, W. T., Ijaz, U. Z. (2018) The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. Microbiome, 6, (doi: 10.1186/s40168-018-0449-9)

Joyce, A., Ijaz, U. Z., Nzeteu, C., Vaughan, A., Shirran, S. L., Botting, C. H., Quince, C., O'Flaherty, V., Abram, F. (2018) Linking microbial community structure and function during the acidified anaerobic digestion of grass. Frontiers in Microbiology, 9, (doi: 10.3389/fmicb.2018.00540)

Vignola, M., Werner, D., Wade, M. J., Meynet, P., Davenport, R. J. (2018) Medium shapes the microbial community of water filters with implications for effluent quality. Water Research, 129, pp. 499-508. (doi: 10.1016/j.watres.2017.09.042)

Heidrich, E.S., Dolfing, J., Wade, M.J., Sloan, W.T., Quince, C., Curtis, T.P. (2018) Temperature, inocula and substrate: contrasting electroactive consortia, diversity and performance in microbial fuel cells. Bioelectrochemistry, 119, pp. 43-50. (doi: 10.1016/j.bioelechem.2017.07.006)

Couto, J. M., McGarrity, A., Russell, J., Sloan, W. T. (2018) The effect of metabolic stress on genome stability of a synthetic biology chassis Escherichia coli K12 strain. Microbial Cell Factories, 17, (doi: 10.1186/s12934-018-0858-2)

Koci, O., Logan, M., Svolos, V., Russell, R. K., Gerasimidis, K., Ijaz, U. Z. (2018) An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights. PeerJ, 6, (doi: 10.7717/peerj.5047)

Yuan, X., Couto, J. M., Glidle, A., Song, Y., Sloan, W., Yin, H. (2017) Single-cell microfluidics to study the effects of genome deletion on bacterial growth behavior. ACS Synthetic Biology, 6, pp. 2219-2227. (doi: 10.1021/acssynbio.7b00177)

Domingo-Felez, C., Calderó-Pascual, M., Sin, G., Plósz, B. G., Smets, B. F. (2017) Calibration of the comprehensive NDHA-N2O dynamics model for nitrifier-enriched biomass using targeted respirometric assays. Water Research, 126, pp. 29-39. (doi: 10.1016/j.watres.2017.09.013)

Ho, A., Ijaz, U. Z., Janssens, T. K.S., Ruijs, R., Kim, S. Y., de Boer, W., Termorshuizen, A., van der Putten, W. H., Bodelier, P. L.E. (2017) Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition. GCB Bioenergy, 9, pp. 1707-1720. (doi: 10.1111/gcbb.12457)

Logan, M., Ijaz, U.Z., Hansen, R., Gerasimidis, K., Russell, R.K. (2017) Letter: reproducible evidence shows that exclusive enteral nutrition significantly reduces faecal calprotectin concentrations in children with active Crohn's Disease. Alimentary Pharmacology and Therapeutics, 46, pp. 1119-1120. (doi: 10.1111/apt.14351)

Blair, R., Waldron, S., Phoenix, V., Gauchotte-Lindsay, C. (2017) Micro- and nanoplastic pollution of freshwater and wastewater treatment systems. Springer Science Reviews, 5, pp. 19-30. (doi: 10.1007/s40362-017-0044-7)

Sinclair, H., Attal, M., Borthwick, A., Budimir, M., Creed, M., Dingle, E., Dugar, S. (2017) Improving understanding of flooding and resilience in the Terai, Nepal.

Parsons, B. N., Ijaz, U. Z., D’Amore, R., Burkitt, M. D., Eccles, R., Lenzi, L., Duckworth, C. A., Moore, A. R., Tiszlavicz, L., Varro, A., Hall, N., Pritchard, D. M. (2017) Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use. PLoS Pathogens, 13, (doi: 10.1371/journal.ppat.1006653)

Ritchie, N. D., Ijaz, U. Z., Evans, T. J. (2017) IL-17 signalling restructures the nasal microbiome and drives dynamic changes following Streptococcus pneumoniae colonization. BMC Genomics, 18, (doi: 10.1186/s12864-017-4215-3)

Su, Q., Ma, C., Domingo-Felez, C., Kiil, A. S., Thamdrup, B., Mark Jensen, M., Smets, B. F. (2017) Low nitrous oxide production through nitrifier-denitrification in intermittent-feed high-rate nitritation reactors. Water Research, 123, pp. 429-438. (doi: 10.1016/j.watres.2017.06.067)

Ijaz, A. Z., Jeffries, T. C., Ijaz, U. Z., Hamonts, K., SinghIjaz, B. K. (2017) Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences. PeerJ, 5, (doi: 10.7717/peerj.3827)

Tsagkari, E., Keating, C., Couto, J. M., Sloan, W. T. (2017) A keystone Methylobacterium strain in biofilm formation in drinking water. Water, 9, (doi: 10.3390/w9100778)

Cho, S.-K., Jung, K.-W., Kim, D.-H., Kwon, J.-C., Ijaz, U. Z., Shin, S. G. (2017) Bacterial community analysis in upflow multilayer anaerobic reactor (UMAR) treating high-solids organic wastes. Biotechnology Progress, 33, pp. 1226-1234. (doi: 10.1002/btpr.2540)

Ulrich, B. A., Vignola, M., Edgehouse, K., Werner, D., Higgins, C. P. (2017) Organic carbon amendments for enhanced biological attenuation of trace organic contaminants in biochar-amended stormwater biofilters. Environmental Science and Technology, 51, pp. 9184-9193. (doi: 10.1021/acs.est.7b01164)

Ma, Y., Domingo-Félez, C., Plósz, B. G., Smets, B. F. (2017) Intermittent aeration suppresses nitrite-oxidizing bacteria in membrane-aerated biofilms: A model-based explanation. Environmental Science and Technology, 51, pp. 6146-6155. (doi: 10.1021/acs.est.7b00463)

Connelly, S., Shin, S. G., Dillon, R. J., Ijaz, U. Z., Quince, C., Sloan, W. T., Collins, G. (2017) Bioreactor scalability: laboratory-scale bioreactor design influences performance, ecology, and community physiology in expanded granular sludge bed bioreactors. Frontiers in Microbiology, 8, (doi: 10.3389/fmicb.2017.00664)

Woodcock, S., Sloan, W. T. (2017) Biofilm community succession: a neutral perspective. Microbiology, 163, pp. 664-668. (doi: 10.1099/mic.0.000472)

Creed, M. J., Draper, S., Nishino, T., Borthwick, A. G. L. (2017) Flow through a very porous obstacle in a shallow channel. Proceedings of the Royal Society of London Series A: Mathematical, Physical and Engineering Sciences, 473, (doi: 10.1098/rspa.2016.0672)

De Vrieze, J., Christiaens, M. E.R., Walraedt, D., Devooght, A., Ijaz, U. Z., Boon, N. (2017) Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure. Water Research, 111, pp. 109-117. (doi: 10.1016/j.watres.2016.12.042)

Harris, K., Parsons, T. L., Ijaz, U. Z., Lahti, L., Holmes, I., Quince, C. (2017) Linking statistical and ecological theory: Hubbell's unified neutral theory of biodiversity as a hierarchical dirichlet process. Proceedings of the IEEE, 105, pp. 516-529. (doi: 10.1109/JPROC.2015.2428213)

Ijaz, U. Z., Quince, C., Hanske, L., Loman, N., Calus, S. T., Bertz, M., Edwards, C. A., Gaya, D. R., Hansen, R., McGrogan, P., Russell, R. K., Gerasimidis, K. (2017) The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically linked kindred. PLoS ONE, 12, (doi: 10.1371/journal.pone.0172605)

Svolos, V., Hansen, R., Ijaz, U.Z., Quince, C., Watson, D., Alghamdi, A., Brejnrod, A., Ansalone, C., Milling, S., Gaya, D., Russell, R., Gerasimidis, K. (2017) Dietary Manipulation of the Healthy Human and Colitic Murine Gut Microbiome by CD-TREAT Diet and Exclusive Enteral Nutrition; A Proof of Concept Studyy. (doi: 10.1093/ecco-jcc/jjx002.045)

Domingo-Félez, C., Pellicer-Nàcher, C., Petersen, M. S., Jensen, M. M., Plósz, B. G., Smets, B. F. (2017) Heterotrophs are key contributors to nitrous oxide production in activated sludge under low C-to-N ratios during nitrification-Batch experiments and modeling. Biotechnology and Bioengineering, 114, pp. 132-140. (doi: 10.1002/bit.26062)

Tsagkari, E., Sloan, W.T. (2017) Effect of Methylobacterium on Chloroform Concentration in Drinking Water.

Vignola, M., Werner, D., Davenport, R.J. (2017) Evaluating Neutral Assembly in the Formation of Water Filters Microbial Communities [oral presentation]

Tsagkari, E., Keating, C., Couto, J., Sloan, W.T. (2017) Impact of a Methylobacterium Species in Drinking Water Biofilms.

Duff, A. M., Zhang, L.-M., Smith, C. J. (2017) Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Scientific Reports, 7, (doi: 10.1038/s41598-017-13583-x)

Creed, M. J., Apostolidou, I.-G., Taylor, P. H., Borthwick, A. G. L. (2016) A finite volume shock-capturing solver of the fully coupled shallow water-sediment equations. International Journal for Numerical Methods in Fluids, 84, pp. 509-542. (doi: 10.1002/fld.4359)

Sinclair, L., Ijaz, U. Z., Jensen, L. J., Coolen, M. J.L., Gubry-Rangin, C., Chroňáková, A., Oulas, A., Pavloudi, C., Schnetzer, J., Weimann, A., Ijaz, A., Eiler, A., Quince, C., Pafilis, E. (2016) Seqenv: linking sequences to environments through text mining. PeerJ, 4, (doi: 10.7717/peerj.2690)

Pedersen, C., Gallagher, E., Horton, F., Ellis, R. J., Ijaz, U. Z., Wu, H., Jaiyeola, E., Diribe, O., Duparc, T., Cani, P. D., Gibson, G. R., Hinton, P., Wright, J., La Ragione, R., Robertson, M. D. (2016) Host–microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intake. British Journal of Nutrition, 116, pp. 1869-1877. (doi: 10.1017/S0007114516004086)

Pedersen, C., Hinton, P., Gallagher, E., Horton, F., Ellis, R., Ijaz, U. Z., Wu, H., Jaiyeola, E., Diribe, O., Gibson, G. R., Duparc, T., Cani, P. D., Wright, J., Russell-Jones, D., La Ragione, R., Robertson, M. D. (2016) Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in Well-controlled Type 2 Diabetes. (doi: 10.1017/S0029665116001191)

Oulas, A., Varsos, C., Patkos, T., Pavloudi, C., Gougousis, A., Ijaz, U. Z., Filiopoulou, I., Pattakos, N., Vanden Berghe, E., Fernández-Guerra, A., Faulwetter, S., Chatzinikolaou, E., Pafilis, E., Bekiari, C., Doerr, M., Arvanitidis, C. (2016) Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab) Biodiversity Data Journal, 4, (doi: 10.3897/BDJ.4.e8357)

Maldonado, S., Creed, M. J., Borthwick, A. G. L. (2016) Bed-slope-related diffusion of an erodible hump. CRC Press

Widder, S. et al. (2016) Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME Journal, 10, pp. 2557-2568. (doi: 10.1038/ismej.2016.45)

Ray, J. L., Althammer, J., Skaar, K. S., Simonelli, P., Larsen, A., Stoecker, D., Sazhin, A., Ijaz, U. Z., Quince, C., Nejstgaard, J. C., Frischer, M., Pohnert, G., Troedsson, C. (2016) Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities. Molecular Ecology, 25, pp. 5585-5602. (doi: 10.1111/mec.13844)

Domingo-Félez, C., Smets, B. F. (2016) A consilience model to describe N2O production during biological N removal. Environmental Science: Water Research and Technology, 2, pp. 923-930. (doi: 10.1039/C6EW00179C)

Quince, C., Connelly, S., Raguideau, S., Alneberg, J., Shin, S. G., Collins, G., Eren, A. M. (2016) De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning. bioRxiv, (doi: 10.1101/073825)

Gerasimidis, K., Ijaz, U. Z., Edwards, C., Russell, R. K., Quince, C., Hansen, R. (2016) Response to Kaakoush et al. American Journal of Gastroenterology, 111, pp. 1033-1034. (doi: 10.1038/ajg.2016.169)

Tatti, E., McKew, B. A., Whitby, C., Smith, C. J. (2016) Simultaneous DNA-RNA extraction from coastal sediments and quantification of 16S rRNA genes and transcripts by real-time PCR. Journal of Visualized Experiments, (doi: 10.3791/54067)

Haig, S.-J., Gauchotte-Lindsay, C., Collins, G., Quince, C. (2016) Bioaugmentation mitigates the impact of estrogen on coliform-grazing protozoa in slow sand filters. Environmental Science and Technology, 50, pp. 3101-3110. (doi: 10.1021/acs.est.5b05027)

Svolos, V., Hansen, R., Hughes, K., Ijaz, U.Z., Quince, C., Gaya, D., Russell, R., Gerasimidis, K. (2016) The Impact of ‘Crohn’s Disease-TReatment-with-EATing’ Diet (CD-TREAT Diet) and Exclusive Enteral Nutrition on Healthy Gut Bacteria Metabolism. (doi: 10.1093/ecco-jcc/jjw019.017)

Bautista-de los Santos, Q., Schroeder, J. L., Blakemore, O., Moses, J., Haffey, M., Sloan, W., Pinto, A. J. (2016) The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales. Water Research, 90, pp. 216-224. (doi: 10.1016/j.watres.2015.12.010)

Schirmer, M., D’Amore, R., Ijaz, U. Z., Hall, N., Quince, C. (2016) Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics, 17, (doi: 10.1186/s12859-016-0976-y)

Torondel, B., Ensink, J. H.J., Gundogdu, O., Ijaz, U. Z., Parkhill, J., Abdelahi, F., Nguyen, V.-A., Sudgen, S., Gibson, W., Walker, A. W., Quince, C. (2016) Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines. Microbial Biotechnology, 9, pp. 209-223. (doi: 10.1111/1751-7915.12334)

Gauchotte-Lindsay, C., Turnbull, S. M. (2016) On-line high-precision carbon position-specific stable isotope analysis: a review. Trends in Analytical Chemistry, 76, pp. 115-125. (doi: 10.1016/j.trac.2015.07.010)

Barrett, M., Sloan, W., Stark, W., Watson, I. (2016) New Developments in Synthetic Biology at the University of Glasgow.

D’Amore, R., Ijaz, U. Z., Schirmer, M., Kenny, J. G., Gregory, R., Darby, A. C., Shakya, M., Podar, M., Quince, C., Hall, N. (2016) A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics, 17, (doi: 10.1186/s12864-015-2194-9)

Keating, C., Chin, J. P., Hughes, D., Manesiotis, P., Cysneiros, D., Mahony, T., Smith, C. J., McGrath, J. W., O’Flaherty, V. (2016) Biological phosphorus removal during high-rate, low-temperature, anaerobic digestion of wastewater. Frontiers in Microbiology, 7, (doi: 10.3389/fmicb.2016.00226)

Bautista-de los Santos, Q. M., Schroeder, J., Sevillano-Rivera, M. C., Sungthong, R., Ijaz, U. Z., Sloan, W. T., Pinto, A. J. (2016) Emerging investigators series: Microbial communities in full-scale drinking water distribution systems – A meta-analysis. Environmental Science: Water Research and Technology, 2, pp. 631-644. (doi: 10.1039/C6EW00030D)

Tsagkari, E., Couto, J., Sloan, W.T. (2016) Methylobacteria: Keystone Species in Biofilm Formation?

Tsagkari, E., Couto, J., Sloan, W.T. (2016) Methylobacteria: Keystone Species in Biofilm Succession?

Vignola, M., Werner, D., Davenport, R.J. (2016) Niche and Neutral Effects in Lab Scale Water Filter Communities [poster]

Abberton, C. L., Bereschenko, L., van der Wielen, P. W.J.J., Smith, C. (2016) Survival, biofilm formation, and growth potential of environmental and enteric escherichia coli strains in drinking water microcosms. Applied and Environmental Microbiology, 82, pp. 5320-5331. (doi: 10.1128/AEM.01569-16)

Gerasimidis, K., Bertz, M., Quince, C., Brunner, K., Bruce, A., Combet, E., Calus, S., Loman, N., Ijaz, U. (2016) The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes, 9, (doi: 10.1186/s13104-016-2171-7)

Tsagkari, E., Keating, C., Sloan, W.T. (2016) Turbulence Promotes Core-and-mantle Structure in Drinking Water Bacterial Aggregates.

Keating, C., Song, Y., Quince, C., Collins, G., Yin, H., Sloan, W. (2016) Understanding Syntrophy in Anaerobic Digestion.