Ruchir Khandelwal Email & Phone Number

Fijnaart, North Brabant, The Netherlands

Wageningen, The Netherlands

Supervised by Prof. Rene Wijffels and Prof. Dirk Martens, my postdoctoral projects included making a Python based software pipeline ‘AlgaePy’, for building and working with the genome-scale metabolic models of micro-algae. AlgaePy takes in newly sequenced genome, performs homology based functional annotations by comparing the genome with metabolic pathway databases like KEGG and MetaCyc, both locally and online. All resulting functional annotations are stored locally as MySQL database along with all respective statistical information. Using these local databases, a genome-scale metabolic model is generated with all the functional annotation evidences. AlgaePy can also be used for working and modifying these models. I have also supervised multiple PhD and thesis students in their experimental planning, data analysis and finally applying various modeling techniques to address their research questions. I have also given classes to masters and PhD students on genome-scale modeling, metabolic engineering and systems biology.

Amsterdam Area, Netherlands

I have done a PhD in Systems Biology from VU University Amsterdam with Prof. Dr. Bas Teusink, Dr. Frank Bruggeman and Dr. Wilfred Röling as my supervisors. In my PhD, I have developed a Python based computational and theoretical framework for constraint based modeling of microbial consortia called, community flux balance analysis. This is a linear programming based modeling approach where genome-scale metabolic models representing all the participating organisms are optimized with an objective function at the level of their consortia. I have also created all the necessary programs to perform this analysis in Python and Mathematica. I have applied this analysis to further understand the complex interactions of lactic acid bacteria of the yogurt consortium. At the same time, I acquired yogurt fermentation data to validate another developed theory that extends our constraint-based approach towards dynamic flux balance analysis.

Greater Boston Area

Planned and developed a recombinant strain of Saccharomyces cerevisiae to make it overproduce succinic acid through synthetic biology techniques. Also, developed a biological hydrogen sensor in bacteria Ralstonia eutropha.

Hyderabad Area, India

Developed a Java based tool called MetCon, which downloads queried metabolic pathway from KEGG database in ‘.sbml’ format and displays it as a SVG (Scalable Vector Graphics) image by using graph theory (yFiles java library).

Doctor Of Philosophy (Phd), Systems Biology

Master Of Science (Msc), Biology/Biological Sciences

Bachelor Of Science (Bsc), Bioinformatics

Molecular Biology, Microbiology and Biotechnology