Subha Team
PhD
Meeta Sunil
Title :
Pushpinder Bhwa
Title :
Suran Nambisan
Title :
Training | Semester Projects | Interns
The success of research-cum-training program was twofold. Students, who were driven by genomics, had a chance to build a research career by securing publications. Also, it helped faculty members to venture and broaden their research in diverse application areas using NGS data from public repository. Since the public repository represents the trend in NGS research, this allowed faculty members at IBAB to keep-up with the trend in technology and applications both in training and research.
Students also played a significant role in validating findings from data mining efforts. Many students, who preferred wet lab work were offered projects to experimentally validate findings from data analysis. This provided IBAB with a continuous stream of students’ year-after-year in advancing research both in bioinformatics and experimental biology. For example, by 2014, when the second batch of MSc students were ready for semester projects, students opted to clone tyrosinase gene from grain amaranths, PCR validate gene expression or correlate lysine content with the expression of aspartate kinase in grain amaranths. Many others ventured mining public data for miRNA expression in lung cancer, alternative splicing in bipolar disorder, differential gene expression in breast cancer, biomarker for testis, prognostics miRNA in renal cancer and more. It is almost like a river running through IBAB.
The first few PhD students lacked infrastructure and had no road map. At that time IBAB and the rest of the world was new to NGS. Even faculty members at IBAB were learning along with students. It was exciting times! The river of students’ year-after-year provided the much-required hands for PhD students in trying various pipelines and protocols. It was like an extended family preparing for a huge wedding. The timetable shows interns/PAs who supported both PhD students (red arrows) and additional ongoing projects.
Learning from talented PhD students attracted significant students towards academic research. Almost all interns were supported by grants to Subha (grey arrows) and the numbers are reflective of training support from grants. For example, well-funded TIGS collaboration attracted large number of students to continue with internship after graduation. The success of the research-cum-training was also acknowledged by students willing to do internship/PA at IBAB for a meager stipend when they could join companies earning handsome salaries.
Many students interested in pursuing academic career in genomics, used a year or two at IBAB until they secured admission into a graduate school of their choice. During this time, they had opportunities to continue their semester projects to a fruitful end leading to a publication and/or gain expertise in NGS data generation. They spent long hours working on various genomics projects including helping with sudden deluge in data from the BioIT center. With a few exceptions majority of these interns secured publications from IBAB in peer reviewed journals increasing the odds of getting admitted in better school (*). Many interns subsequently secured admissions in graduate schools abroad. These interns include:
Many interns subsequently secured admissions in graduate schools abroad. These interns include:
• Samathmika Ravi, University of Padova, Italy (MSc04) Graduated *
• Saptharathi Dev, University of Padova, Italy (MSc06) *
• Aditi Takare, University of Padova, Italy (MSc06), Marie Curie Fellow *
• Tejashwini Alalamath, John’s Hopkins, USA (MSc07) *
• J. Suvratha, University of Jena, Germany (MSc04) *
• Jeyshmita Saha, University of Belgium, Belgium (MSc07) *
• Chinjusha Suresh, University of Poland, Warsaw (MSc07) *
• Mohit Verma, University of Leusiana, USA, (PGDB 2011) Graduated *
• Arun Patil, IOB plus John’s Hopkins, USA, (PGDB, 2010) Graduated *
Many others chose to register for PhD or secure jobs in genomics in Bangalore including at IBAB
• Nivedita Hariharan, NCBI, Bangalore (MSc02) *
• Sowmya Nayak, NCBI, Bangalore (PGDB 2011) *
• Jayanth B, GSK, metagenomics (PGDB 2010)
• Sasi Kumar, Thermo Fisher, genomics researcher
• Kiran Paul, TIGS, genomics researcher *
• Meeta Sunil, Plant Genomics, IBAB, (PGDB 2011) Graduated *
• Suran Nambisan, Metagennomics, IBAB, (PGDB 2011) Graduated *
• Pushpinder Bawa, Cancer, IBAB, (MSc01) Graduated *
• Manjari Deshmukh, Indegene (PGDB 2010) *
• Neeraj Singh, Infosys, SME in genomics (PGDB 2010) *
Yet others did internship at national labs before moving abroad. These include,
• Rachita Srivatsava, Max Plank Institute for Plant Breeding (MSc06)
• Tejas Shinde, University of Austria, Austria (MSc07)
• Muktai Kuwalekar, University of Helsinki, Finland (MSc07)
• Harsh Shukla, University to California, USA (MSc06) *
• Saurabh Gupta, University of Potsdam, Marie Curie Fellow, Germany (PGDB 2011) Graduated *
• Ameer Washib Khan, University of Western Australia, (PGDB 2011) Graduated
There are others who were hired to work as interns and ended up going abroad for graduate school. These include,
• Afiya Chida, University of Calgary, Canada *
• Savita Kartikeyan, University of Oxford, UK *
As IBAB research-cum-training program matured a number of students from more recent batches were able to secure authorship in peer reviewed journal based on their 4th sem projects. These include Shrestha Das. Himani Narang, Shweta Shrotri and Siddarth Singh from MSc09 and Harsh Mahavir, Aadhaya Jaisimha, Mohanapriya Ksrishna, Artra Chattopadhyay, Rishima Borah. And Vikranth Singh from MSc10.
With a handful of faculty members to handle labs, interns/PAs are important component of our training programs. This also provided the TAs to sharpen the concepts missed during their course work. To name a few effective TAs, Sagar Desai (did intern before registering for a PhD), Pushpinder Bawa (PhD student), Aditi Takare, Saurabh Gupta, Savita Kathikeyan, Saptarathi Dev, Suvratha J, and Afiya Chida played critical role over the years like they were part of a relay race in the success of IBAB training and research program.
The timetable above demonstrates that the research funding related to training people in NGS applications, such as TIGS, had a larger impact on people pursuing genomics research as their career option. The novelty in applying genomics to control malaria with direct impact to health benefits in India was attractive to students. Furthermore, data generated using the then state of the art technology like PacBio and HiC provided an unprecedented opportunity to learn. Early 2020, the success of retaining interns and attracting 4th sem students resulted in 14 students/interns (see left) working with Subha in TIGS related projects.
It also required intensive training in bioinformatics because An. stephensi, an urban malaria vector endogenous to India, has never been studied using genomics. This means that students are looking for both interesting projects that addresses bottom-line problems related to India and take upon the challenges from the burgeoning NGS technologies with steady funding source from TIGS. As is obvious from the timeline, it was easier to retain interns with the promise of publication and guaranteed funding.