Article

Saleem, Farrukh and Ameer, Aqsa and Afzal, Farhan and Usman, Muhammad and Irshad, Hamid and Sattar, Sadia and Ijaz, Umer Zeeshan and Javed, Sundus (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18: 144. ISSN 1756-0500

Badar, Ayesha and Aqueel, Rhea and Nawaz, Ali and Ijaz, Umer Zeeshan and Malik, Kauser Abdulla (2025) Microbiota transplantation for Cotton Leaf Curl Disease suppression - core microbiome and transcriptome dynamics. Communications Biology, 8 (1): 380. ISSN 2399-3642

Zainy, Zainy and Hyder, Muhammad Zeeshan and Uzma, Uzma and Fayyaz, Muhammad and Ijaz, Umer Zeeshan and Farrakh, Sumaira (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 (1): 2481853. ISSN 1742-9145

Milling, Simon and Ijaz, Umer Zeeshan and Venieri, Danae and Christidis, George E. and Rattray, Nicholas J. W. and Gounaki, Iosifina and Andrusaite, Anna and Hareendran, Aravind and Knapp, Charles W. and Jones, Alexander X. and Photos-Jones, Effie (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 (12): e0313090. ISSN 1932-6203

Ashraf, Hajra and Dikarlo, Plamena and Masia, Aurora and Zarbo, Ignazio R. and Solla, Paolo and Ijaz, Umer Zeeshan and Sechi, Leonardo A. (2024) Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with Multiple Sclerosis. Scientific Reports, 14: 24027. ISSN 2045-2322

Bibi, Sara and Kerbiriou, Caroline and Uzma and Mckirdy, Shona and Kostrytsia, Anastasiia and Rasheed, Hifza and Eqani, Syed Ali Musstjab Akber Shah and Gerasimidis, Konstantinos and Nurulain, Syed Muhammad and Ijaz, Umer Zeeshan (2024) Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan. Ecotoxicology and Environmental Safety, 284: 116959. ISSN 0147-6513

Martin, Signe and Smith, Cindy and Stewart, Kelly and Barr, William and Cheslett, Deborah and O'Connor, Ian and Swords, Fiona and Ijaz, Umer Zeeshan and O'Dwyer, Katie (2024) The hepatopancreas microbiome of velvet crab, Necora puber. Environmental Microbiology Reports, 16 (5): e70014. ISSN 1758-2229

Trego, Anna and O'Sullivan, Sarah and O'Flaherty, Vincent and Collins, Gavin and Ijaz, Umer Zeeshan (2024) Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues. Environmental Microbiome, 19: 68. ISSN 2524-6372

Trego, Anna and Palmeiro-Sánchez, Tania and Graham, Alison and Ijaz, Umer Zeeshan and O'Flaherty, Vincent (2024) First evidence for temperature influencing the enrichment, assembly and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities. Frontiers in Systems Biology, 4: 1375472. ISSN 2674-0702

Aqueel, Rhea and Badar, Ayesha and Roy, Nazish and Ijaz, Umer Zeeshan and Malik, Kauser Abdulla (2024) Disease resistance correlates with core microbiome diversity in cotton. Current Microbiology, 81 (9): 302. ISSN 0343-8651

Ashraf, Hajra and Dikarlo, Plamena and Masia, Aurora and Zarbo, Ignazio R. and Solla, Paolo and Ijaz, Umer Zeeshan and Sechi, Leonardo 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 (1): 37. ISSN 1757-4749

Corbett, Erin and Ijaz, Umer Zeeshan and Jackson, Isla and Phoenix, Vernon R. (2024) Stormwater quality and microbial ecology in an urban rain garden system. Frontiers in Water, 6: 1383382. ISSN 2624-9375

Koci, Orges and Russell, Richard K. and Shaikh, M. Guftar and Edwards, Christine and Gerasimidis, Konstantinos and Ijaz, Umer Zeeshan (2024) CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets. Microbiome, 12 (1): 117. ISSN 2049-2618

Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data In Brief, 54: 110487. ISSN 2352-3409

Saleem, Farrukh and Ameer, Aqsa and Star-Shirko, Banaz and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (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: 110552. ISSN 2352-3409

Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (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 (4). pp. 885-895. ISSN 0002-9165

Gul, Farzana and Herrema, Hilde and Davids, Mark and Keating, Ciara and Nasir, Arshan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathogens, 16: 5. ISSN 1757-4749

Aqueel, Rhea and Badar, Ayesha and Roy, Nazish and Mushtaq, Qandeel and Ali, Aimen Fatima and Bashir, Aftab and Ijaz, Umer Zeeshan and Malik, Kauser Abdulla (2023) Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated. npj Biofilms and Microbiomes, 9 (1): 100. ISSN 2055-5008

Craven, Hannah and Erlandsson, Helen and McGuinness, Dagmara and McGuinness, David and Mafra, Denise and Ijaz, Umer Zeeshan and Bergman, Peter and Shiels, Paul G. and Stenvinkel, Peter (2023) A normative microbiome is not restored following kidney transplantation. Clinical Science, 137 (20). pp. 1563-1575. ISSN 0143-5221

Vignola, Marta and Lenselink, Jeanine and Quinn, Dominic and Ijaz, Umer Zeeshan and Pereira, Ryan and Sloan, William T. and Connelly, Stephanie and Moore, Graeme and Gauchotte-Lindsay, Caroline and Smith, Cindy J. (2023) Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communities. AQUA: Water Infrastructure, Ecosystems and Society, 72 (10). pp. 1837-1851. ISSN 2709-8028