Contact Professor Fady Mohareb
- Tel: 01234 754807
- Email: f.mohareb@cranfield.ac.uk
- ORCID
Areas of expertise
- Bioinformatics
- Computing, Simulation & Modelling
- Digital Agriculture
- Drug Discovery & Development
- Food Quality
- Food Safety
Background
Professor Mohareb is Head of the Bioinformatics Group at Cranfield University. He has over 20 years of experience as academic and Principal Investigator with extensive technical skill and detailed knowledge across a broad range of genome analysis and Artificial Intelligence techniques. Proven track record in the management and delivery of large-scale genomics, machine learning and AI international projects.
Research opportunities
1. Next-Generation Sequencing (NGS) informatics: Prof Mohareb's lab is responsible for all the genome informatics work at Cranfield University. He led several genome projects for plant, fungal , and insect species. Research activities also include functional annotation and gene expression profiling of these organisms under various environmental stresses and conditions. Prof Mohareb specialises in complex and computationally challenging species, often requiring the development of tailored assembly strategies and/or purpose-built bioinformatics software
2. Artificial Intelligence and Machine Learning: Prof Mohareb has over 20 years of experience in the field of data science and machine learning for profiling food quality, safety and authentication. The advances in this field achieved through his research has been internationally recognized through key publications, invitations as keynote speaker at high-profile international food conferences, as well as several national and international research collaborations.
3. Bioinformatics algorithms and software development: Prof Mohareb Lab led the development, and continues to maintain several standalone and web-based bioinformatics tools and platforms for the benefit of the wider research community. This includes MapOptics (https://github.com/FadyMohareb/mapoptics), Tersect (https://github.com/tomkurowski/tersect), Vargen (https://github.com/MCorentin/VarGen) and SorfML (http://elvis.misc.cranfield.ac.uk/sorfml/home).
Clients
- European Bioinformatics Institute
- London School of Hygiene and Tropical Medicine
- Wellcome Sanger Institute
- Rothamsted Research
- Unilever PLC
- GSK plc
- Syngenta AG
- Pepsico
- AstraZeneca PLC
- Health Education England (NHS)
Publications
Articles In Journals
- Kevei Z, Larriba E, Romero-Bosquet MD, Nicolás-Albujer M, Kurowski TJ, .... (2024). Genes involved in auxin biosynthesis, transport and signalling underlie the extreme adventitious root phenotype of the tomato aer mutant. Theoretical and Applied Genetics, 137(4)
- Molitor C, Kurowski TJ, Fidalgo de Almeida PM, Kevei Z, Spindlow DJ, .... (2024). A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought. Frontiers in Plant Science, 15
- Ramos-Garcia V, Ten-Doménech I, Moreno-Giménez A, Campos-Berga L, Parra-Llorca A, .... (2023). Fact-based nutrition for infants and lactating mothers—The NUTRISHIELD study. Frontiers in Pediatrics, 11
- Okyere FG, Cudjoe D, Sadeghi-Tehran P, Virlet N, Riche AB, .... (2023). Machine Learning Methods for Automatic Segmentation of Images of Field- and Glasshouse-Based Plants for High-Throughput Phenotyping. Plants, 12(10)
- Okyere FG, Cudjoe D, Sadeghi-Tehran P, Virlet N, Riche AB, .... (2023). Modeling the spatial-spectral characteristics of plants for nutrient status identification using hyperspectral data and deep learning methods. Frontiers in Plant Science, 14
- Vicente MH, MacLeod K, Zhu F, Rafael DD, Figueira A, .... (2023). The ORGAN SIZE (ORG) locus modulates both vegetative and reproductive gigantism in domesticated tomato. Annals of Botany, 132(7)
- Cudjoe DK, Virlet N, Castle M, Riche AB, Mhada M, .... (2023). Field phenotyping for African crops: overview and perspectives. Frontiers in Plant Science, 14
- Bailey E, Field L, Rawlings C, King R, Mohareb F, .... (2022). A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus (Hemiptera: Anthocoridae), and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests. BMC Genomics, 23(1)
- Kevei Z, Ferreira SDS, Casenave CMP, Kurowski T, Mohareb F, .... (2022). Missense mutation of a class B heat shock factor is responsible for the tomato bushy root-2 phenotype. Molecular Horticulture, 2(1)
- Zuo Y, Verheecke-Vaessen C, Molitor C, Medina A, Magan N, .... (2022). De novo genome assembly and functional annotation for Fusarium langsethiae. BMC Genomics, 23(1)
- Bailey E, Field L, Rawlings C, King R, Mohareb F, .... (2022). A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution. BMC Genomics, 23(1)
- Kourani M, Mohareb F, Rezwan FI, Anastasiadi M & Hammond JP. (2022). Genetic and Physiological Responses to Heat Stress in Brassica napus. Frontiers in Plant Science, 13(April)
- Molitor C, Kurowski TJ, Fidalgo de Almeida PM, Eerolla P, Spindlow DJ, .... (2021). De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance. Bioinformatics, 37(14)
- Spyrelli ED, Ozcan O, Mohareb F, Panagou EZ & Nychas G-JE. (2021). Spoilage assessment of chicken breast fillets by means of fourier transform infrared spectroscopy and multispectral image analysis. Current Research in Food Science, 4
- Fengou L-C, Lianou A, Tsakanikas P, Mohareb F & Nychas G-JE. (2021). Detection of Meat Adulteration Using Spectroscopy-Based Sensors. Foods, 10(4)
- Martínez‐Andújar C, Martínez‐Pérez A, Albacete A, Martínez‐Melgarejo PA, Dodd IC, .... (2021). Overproduction of
ABA in rootstocks alleviates salinity stress in tomato shoots. Plant, Cell & Environment, 44(9) - Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, .... (2021). Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus. Parasites & Vectors, 14(1)
- Collings ER, Alamar MC, Márquez MB, Kourmpetli S, Kevei Z, .... (2021). Improving the Tea Withering Process Using Ethylene or UV-C. Journal of Agricultural and Food Chemistry, 69(45)
- Kurowski TJ & Mohareb F. (2020). Tersect: a set theoretical utility for exploring sequence variant data. Bioinformatics, 36(3)
- Anastasiadi M, Bragin E, Biojoux P, Ahamed A, Burgin J, .... (2020). CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances. Bioinformatics, 36(11)
- Molitor C, Brember M & Mohareb F. (2020). VarGen: an R package for disease-associated variant discovery and annotation. Bioinformatics, 36(8)
- Alamar MC, Anastasiadi M, Lopez-Cobollo R, Bennett MH, Thompson AJ, .... (2020). Transcriptome and phytohormone changes associated with ethylene-induced onion bulb dormancy. Postharvest Biology and Technology, 168
- Libiseller-Egger J, Phelan J, Campino S, Mohareb F & Clark TG. (2020). Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers. PLOS Computational Biology, 16(12)
- Cazzola H, Lemaire L, Acket S, Prost E, Duma L, .... (2020). The Impact of Plasma Membrane Lipid Composition on Flagellum-Mediated Adhesion of Enterohemorrhagic Escherichia coli. mSphere, 5(5)
- Kangara N, Kurowski TJ, Radhakrishnan GV, Ghosh S, Cook NM, .... (2020). Mutagenesis of Puccinia graminis f. sp. tritici and Selection of Gain-of-Virulence Mutants. Frontiers in Plant Science, 11
- Manthou E, Lago S-L, Dagres E, Lianou A, Tsakanikas P, .... (2020). Application of spectroscopic and multispectral imaging technologies on the assessment of ready-to-eat pineapple quality: A performance evaluation study of machine learning models generated from two commercial data analytics tools. Computers and Electronics in Agriculture, 175
- Burgin J, Molitor C & Mohareb F. (2019). MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment. Bioinformatics, 35(15)
- González-Arcos M, de Noronha Fonseca ME, Zandonadi DB, Peres LEP, Arruabarrena A, .... (2019). A loss-of-function allele of a TAC1-like gene (SlTAC1) located on tomato chromosome 10 is a candidate for the Erectoid leaf (Erl) mutation. Euphytica, 215(5)
- Silva Ferreira D, Kevei Z, Kurowski T, de Noronha Fonseca ME, Mohareb F, .... (2018). BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene. Journal of Experimental Botany, 69(10)
- Benavente ED, Oresegun DR, de Sessions PF, Walker EM, Roper C, .... (2018). Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development. Scientific Reports, 8(1)
- Balani J, Hyer SL, Shehata H & Mohareb F. (2018). Visceral fat mass as a novel risk factor for predicting gestational diabetes in obese pregnant women. Obstetric Medicine, 11(3)
- Estelles-Lopez L, Ropodi A, Pavlidis D, Fotopoulou J, Gkousari C, .... (2017). An automated ranking platform for machine learning regression models for meat spoilage prediction using multi-spectral imaging and metabolic profiling. Food Research International, 99(Pt 1)
- Anastasiadi M, Mohareb F, Redfern SP, Berry M, Simmonds MSJ, .... (2017). Biochemical Profile of Heritage and Modern Apple Cultivars and Application of Machine Learning Methods To Predict Usage, Age, and Harvest Season. Journal of Agricultural and Food Chemistry, 65(26)
- Diez Benavente E, Ward Z, Chan W, Mohareb FR, Sutherland CJ, .... (2017). Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure. PLOS ONE, 12(5)
- Nychas G-JE, Panagou EZ & Mohareb F. (2016). Novel approaches for food safety management and communication. Current Opinion in Food Science, 12
- Mohareb F, Papadopoulou O, Panagou E, Nychas G-J & Bessant C. (2016). Ensemble-based support vector machine classifiers as an efficient tool for quality assessment of beef fillets from electronic nose data. Analytical Methods, 8(18)
- Motawi TMK, Sadik NAH, Shaker OG, El Masry MR & Mohareb F. (2016). Study of microRNAs-21/221 as potential breast cancer biomarkers in Egyptian women. Gene, 590(2)
- Mohareb F, Iriondo M, Doulgeraki AI, Van Hoek A, Aarts H, .... (2015). Identification of meat spoilage gene biomarkers in Pseudomonas putida using gene profiling. Food Control, 57
- Kevei Z, King RC, Mohareb F, Sergeant MJ, Awan SZ, .... (2015). Resequencing at ≥40-Fold Depth of the Parental Genomes of a Solanum lycopersicum × S. pimpinellifolium Recombinant Inbred Line Population and Characterization of Frame-Shift InDels That Are Highly Likely to Perturb Protein Function. G3 Genes|Genomes|Genetics, 5(5)
- Ropodi AI, Pavlidis DE, Mohareb F, Panagou EZ & Nychas G-JE. (2015). Multispectral image analysis approach to detect adulteration of beef and pork in raw meats. Food Research International, 67
- Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, .... (2015). PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics, 16(1)
- Papadopoulou OS, Panagou EZ, Mohareb FR & Nychas G-JE. (2013). Sensory and microbiological quality assessment of beef fillets using a portable electronic nose in tandem with support vector machine analysis. Food Research International, 50(1)
- Fan J, Mohareb F, Bond NJ, Lilley KS & Bessant C. (2012). MRMaid 2.0: Mining PRIDE for Evidence-Based SRM Transitions. OMICS: A Journal of Integrative Biology, 16(9)
- Fan J, Mohareb F, Jones AME & Bessant C. (2012). MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species. Frontiers in Plant Science, 3(JUL)
Conference Papers
- Cudjoe DK, Okyere FG, Virlet N, Castle M, Buchner P, .... (2023). Using proximal sensing parameters linked to the photosynthetic capacity to assess the nutritional status and yield potential in quinoa
- Lytou A, Fengou L-C, Schultz N, Carstensen JM, Zhang Y, .... (2023). An overview of implementing Multispectral Imaging coupled with machine learning for the assessment of microbiological quality and authenticity in foods
- Panagou EZ, Mohareb FR, Argyri AA, Bessant CM & Nychas G-JE. (2011). A comparison of artificial neural networks and partial least squares modelling for the rapid detection of the microbial spoilage of beef fillets based on Fourier transform infrared spectral fingerprints
- Mohareb F, Bessant C & Nychas GJ. (2009). Symbiosis: a Web-based framework for managing and analysing high throughput metabolomic data
- Argyri A, Mohareb F, Panagou EZ, Bessant C & Nychas GJ. (2009). An artificial neural networks approach for the rapid detection of the microbial spoilage of beef fillets based on Fourier transform infrared spectroscopy data
- Mohareb F, Sattlecke M, Argyri A, Panagou EZ, Nychas E, .... (2009). Identification of Meat Spoilage from FTIR Data Using the Symbiosis Data Analysis Framework
