Statement of Purpose
During my sophomore year at University of agriculture Faisalabad, I enrolled in my first course on
molecular plant pathology. The course elaborated on the potential applications of molecular techniques
to life sciences. Inspired, I set out to learn more about this area with a focus on molecular virology.
For that, I joined a summer internship program at Crop Diseases Research Institute (CDRI) at National
Agriculture and Research Centre (NARC) for three months (March 2015-May 2015) Dr. Shahid
Hameed ‘s lab. After my bachelors I had an opportunity to work as a research internee at RNA silencing
and plant functional genetics laboratory at Lahore University of management sciences (LUMS) for 8
months (Oct 2015-May 2016) under the supervision of Dr. Sadia Hamera. Her knowledge-driven
capabilities and experience provided me tremendous learning opportunities and a chance to explore
and apply my concepts practically. During this tenure, my research project involved investigating the
role of tomato AGO4 paralogues in pathogen resistance. We strived to unravel AGO4 role in host
defense against Pst besides focussing on developing a visual readout reporter system in tomato to
examine the role of pathogens in host epigenetics.
While I was working with Dr. Hamera, she had to move to Germany and subsequently, I got received
an offer for Research Associate position at Biomedical Informatics Research Lab (BIRL) under the
supervision of Dr. Safee Ullah Chaudhary. Dr Safee’s lab focus on health informatics, systems biology
and bioinformatics. Given my background in basic biology I was excited at the prospect of using
computational modalities to solve biological problems. The major focus of my project at BIRL was on
on the Hepatitis C virus which is a major cause of chronic liver disease worldwide. In addition to my
experimental proficiency, I also obtained experience in developing computational methods for
analyzing protein structures. While exploring in depth literature, we worked on a review article
“Evolution of Efficacious Pan-Genotypic HCV Therapies” which got published in “Medicinal
Research Reviews”.
As part of a Higher Education Commission (HEC) funded project, an integrated computational and
experimental study of Hepatitis-C Virus (genotype 3a) was undertaken to mark the sequence
heterogeneity, protein-drug interactions and immune responses. Towards this goal, conserved regions
of NS3 were identified based on the information obtained from ELISA and immunodominant peptides.
The variations in local sequences were mapped to protein structures followed by the prediction of
inhibition affinities. Various online tools were accessed for the sake of homology modeling, structure
validation, docking and pose analysis. This enabled us to make an in-silico prediction of
immunodominant regions of NS3 and NS5B.
The second part of this project aimed to explore the effect of CRISPR/Cas mediated HCV targeting in
Huh-7.5 cells is “CRISPR/Cas13-Mediated Targeting of Hepatitis C Virus RNA in Eukaryotic Cells”
and is published recently. To design broad genotypic high-efficiency crRNAs (CRISPR RNA), we
systematically determined the optimum target sites in HCV IRES using IRES sequence (nt 1–370) of
genotype 2a (isolate JFH-1; AB047639.1) as a template to predict the all possible 28 nt crRNAs using
CRISPR RNA-Targeting Prediction and Visualization tool (CRISPR- RT).
Finally, we selected five different crRNAs to target the unpaired bases of the IRES element for
experimental evaluation. We also performed multiple sequence alignment (MSA) of 114 complete
HCV genomes (covering genotypes one to seven) using MAFFT by Geneious Prime software
(Geneious 2020.0.3). Consequently, C2c2 and sgRNA expression vectors were constructed and
transfected into Huh.7.5 cells. Ultimately, HCV sub genomic replicon RNA were employed to
evaluate the intensity of CRISPR/Cas mediated HCV targeting on viral replication and translation.
Moreover, we have planned to target multiple infectious diseases through an integrated
computational-experimental pipeline. Towards this approach, we aim to identify highly
immunogenic epitopes which will aid in the design and development of potential in silico vaccines
and therapeutic strategies (in process).
Taken together, my research journey from an undergraduate to a senior research associate has
allowed me to gain diverse range of experiences as a team member as well as an independent thinker.
Even during COVID-19, with wet lab shut down for six months, we worked from home and right
after university re-opened, we managed to publish two manuscript with one in preparation. My
background, areas of study, along with my work experience in laboratories and academic setting has
equipped me to be a good fit in your esteemed institute. Moreover, I believe that having worked
extensively over the four years in a Bioinformatics lab that offers a conducive environment for
conducting research in Bioinformatics and Computational Biology thus giving me the essential
training for advanced study and research in this area.
With the experienced gained, my thirst for this field is ever-growing, seeing how much potential it
holds to merge the field of Molecular Cell Biology with wet lab biology, i am passionate to pursue
further in this to utilize the information obtained from biological systems in a more meaningful and
productive manner.