Bioinformatics Centre
A.J.C. Bose Centenary Building,
P-1/12, CIT Scheme - VII M,
Kolkata - 700 054, India

Sudipto Saha, Ph.D.

[Lab Link]

Assistant Professor


Centre for Excellence in Bionformatics


Tel:+91-33-2569 3333

Fax:+91-33-2355 3886



 Research Interests:

  1. Discover novel motifs mediating protein-protein interactions (PPIs) through analysis of protein interaction networks. PPIs are reported in the literature to be regulated by linear motifs (LMs), which are short elements embedded witin large protein sequences (Petsalaki and Russel, Curr Opin Bitechnol, 2008). These short linear peptide sections are often present in disordered regions in eukaryotic proteins and are responsible for thousands of protein-protein interactions.

  2. Systematic discovery of biomarkers of asthma caused by common environmental allergens using human plasma proteomics, cytokine profiling and network biology- a systems approach to drug discovery. Asthma is characterized by a specific pattern of inflammation in the airway mucosa which involves the infiltration of eosinophils, increased numbers of TH2 cells relative to TH1 cells and increased numbers of activated mast cells. Specific aims of this project are: i) Study and compare the plasma proteome and cytokine profile between atopic and non-atopic asthma vs healthy subjects. ii) Study the integrated profile derived from plasma proteomics and cytokine assay among asthma patients before and after drug treatment iii) Discover asthma related biomarkers by differential proteome expression profile. iv) Identify the active networks (based on protein-protein interactions) and pathways, affected and altered in asthma patients.

Positions Available:

*Position for Research Assistant is currently avilable

Positions will be open for individuals with NET (CSIR/UGC/ICMR/DBT) fellowships to conduct research. Interested candidate may contact me directly.

Key Publications:

Saha S, Dazard JE, Xu H, Ewing RM. A computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. J Proteome Res. 2012 Jul 30. [PMID: 22845868]

Song J, Saha S, Gokulrangan G, Tesar PJ, Ewing RM. DNA and Chromatin Modification Networks Distinguish Stem Cell Pluripotent Ground States. Mol Cell Proteomics. 2012 Jul 22. PMID: 22822199

Dazard JE*, Saha S*, Ewing RM. ROCS: A reproducibility index and confidence score for interaction proteomics. BMC Bioinformatics. 2012 Jun 8;13(1):128. [Equal Contribution]

Saha S, Kaur P, Ewing RM. The bait compatibility index: computational bait selection for interaction proteomics experiments. J Proteome Res. 2010 Oct 1;9(10):4972-81.

Saha S, Harrison SH, Chen JY. Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics. 2009 Jan;9(2):470-84.

Saha S, Harrison SH, Shen C, Tang H, Radivojac P, Arnold RJ, Zhang X, Chen JY. HIP2: an online database of human plasma proteins from healthy individuals. BMC Med Genomics. 2008 Apr 25;1:12.

Saha S, Raghava GP. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins. 2006 Oct 1;65(1):40-8.

Saha S, Raghava GP. AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W202-9.

Saha S, Bhasin M, Raghava GP. Bcipep: a database of B-cell epitopes. BMC Genomics. 2005 May 29;6:79.

 Publications in Pubmed

Bioinformatics Centre (BIC), Bose Institute, Kolkata 2011, Last updated on: January 30, 2011