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
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.
*Position for Research Assistant is currently avilable
will be open for individuals with NET (CSIR/UGC/ICMR/DBT) fellowships
to conduct research. Interested candidate may contact me directly.
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.
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.
Harrison SH, Chen JY. Dissecting the human plasma proteome and
inflammatory response biomarkers. Proteomics. 2009 Jan;9(2):470-84.
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.
Raghava GP. Prediction of continuous B-cell epitopes in an antigen
using recurrent neural network. Proteins. 2006 Oct 1;65(1):40-8.
Raghava GP. AlgPred: prediction of allergenic proteins and mapping of
IgE epitopes. Nucleic Acids Res. 2006 Jul 1;34(Web Server
Bhasin M, Raghava GP. Bcipep: a database of B-cell epitopes. BMC
Genomics. 2005 May 29;6:79.
Publications in Pubmed