Frameshift – Physicist Dr. Nita Parekh’s curious trail to computational biology

Prof. Nita Parekh has witnessed IIIT Hyderabad’s evolving avatars, from its fledgling years to the smart connected and buzzing research hub that it is today. With over two decades at IIITH’s CCNSB, her core expertise in computational biology and bioinformatics delves into next generation sequencing and multi-omics data analysis, developing ML-based tools and databases for biological problems like cancer detection.

“When I joined the iGenomics division at iLabs, I did not know the B of Bioinformatics. I loved Math, hated biology and the thought of dissecting frogs horrified me”, laughs the physicist who clocked six years of diverse post-doctoral research in computational methods in physical, chemical and biological systems. “Even during my post-doc tenure at the Center for Cellular and Molecular Biology (CCMB), my work was mostly in non-linear dynamics”.

Nita and her husband Shrish Tiwari returned home from USA when her husband joined CSIR Lab at CCMB as a scientist. This was during the Boom of biological data; when the genome was sequenced and there was a lot of talk about precision medicine. She joined iGenomics division of iLABS, as they needed a scholar who understood algorithms for biological data analysis to help their coders. While at iLABS , the Genomics specialist gave guest lectures in bioinformatics to MSIT students at IIIT Hyderabad and found the research environment invigorating.  She joined the Institute in 2003, the year that the human genome was sequenced. Within a year, the M. Tech, MS by Research and Ph.D in Bioinformatics programs commenced. The erstwhile Bioinformatics Research Center with its skeletal faculty and CCMB’s visiting scientists would eventually evolve into CCNSB.

The things that I do
Advancements in biotechnology have led to different types of data being generated for different omics, like genomics, transcriptomics, proteomics and metabolomics, explains the professor. When the study of biology became quantitative, the need arose for cross-disciplinary experts who understood biology and could write algorithms or build models.  The development of tools, databases and analysis was happening and somebody had to do the lab testing. “My work in computational biology was somewhere in that interface. Being a Ph. D in physics, well-versed in computational physics, I wrote models and equations and solved them on computers. I was thus a good fit in this new area that had just come up in biology”, explains Dr. Parekh. 

 “It was fun in the early days on campus, when everybody knew everybody. My room was on the third floor of the old main building. Lunches in the canteens, a quick walk around campus or catching up at the small tea stall at the basketball court before heading back to our labs and lessons, were great memories. We had a makeshift tea stall under the staircase and one had to just call out, ‘Babu Chai dena’ and he would bring us our tea”, she reminisces fondly.

Advancements in biotechnology have led to different types of data being generated for different omics, like genomics, transcriptomics, proteomics and metabolomics, explains the professor. When the study of biology became quantitative, the need arose for cross-disciplinary experts who understood biology and could write algorithms or build models.  The development of tools, databases and analysis was happening and somebody had to do the lab testing. “My work in computational biology was somewhere in that interface. Being a Ph. D in physics, well-versed in computational physics, I wrote models and equations and solved them on computers. I was thus a good fit in this new area that had just come up in biology”, explains Dr. Parekh. 

 “It was fun in the early days on campus, when everybody knew everybody. My room was on the third floor of the old main building. Lunches in the canteens, a quick walk around campus or catching up at the small tea stall at the basketball court before heading back to our labs and lessons, were great memories. We had a makeshift tea stall under the staircase and one had to just call out, ‘Babu Chai dena’ and he would bring us our tea”, she reminisces fondly.

Of Alleles and unusual range of projects
Dr. Parekh enjoys working with transcriptomics data, which is basically gene expression data. “There’s a lot to learn in this field and what really excited me was understanding networks of genes using graph theory”, notes the professor who takes various courses in Bioinformatics at CCNSB. Continuous learning keeps her at the top of her game, thanks to the diverse research topics of her Ph.D. students, that range from Plant stress to working with cancers, the spread of swine flu and COVID-19. A few papers and an online tool, NetREx, came out of their work on Gene co-expression network analysis of abiotic and biotic stress conditions in rice for identifying stress-specific biomarkers.

During the pandemic, Nita worked on Covid-19 demographic analysis of SARS-CoV-2 mutations for the three waves, using Indian samples data and developed an epidemiological model of transmission for the different waves and its impact. With computer science Ph.D. student, Suba, who recently graduated, she worked on the analysis of chest X-rays and CT-scan images for diagnosis of COVID-19 using ML approaches, that resulted in couple of journal and conference publications.

With Ph.D. student Prashanthi, they analyzed different types of variations in cancer genomics; genetic variation analysis using next generation sequencing data to do subtyping of the cancer. “We integrated all types of mutation data to create a mutation profile for the patient and proposed subtype-specific pathways affected DLBCL cancer. Couple of tools and MS theses came out of this project. Currently she is extending this work, integrating various omics data for breast cancer subtyping with PhD student, Sri Lakshmi. She developed a tool called Network Analysis of Protein Structures (NAPS) that was subsequently updated with more features, with PhD student Broto. This was an extensively used tool by researchers during the COVID era for modeling SARS-CoV-2 proteins and we have the maximum number of citations for that paper”, observes Dr. Parekh who has co-authored 40 journal publications, contributed book chapters and has three MS thesis published as monographs in nonlinear physics and bioinformatics. “Over 30 papers were published in conference proceedings and a couple of journal and conference papers are still in the pipeline” says the associate editor of the Journal of Genetics, published by the Academy of Sciences.

Simple living marred by tragedy, and a circuit ticket
Since her father was in a transferable job, Dr. Parekh moved around many small towns till the family settled in Jabalpur. From Class eight, she studied at Jabalpur’s St. Joseph’s Convent Girl’s Sr. Sec. School (1977-81).  “Growing up, we stayed in very small government estates, away from city life. It was a very nice small community, with all of us going to the same school, the local club and movie hall. There were jungles around us and we had nothing to do except play, study, sleep and go for walks along jungle trails. I was always good in studies and for me, academics was just a seamless journey of acquiring one degree after another. I was very good in Maths but opted for Physics since it had better job opportunities”.

She was slated to join IIT Roorkee but the tragic demise of her father and sister in a car crash derailed that dream. Dr. Parekh would stay back in Jabalpur to complete her M.Phil. (1984-1988) in Physics from Rani Durgavati Vishwavidyalaya. It was her mother, who went against all relatives who wanted to marry her off, and encouraged her to pursue her Ph. D and become financially independent first. “Without her constant support through all these years, not to mention the sacrifices and support of my husband and daughter, this journey wouldn’t have been possible”, says Dr. Parekh gratefully. She received her doctorate in Physics (1986 – 94) from Jawaharlal Nehru University, Delhi. After submitting her Ph. D, she embarked on a Theoretical Physics Seminar Circuit, to give talks in Physics department of various Institutes. “I actually travelled across India on what was called a circuit ticket. It was the most memorable round trip from Delhi to PRL & IPR Ahmedabad, Bose Institute and SINP, Kolkata, IOP Bhubaneshwar, IIT Madras and Ins. Math Sci Chennai, University of Trichy, and a conference in Cochin on the way to IISc and JNCASR, Bangalore where I completed the circuit”.

A switch in Time
An overarching desire to explore more viable career avenues would prompt Dr. Parekh’s decision to join National Chemical Laboratory, Pune (1994-97). At her first post-doctoral stint, she worked on a chemical reaction diffusion system for big reactors for the chemical engineering department. At her second post-doc stint at CCMB (1997-99) she worked on population biology.

“When we moved to USA with our baby daughter, Nikita, it was initially an adjustment in a new country”, she recalls. “However, since my post-doctoral supervisor was also on sabbatical at NIH for 6 months, my research work continued with her on weekends, while Nikita was being taken care by Shrish”. At that time, The Institute of Genome Research (TIGR), a tantalizing half kilometer from her house, was doing pioneering work in the human genome. Dr. Parekh soon joined NIST at Maryland and got to work on stress-strain analysis of phase segregating systems. Within a year, the young family relocated to India and after a brief stint at iLabs, Dr. Parekh joined IIIT Hyderabad. A few years later, she would complete a year’s tenure at the Center for DNA fingerprinting and Diagnostics while juggling two classes a week at IIIT Hyderabad.

The professor who walks
“I love walking, alone or with company. I take short walks in the morning, lunchtime and sometimes before heading home”, admits the professor who has finessed the art of switching off when she leaves campus. “Once home, a quick evening constitutional walk and then I’m ready to start my cooking. When my daughter was younger, I would walk circuits around the tennis court, while she practiced.  I also enjoy yoga and cycling.  During the pandemic lockdown, I gifted myself a cycle. I recently recovered from a meniscus tear in my knee and a broken ankle and am getting back to my routine. Online yoga is my latest fitness fad. I generally put on old Hindi music when I do my morning exercises”, notes Dr. Parekh, once an avid reader of Agatha Christie, Wodehouse, Alistair McLean, etc. who now struggles to plough through a book.

 “Working alongside my students gives me the most joy. They are my lifeline”, she observes. “I feel that honest hard work is a cherished value that every student should strive for in today’s OpenAI era. How to learn is more important than memorizing and reproducing it for the exam”.

“How should I identify important features and attributes using domain knowledge to intelligently use ML-based approaches? That is a challenge given the heterogeneity in biological systems”, points out Dr. Parekh. One big item on her wish list is to keep up with advancements in machine learning and connect it back to her work in the Lab.