Projects
Past research experiences
Elucidating the role of protein phosphorylation in regulating Escherichia coli metabolism
Aug 2013 – Feb 2014 (6 months)
Master Thesis Under the supervision of Prof. Uwe Sauer and Dr. Zrinka Raguz Nakic (IMSB, ETH Zürich)
Performed physiological growth experiments on 96 phospho-mutants (generated by site directed mutagenesis*) of proteins involved in central metabolic pathways of the gram-negative bacteria, E. coli.
Captured metabolic changes at the intracellular and extracellular level by untargeted mass spectrometry (LC and GC-MS) and analyzed the high throughput data using MATLAB.
*In collaboration with Dr. Harris Wang, Department of Systems Biology, Columbia University, USA
Bioinformatics tool for computing correlation statistics and the analysis of siRNA in Arabidopsis thaliana
Mar 2013 – Apr 2013 (2 months)
Lab rotation: Under the supervision of Dr. Antonin Marchais (Vionnet group, RNA Biology, ETH Zürich)
Developed a small bioinformatics tool to compute the auto-correlation and cross-correlation between siRNA (small interfering RNA) fragments and analysed the whole genome of Arabidopsis thaliana for identification of the abundance, phasing and overhangs of the siRNAs.
Programmed in PERL and R statistical software
Exploring nuclear localization and functions of Argonaute proteins
Mar 2013 – Apr 2013 (2 months)
Lab rotation: Under the supervision of Dr. Alexis Sarazin (Vionnet group, RNA Biology, ETH Zürich)
Analysed and benchmarked bioinformatics tools available for the identification of RISCs (RNA-induced silencing complexes) and microRNA targets such as PAREsnip and SeqTAR.
Performed statistical and differential expression analysis of small RNA using R statistical software.
Molecular Screening of Rice for presence of blast resistant genes
Oct 2012 – Nov 2012 (2 months)
Lab rotation: Under the supervision of Dr. Kumar Vasudevan and Dr. Navreet Bhullar (Gruissem group, Plant Biotechnology, ETH Zürich).
Characterized eight hundred rice accessions by extracting genomic DNA followed by PCR based diagnosis for the presence of major blast resistance genes (using specific molecular markers).
Validation of a new GROMOS force field parameter set genes
Sept 2011 – Dec 2011 (3 months)
Lab rotation: Under the supervision of Dr. Jozica Dolenc (IGC, Group for computer-aided chemistry, ETH Zürich)
Validated and and analyzed the parameter sets of the new GROMOS (GRoningen MOlecular Simulation) package by simulating the DNA Dickerson-Drew dodecamer.
The simulation investigated the role of salt concentration on the stability of the DNA duplex at 10 ns.
Undergraduate research experience
Drug Development for Alzheimer’s disease
May 2010 – Jul 2010 (3 months)
Undergraduate research fellowship sponsored by University Grants Commission, Government of India
Under the supervision of Prof. Dr. R. Boopathy (Head, Department of Biotechnology, Bharathiar University, India).
Screened small drug like molecules which serve as a hybrid inhibitor for both Acetyl-cholinesterase and Beta-secretase (causal proteins of Alzheimer’s disease) and performed molecular docking to study the inhibitory effects of the screened molecules.
Simulation packages from Schrödinger Maestro, ChemSketch and small molecule/ protein visualisation tool (PyMOL) were used.
Development and maintenance of in-house databases using PERL programming
June 2009 (1 month)
Summer Training: Structural and Bio-Computing Laboratory, Indian Institute of Sciences (IISc.), Bangalore, India
Short training on the utilization of PERL programming for development and maintenance of value added knowledge bases.
Student supervision
Elucidating the importance of biosynthesis and salvage of an essential vitamin, VitB6 (pyridoxal-5-phosphate) in T. gondii. With Dr. Damien Nicolas (2018)
Creation of a 2gRNA CRISPR-Cas9 based genetic tool to knock-out any gene of interest in T. gondii. With Myriam Roth (2016)
Acquired skills
Computational
Programming in Python, R, MATLAB, PERL; Plot.ly, GraphPad Prism; Metabolic modeling and simulation; Molecular dynamics and docking (Schrödinger Maestro, AutoDock Vina, DOCK6); Adobe Illustrator and MS Office suite; Web and graphics design
Experimental
High-throughput screening; Molecular biology (plasmid design, cloning, DNA extraction, PCR), gel electrophoresis, immunofluorescence and immunoblotting, microscopy, FACS); Enzymatic assays; Cell culture, transfections, phenotyping; CRISPR-Cas9 gene editing; Metabolomics sampling and analysis (LC/GC-MS)
General
Project management; Events and meeting organisation; Collaborating and networking; Student supervision; Presentation and scientific communication