Brief CV

Syed Asad Rahman

I am a Research Scientist in the Thornton group at EMBL-EBI. My current research theme involves the investigation of small molecules and reaction mechanism. The focus of my work is to develop new algorithms and tools for understanding small molecules and their function and contribution with regards to Systems Biology.

General interest: Chem-Informatics, Bioinformatics, Systems Biology, Algorithm design, BioMarker Discovery, Modelling and Machine Learning Systems, Integration and Analysis of Genomic, Proteomic, Functional and Metabolic data.


  • 2003-2006: PhD (Comp. Science) at CUBIC, University of Cologne, Germany. My thesis involved investigating and developing new methods/tools for the analysis of metabolic networks. Finding new potential drug targets against pathogens [Pathway Hunter Tool] using metabolic networks.
  • 2002-2003: PG-MS (Bioinformatics) at CUBIC, University of Cologne, Germany. My graduation thesis was based on Gene function prediction by sequence patterns.
  • 1995-2000: B. Engg. (Comp. Science) at BVBCET, Karnatak University, India. My undergrad thesis was based on an E-Commerce portal development for e-books.
1. SA Rahman, Y Singh, S Kohli, J Ahmad, NZ Ehtesham, AK Tyagi, SE Hasnain (2014) Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis. mBio 5 (6), e02020-14
2. SM Cuesta, N Furnham, SA Rahman, I Sillitoe, JM Thornton (2014) The evolution of enzyme function in the isomerases. Current opinion in structural biology. 26, 121-130
3. Y Singh, S Kohli, DT Sowpati, SA Rahman, AK Tyagi, SE Hasnain (2014) Gene cooption in Mycobacteria and search for virulence attributes: comparative proteomic analyses of Mycobacterium tuberculosis, Mycobacterium indicus pranii and other mycobacteria. International Journal of Medical Microbiology. 304, 5–6
4. GL Holliday, SA Rahman, N Furnham, JM Thornton (2014) Exploring the Biological and Chemical Complexity of the Ligases. Journal of Molecular Biology. 426 (10), 2098-2111
5. SA Rahman, SM Cuesta, N Furnham, GL Holliday, JM Thornton (2014) EC-BLAST: a tool to automatically search and compare enzyme reactions. Nature Methods. 11 (2), 171-174
6. A Ala, D Brown, K Khan, R Standish, JA Odin, MI Fiel, TD Schiano, KJ Hillan, SA Rahman, Humphrey JF Hodgson, AP Dhillon (2013) Mucosal Addressin Cell Adhesion Molecule (MAdCAM-1) Expression Is Upregulated in the Cirrhotic Liver and Immunolocalises to the Peribiliary Plexus and Lymphoid Aggregates. Digestive Diseases and Sciences. 58 (9), 2528-2541
7. R Alcántara, J Onwubiko, H Cao, P de Matos, JA Cham, J Jacobsen, GL Holliday, JD Fischer, SA Rahman, B Jassal, M Goujon, F Rowland, S Velankar, R López, JP Overington, GJ Kleywegt, H Hermjakob, C O’Donovan, MJ Martín, JM Thornton, C Steinbeck (2012) The EBI enzyme portal. Nucleic Acids Research. 41 (D1): D773-D780
8. GL Holliday, C Andreini, JD Fischer, SA Rahman, DE Almonacid, ST Williams, WR Pearson (2011) MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Research. 40 (D1): D783-D789
9. N Furnham, I Sillitoe, GL Holliday, AL Cuff, SA Rahman, RA Laskowski, CA Orengo, JM Thornton (2011) FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Research. 40 (D1): D776-D782
10. SA Rahman, G Torrence, F Fenninger, L Baldacci, N Gopal, GL Holliday, JM Thornton (2011) Automated analysis of enzyme reaction mechanisms. ECCB/ISMB F1000 Posters, 2: 1349
11. JD Fischer, GL Holliday, SA Rahman, JM Thornton (2010) The structures and physicochemical properties of organic cofactors in biocatalysis. Journal of Molecular Biology. 403 (5), 803-824
12. J Thornton, G Holliday, SA Rahman, J Mitchell (2009) The evolution of enzyme mechanisms and functional diversity. FEBS JOURNAL. 276, 9-9
13. SA Rahman, M Bashton, GL Holliday, R Schrader, JM Thornton (2009) Small Molecule Subgraph Detector (SMSD) toolkit. Journal of Cheminformatics. 1, 12
14. SA Rahman (2007) Pathway Hunter Tool (PHT): A Platform for Metabolic Network Analysis and Potential Drug Targeting University of Cologne, Koeln, Germany. PhD thesis. hbz:38-24504
15. SM Devi, I Ahmed, AA Khan, SA Rahman, A Alvi, LA Sechi, N Ahmed (2006) Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island. BMC Genomics. 7 (1), 191
16. SA Rahman, D Schomburg (2006) Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics. 22 (14), 1767-1774
17. SA Rahman, PS Jonnalagadda, J Padiadpu, K Hartmann, R Schrader, D Schomburg (2005) Metabolic network analysis: implication and application. BMC Bioinformatics. 6 (Suppl 3), S12
18. SA Rahman, P Advani, R Schunk, R Schrader, D Schomburg (2005) Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics. 21 (7), 1189-1193
19. N Ahmed, M Alam, AA Majeed, SA Rahman, A Cataldi, D Cousins, SE Hasnain (2003) Genome sequence based, comparative analysis of the fluorescent amplified fragment length polymorphisms (FAFLP) of tubercle bacilli from seals provides molecular evidence for a new species within the Mycobacterium tuberculosis complex. Infection, Genetics and Evolution. 2 (3), 193-199
20. N Ahmed, A Bal, AA Khan, M Alam, A Kagal, V Arjunwadkar, A Rajput, AA Majeed, SA Rahman, S Banerjee, S Joshi, R Bharadwaj (2002) Whole genome fingerprinting and genotyping of multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from endophthalmitis patients in India. Infection, Genetics and Evolution. 1 (3), 237-242
Selected Book Chapters
  • 1) N Ahmed, SH Devi, S Tenguria, M Majid, SA Rahman and SE Hasnain. Genomic Fluidity of the Human Gastric Pathogen Helicobacter pylori, Genome Plasticity and Infectious Diseases, Publisher American Society for Microbiology (2012)
  • 2) Niyaz Ahmed, Singamaneni Haritha Devi, Shivendra Tenguria, Mohammed Majid, Syed Asad Rahman, and Seyed E. Hasnain. Genomic Fluidity of the Human Gastric Pathogen Helicobacter pylori; Genome Plasticity and Infectious Diseases of the American Society for Microbiology (2012)
  • SA Rahman et-al. (2014) “Genetic Markers for Diagnosis of Tuberculosis caused by Mycobacterium tuberculosis”- WIPO PCT System- PCT/IB2014/066469


I am always open to new ideas, after all that’s what SCIENCE is all about!


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