Brief CV

Syed Asad Rahman

I am working as 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 E-Commerce site development for e-books.

Selected Publications:

9. EC-BLAST: a tool to automatically search and compare enzyme reactionsSA Rahman, SM Cuesta, N Furnham, GL Holliday, JM Thornton; Nature methods (2014)

8. MACiE: exploring the diversity of biochemical reactions: S. A. Rahman with Gemma L. Holliday Nucleic Acids Research (2011) 

7. FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies: S. A. Rahman with N. Furnham Nucleic Acids Research (2011) 

6. Small molecule Subgraph Detector (SMSD) Toolkit: S. A. Rahman  Journal of Cheminformatics (2009) 1:12

5. Observing local and global properties of metabolic pathways: “Load points” and “Choke points” in the metabolic network: Syed Asad Rahman and Dietmar Schomburg Bioinformatics (2006) 22: 1767-1774

4. Genomics of Helicobacter Pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island:  Syed A. Rahman with Ahmed N et. al. BMC Genomics (2006): 1471-2164-7-191

3. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC):  S. A. Rahman Bioinformatics (2005) 21: 1189-1193

2. Genome sequence based, comparative analysis of fluorescent amplified fragment length polymorphism (FAFLP) of tubercle bacilli from seals provides molecular evidence for a new species within the Mycobacterium tuberculosis complex:  S. A. Rahman, with Ahmed N et. al. Infection, Genetics and Evolution 2 (2003) 193-199

1. Whole genome fingerprinting and genotyping of multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from endophthalmitis patients in India:  S. Asad Rahman with Ahmed N et. al. Infection, Genetics and Evolution 1 (2002) 237-242

Book Chapters:

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).


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