Nisha Singh is an Assistant Professor at Department of Bioinformatics of the Gujarat Biotechnology University, Gandhinagar. In the eighth article of our JOYI series, she shares her inspiring journey of transitioning from wet lab to bioinformatics as a young investigator in India.
As a child, I wanted to become a doctor and had a keen interest in biology. I used to love the subject and had an indomitable instinct to know the “what, how, and why” of natural beings. This constant inquiry annoyed my mother, leading me to redirect my questions to my teachers, fellows, and others. My nature remained the same, but my questions evolved.
During the summer vacation of my undergraduate biotechnology program, I caught on to the popular subject of programming. I learned the basics of computer systems and programming languages C, C++, and Java, which kindled my interest in programming alongside biology.
During my bachelor’s degree in biotechnology, I found much to explore in genetics, evolution, and biochemistry. I always found pleasure in performing experiments and noting down outcomes. However, merging the study outcomes was painstaking; manual analysis and data interpretation seemed a herculean task to me.
This struggle was a source of discontentment. Although experimental research generated much data, there was a lack of a clear pipeline for its analysis. There also was a need for validating data authenticity. Thus, combining my interest in programming languages with the need for automated data analysis, I decided to pursue a masters in bioinformatics. The decision was challenging on many fronts:
I had to shift to a new city, away from my parents. Since I was a girl from a small town with a humble and orthodox background, I faced challenges that tested my determination.
I was the first among my peers to pursue a transition to bioinformatics.
There was a general lack of awareness about bioinformatics as a course.
Bioinformatics at that time was not considered applicable to plant/agricultural sciences (only to medical research/animal sciences).
Only a few universities offered a Ph.D. in bioinformatics.
At times my determination seemed fragile. However, my perseverance and focus kept me going. By the time I completed my post-graduation, I had thought of agility as my strong suit — I could combine experiments in the laboratory with the tools/languages of computers.
My doctorate in biotechnology and bioinformatics was an apt opportunity to test my agility. I had fostered a dream of joining one of the labs at the National Institute for Plant Biotechnology, IARI, which was soon actualised. At NIPB, I was a naïve amateur student within a large group of researchers. It was challenging and enlightening at the same time.
Graduating from a small dry setup to an advanced and well-equipped lab was difficult. It challenged me to work harder: I self-learned and updated on R, Python, and NGS data analysis. I had an added advantage due to my background in biology which enabled me to integrate wet and dry science. My hard work bore fruits and I published a patent and several research papers.
I furthered with an international research experience as a post-doctoral scholar at the Institute of Genomic Diversity, Cornell University, USA. It was an experience in leadership qualities, lab management, and maintaining a healthy lab culture. I was inspired here by a seminar on Alpha Fold (a deep learning system to predict protein structure) to focus on machine learning and artificial intelligence. I investigated the genome of the root vegetable cassava and utilised machine learning models to develop its HapMap3. I also contributed to the genetic improvement of crops by creating novel genomic elements for desirable functions using deep learning in synthetic biology.
I wanted to serve the country with the skill sets and expertise acquired during my postdoctoral training. Thanks to the DST-INSPIRE Faculty award, I could walk the talk. I returned to India, formed my research group, and mentored postgraduate and Ph.D. students.
Currently, I am serving as an Assistant Professor at Department of Bioinformatics of the Gujarat Biotechnology University, Gandhinagar, where my group is focused on the battle against hidden hunger (undernutrition) and malnourishment through biofortified crop development.
My interest lies in developing cost-effective and high-throughput genotyping technologies. It enables routine genomic selection in breeding programs for the fast-track development of superior crop breeds.
I investigate the use of biomarkers to evaluate plant protein variation. I have also contributed in the following avenues:
Developed the first patented 50,000 SNP genotyping chip “OsSNPnks” for genetics and molecular breeding applications in rice. This chip is bridging the yield gap by helping develop flood-tolerant varieties of rice.
Investigated the origin of rice and its domestication based on agronomically important genes.
Identified seven genes responsible for the resistance of root-knot nematodes (Meloidogyne graminicola) in rice.
Constructed the first haplotype map (HapMap‑1) of tea and developed genomics and bioinformatics tools and pipelines (heterozygous genome assembly, gene-based haplotype pipelines, SNPs assay development tools).
Worked on international genome-sequencing projects (Wild rice, Wheat, Mango, Jute, Pigeonpea, and Tea), genome-wide association mapping, haplotype analysis, synteny analysis, and genic SNP chip development. I have made a significant contribution to the “omics” resource development of pigeon pea (62K CcSNPnks) and mango (80K MiSNPnks). Currently, my group is exploring the tissue-specific proteome atlas of pigeon peas.
Using multi-omics approaches, I have identified high protein lines in pigeon peas, without any gene editing and genetic modifications. These genotypes boost protein gain in the human diet, especially in developing countries, leading to a growth in the farmer’s income.
I have been conferred national and international awards and recognitions. I have been a recipient of the INSA Young Scientist Medal 2020, National Environmental Science Academy, Women Excellence Award-2022, and the NASI Platinum Jubilee Young Scientist Award 2022.
The journey in research and learning is still on and my passion for the same has grown many folds.