Bioinformatics Group Leader

(Senior Research Fellow)
Warwick Medical School, Bioinformatics RTP, SBIDER,
University of Warwick,
A142, Gibbet Hill Campus,
Coventry, CV4 7AL, UK
Office: +44 (0)24 76528291
Email: t.alam@warwick.ac.uk 

My research interests are in the field of Systems Biology and Bioinformatics where my focus is to understand regulatory mechanisms within a metabolic system; more specifically I am interested in how cell reorganizes its metabolism due to genetic or environmental perturbations. In my research, I analyse a variety of Omics datasets and by combining with mathematical models (Genome-scale metabolic models, ODE models) I study metabolic regulations in both pro- and eukaryotes.

Current PhD and Master students:

(1) Swati Mahapatra, final year PhD student, co-supervising with Dr Chrystala Constantinidou and Dr Emma Denham.
(2) Stephen Li, 2nd year PhD student, co-supervising with Dr Chrystala Constantinidou.
(3) Elena Carter, MRC-DTP Master student.

Past PhD and Master students:

(1) Jenna Hoi-Yan Lam, PhD student, co-supervised with Dr Chrystala Constantinidou.
(2) AdamCallan-Sidat, MRC-DTP Master student.
(3) Rebecca Mackley, MRC-DTP Master student.

Research experties:

1. Analysis of multi-dimensional ‘–Omics’ data (NGS sequence analysis, RNAseq, proteomics, metabolomics data, miRNA data, microarray data and metagenomics data).
2. Reconstruction and analysis of mathematical models (genome scale models, Flux Balance analysis, FVA, ODE based models).
3. Biological network analysis (enzyme-metabolite metabolic interactions, enzyme-metabolite regulatory interactions, genetic interactions, protein-protein interactions).
4. Microbial metabolic interactions between different strains/species/cells using metabolic models (FBA, FVA).
5. Metabolic pathway engineering in order to examine the production of interesting compounds, Microbial strain improvement
6. Comparative modeling of a large scale to examine metabolic evolution, metabolic commanality and differences between species.
7. Comparative genomics sequence analysis - motif/domain finding, alighnment, homolgy such as BLAST search.
8. Machine learning algorithms, Statistical analysis and data mining.
9. Chemoinformatics, Drug structure comparison
10. Programming languages such as R, MATLAB, Perl.

Recent interesting publications:

1. Alam MT#, Amos GCA, Murphy A, Murch S, Wellington EMH#, Arasaradnam R: Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels. Gut Pathogens (2020) 12:1 # corresponding authors. https://link.springer.com/article/10.1186/s13099-019-0341-6
2. Olin-Sandoval M, Yu JSL, Miller-Fleming L, Alam MT, Kamrad S, Correia-Melo C, Haas R, Segal J, Navarro DAP, Herrera CL, Méndez-Lucio O, Vowinckel J, Mülleder M, Ralser M: Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism. Nature 572, 249–253 (2019), https://www.nature.com/articles/s41586-019-1442-6
3. Alam MT, M-V. Olin-Sandoval, Keller MA, Zelezniak A, Luisi BF, Ralser M: The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization. Nature communications (2017), 8:6018. https://www.nature.com/articles/ncomms16018
4. Mülleder M, Calvani E, Alam MT, Wang RK, Eckerstorfer F, Zelezniak A, Ralser M: Functional Metabolomics Describes the Yeast Biosynthetic Regulome. Cell (2016), 167, 1–13. http://www.cell.com/cell/fulltext/S0092-8674(16)31237-5
5. Alam MT*, Zelezniak A*, Mülleder M*, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krueger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M: The metabolic background is a global player in Saccharomyces gene expression epistasis. Nature Microbiology (2016), Article number:15030. http://www.nature.com/articles/nmicrobiol201530 

List of full publications

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