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