Ritu Kundu, Postgraduate at Georgia Institute of Technology, 2017-18

Degree programme at King’s

PhD (Computer Science)

Which institution did you go to and why?

Georgia Tech (Georgia Institute of Technology). For internship/research-collaboration as the team working there is among the experts on my research topic – string algorithm for bioinformatics. Networking and exploring the post-doctoral opportunities were other significant criteria for choosing Georgia Tech.

What did the grant cover and what did it enable you to do?

The grant covered part of travel and accommodation costs.

If not for the grant, I would have missed the opportunity of visiting Georgia Tech and meeting Dr. Thankachan who was visiting the university at the same time. He is the person who informed me as well as recommended me for the post-doctoral position with one of the pioneers in my research-field (Prof. Wing-Kin Sung at NUS). I am most grateful to King’s Worldwide and my department for providing me with this wonderful opportunity that has proved to be significant for my career.

How did your research align with one or more of the four global themes in the fourth strand of the King’s International Strategy: Defence & Security; Global Health; Sustainable Cities; Culture & Identity

The design of algorithms for bioinformatics, also known as computational biology, falls within the remit of the Global Health Theme. The Algorithms & Bioinformatics Group at King’s College London (KCL) and the respective group at Georgia Institute of Technology (Georgia Tech) specialise in the design of the algorithms specifically focussing on biological sequences, such as DNA or proteins. Ongoing advancements in bioinformatics, accentuated by sequencing of human genome, has immense potential to influence health globally. However, there is a long way to go before computational biology attains its goal to drastically improve the way diseases are prevented, diagnosed, and treated. Furthermore, drawbacks like low accuracy and inefficiency of the current methods used in sequencing and analysis of genomic sequences restrict their efficacy.

My research focuses on developing algorithmic and data-driven solutions to address specific issues associated with next generation DNA sequencing technologies (Please refer to my web-page for further details on the “problems” handled heretofore).

The research-visit was aimed to work with the team of Professor Srinivas Aluru (School of Computational Science and Engineering, Georgia Tech). He serves as co-Executive Director for the Georgia Tech Interdisciplinary Research Institute (IRI) in Data Engineering and Science (IDEaS), and co-leads the National Science Foundation (NSF) South Big Data Regional Innovation Hub.

The research work undertaken during the visit was focused on developing bioinformatics methods for high-throughput DNA sequencing, particularly error correction in genome assembly.

Please summarise any expected benefits of the research conducted

Various brain-storming sessions started a new line of research problems. A few of them were dropped because of various reasons. But one–using a new data-structures called special-bridges–looked promising. We (a couple of members of the team at Georgia Tech and University of Central Florida, and myself) pursued that problem and are now following up using Skype for discussions. I developed a small prototype for the construction of this data-structure.

In addition, I presented my research work and exchanged research-ideas with other members of the team who are working in the same and related fields. It has helped me in developing better insights of the current overall picture of bioinformatics (genomics in particular) as a research field and possible future directions it might take.

Please summarise the strategic value of your project in deepening the relationship between King’s and your host institution

This visit not only strengthened the connection between the two departments at KCL and Georgia Tech, but also established new ones with the departments at other universities. Prof. Narasimhan from Florida International University (FIU) and another team from the University of Central Florida (CFU) headed by Dr. Thankachan were also visiting Georgia Tech at the time.

The consolidation of the networks between our team at KCL and the aforementioned teams could be assessed from the following: (1) The Royal Society joint research application with Prof. Aluru (Georgia Tech) has been applied. (2) Prof. Narasimhan (FIU) visited us and gave a talk at KCL in April. (3) A joint workshop is being conducted at CFU in October.

Please describe the social and cultural advantages of your time away

I visited the aquarium and socialised with other students at Georgia Tech. I also attended the St. Patrick’s Day parade. The composition of the city, and the university itself, provided quite an amazing experience. I remember a shocking contrast as compared to the UK – people there do not wish a tube-station near their homes. They fear that better transportation connectivity would bring the criminal activities closer!

Please describe any possible impacts of the trip on the advancement of your research career at King’s and beyond?

As I have stated before, this trip is indirectly the reason that I got one of the best post-doctoral positions in my field. In fact, exploring those opportunities was one of the primary reasons of this trip. In addition, I could expand my professional network with several great connections. The proposed research work is progressing at a satisfactory pace. Overall, I would call this a successful trip and can’t thank King’s worldwide and my department enough for this “game-changing” opportunity.

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