Glasgow, Scotland, United Kingdom
With over 26 years of experience, I am a Research Leader specialising in the development of scientific software, bespoke analytical strategies, and engineered systems. For the past 14 years, my work has focused on applying Numerical Ecology and Machine Learning to large-scale "omics" datasets, with high-impact applications across environmental, agricultural, and medical sciences. To date, I have secured over £22M in research funding as a Principal, Co-Investigator, or an Academic Participant. This support has fuelled over 265 publications, garnering over 13K citations. According to Google Scholar, I am currently ranked as the 3rd most-cited researcher globally in Information Engineering and 4th in Numerical Ecology. Beyond my technical output, I am a dedicated mentor committed to empathy, inclusivity, and collegiality. I have supervised over 250 students and staff across all career stages, including 53 PhD candidates who successfully defended their theses under my guidance. My work extends beyond academia; it has informed policy documents, clinical guidelines, and the formation of multiple spin-offs. My non-academic impact is further evidenced by citations in patents and international media, as well as a presence in public discourse via Wikipedia and global news outlets.
The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. With MoyPark (UK’s largest producer of organic and free range chicken, and one of the the UK’s top 15 food companies), three papers on chicken microbiomes (DOI: 10.3389/fmicb.2018.02452; DOI: 10.1186/s40168-020-00908-8; DOI: 10.3389/fmicb.2023.1197838) have led to exploring the diet and their industrial parameters to help control the pathogen Campylobacter. My current work with MoyPark is towards alternatives to antibiotics (ATAs) that can be utilised in animal production for maintenance of gut health, reduction of pathogen load, and improved feed efficiencies (DOI: 10.1101/2024.08.02.606333). These works led to this advisory role where with the Poultry Research Institute, and National Veterinary Laboratory (NVL), I am taking a leading role in understanding the microbial ecology of local/indigenous breeds, improving commercial and backyard farming setups in Pakistan, and reducing antimicrobial resistance (DOI: 10.1016/j.dib.2024.110552; DOI: 10.1016/j.dib.2024.110487; DOI: 10.3389/fmicb.2023.1197838)
Member Supervisory Committee Delivery of Annual Seminars (2023, 2024) on OMICS technologies With Professor Kauser Abdula Malik (https://en.wikipedia.org/wiki/Kauser_Abdullah_Malik), a noted agricultural scientist, I am co-directing several PhD projects on improving crop resilience and food security in Pakistan. For instance, with Rhea Aqueel (Visiting PGR to University of Glasgow under Higher Education Commission, Pakistan Project No. 1-8/HEC/HRD/2023/12777 (University of Glasgow Student ID: 2914245), we have successfully suppressed Cotton Leaf Curl Disease (CLCuD) by isolation of Salicylic Acid producing bacteria [(DOI: 10.1038/s41522-023-00470-9; 2023); (DOI: 10.1007/s00284-024-03827-1; 2023), (DOI: 10.3389/fmicb.2024.1381883; 2024)]. The work was very significant, and was picked up by ISAAA (a not-for-profit organization in which publishes a Biotech Updates newsletter with over 22,000 subscribers worldwide): https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=20580). Recent work with Ayesha Badar is on interspecies microbiome transplantation (DOI: 10.1038/s42003-025-07812-7) as an alternative to Salicylic Acid application. CLCuD is transmitted by the whitefly Bemisia tabaci, and has devastated Pakistan’s cotton crop for the past three decades with economic losses reaching approximately 2 billion USD per annum in Pakistan.
Under this group, I am trying to understand and target interventions to mitigate the effects of an advancing ageing process and the resultant "diseasome of ageing". I have directed several interdisciplinary research projects (in some cases involving NHS) where the focus is on the mechanistic basis of how the exposome [e.g. socioeconomic position (SEP), nutrition, the microbiome, lifestyle and environment] dysregulate ageing and cause ill health (including those diseases where microbial dysbiosis is implicated) (DOI: 10.1186/s13099-024-00627-7; DOI 10.1042/CS20230779; DOI: 10.1038/s41598-021-92042-0; DOI: 10.1101/2023.05.18.23289979; DOI: 10.1101/2023.05.18.23289979; DOI: 10.1080/19490976.2021.1930871).
The Scottish Pakistani Association (SPA) was founded in 1982, led by late Mr Bashir Maan, CBE. Its aim is to develop communications and friendly relations between the Pakistani community and all other people in Scotland and actively engaged in promoting and fostering cultural and social activities, in order to develop a greater understanding at all levels, national and international. The patrons include The High Commissioner of Pakistan to the United Kingdom and His Grace, The Duke of Montrose. The facebook page has over 1K followers.
I teach the following courses: ENG5322: Engineering Skills M (2018-; Course Coordinator; Offered twice a year: Jan/Sep) ENG2079: Civil Engineering Skills 2 (2018-) ENG2078: Environmental Processes 2 (2024-) BIOL5172: Metagenomics (2015-2017; Course Coordinator) ENG4085: Integrated Systems Design Project 4 ISDP4 Business Plans (2024; Assessor) BIOL5173P: MSc Bioinformatics Projects (2017-; Supervisor & Assessor) SIT4017P (Individual Project 4S) (2018-2020) ENG4110P: Individual Project 4 (2018-) ENG5041P: Individual Project 5 (2020-) ENG5059P: MSc Projects (2019-) BIOL5173P: MSc Bioinformatics Projects (2017-) MSc in Product Design Engineering Project Supervision (2018)
I lead a team of 41 editors, and under my guidance, the Integrative Systems Microbiology section encourages submissions that span the various subdisciplines of microbiology research which apply systems biology concepts and approaches, with the aim to provide a comprehensive understanding of microbial communities and their interactions.
High throughput DNA sequencing is now fundamental to the microbiology of everything from environmental engineering through medicine to agriculture. Prior to my research comparing different sequencing technologies, starting in 2014 and funded by Innovate UK (Project No. 100969, £2.3M), no one knew which technology was the most accurate or what were the optimal strategies for sample processing. In a series of, now highly cited (>1400 citations) papers, I helped to establish the Illumina platforms as the leaders in the field. My recommendations on next generation sequencing technology and protocols for microbial community profiling are being adopted by many sequencing centres including Centre for Genome Research, Liverpool. An SME (Eagle Genomics), subsequently implemented my algorithms in Unilever’ R&D centre's systems to facilitate them in their search of next generation personal care products involving microbiology. For these reasons, and contribution to a growing shared research portfolio with several investigators at University of Liverpool, I was awarded the position to recognize my impact.