Meet Dr. Soham Sengupta, a bioinformatics research scientist who was conferred for his doctoral degree at the University of North Texas in December 2022. For the past seven years, Dr. Sengupta has been conducting research in the lab of Dr. Rajeev Azad in the Department of Biological Sciences. Throughout his studies, he has been developing his passion for applying computational techniques and algorithms to analyze complex biological data and gain insights into the underlying biological mechanisms. He said his love for computer science has given him a unique perspective on how computational techniques can be applied to solve biological problems.
"I have always been fascinated by the complexity and diversity of biological systems, and I am passionate about understanding the underlying mechanisms that govern their behavior," he said. "I am inspired by the potential impact that bioinformatics research can have on human health and the environment, and I am driven by a desire to make meaningful contributions to these fields."
Dr. Sengupta's journey began with a Bachelor of Technology degree in Biotechnology from Haldia Institute of Technology in India. This program provided him with a strong foundation in the biological sciences, and it was during this time that he became interested in the intersection between biology and computer science. His next stop was the University of North Texas to pursue a PhD in Biology with a specialization in Bioinformatics.
"During my time at UNT, I gained expertise in the analysis of biological data using computational methods, and I had the opportunity to work on several exciting research projects," said Dr. Sengupta. "These experiences have equipped me with the skills and knowledge necessary to contribute to this exciting and rapidly-evolving field."
Dr. Sengupta's dissertation research focused on investigating the mechanisms and implications of horizontal gene transfer (HGT) in bacterial pathogens, which led to the recent publication of two papers. The first one, titled "Leveraging Comparative Genomics to Uncover Alien Genes in Bacterial Genomes," appeared in Microbial Genomics. The second one, entitled "Reconstructing Horizontal Gene Flow Network to Understand Prokaryotic Evolution," was published in Open Biology.
"This research could have important implications for understanding the evolution of bacterial pathogens, including how they acquire new traits and develop antibiotic resistance," said Dr. Sengupta. "I hope that our work serves as a step forward in this direction and can potentially provide valuable insights to other researchers in developing more effective treatments and interventions to address the growing threat of antibiotic resistance and other challenges posed by bacterial pathogens."
Dr. Sengupta is currently working as a Bioinformatics Research Scientist at the St. Jude Children's Research Hospital in Memphis, Tennessee. In the following interview, he discusses his newly published papers, the nuances of his work, and experience as a research scientist at the University of North Texas.
Q: Can you tell us a little bit about the papers you recently published?
A: Bacterial pathogens are notorious for their ability to spread infections and develop resistance to drugs, often through a process called horizontal gene transfer (HGT). HGT enables bacteria to acquire new traits and adapt to new environments by exchanging genetic material with other species, even across domains. Despite significant progress in this field, our current understanding of bacterial evolution through HGT and the dissemination of traits remains limited. This highlights the need for further research and exploration into the mechanisms underlying this process with the goal of developing new strategies to combat antibiotic resistance and other challenges posed by bacterial pathogens.
In our first recently published paper in Microbial Genomics, we introduce a novel method called Alienness by Phyletic Pattern (APP), for identifying horizontally acquired genes (foreign/alien) in bacterial genomes. This approach involves comparing genes across different taxa to detect genetic material that has been acquired horizontally. APP demonstrated overall superior performance compared to existing methods (~7-68% in overall accuracy) and can detect both recent and ancient transfer events. APP is versatile, user-friendly, and can be used as a standalone tool or in cohort with other complementary pipelines, for more efficient HGT detection.
Our second paper, published in Open Biology, utilized APP in an integrative approach to infer the horizontal transfer of alien genes. This study reveals new insights understanding about HGT and how it contributes to the evolution of prokaryotes. We introduce a new approach for investigating HGT enabling researchers to identify the specific donor and recipient organisms involved in gene transfer, including the movement of not only alien genes but also native genes. As a result, the approach provides a more comprehensive view of the intricate web of genetic exchange occurring between various bacterial taxa.
Q: What is one of the most challenging aspects of your research?
A: One of the most challenging aspects of my research is dealing with the vast amounts of data that are generated by modern high-throughput sequencing technologies. These datasets are complex and require advanced computational tools and methods to extract meaningful information. In addition, the biological data can be noisy, which can make it difficult to distinguish true biological signals from background noise or artifacts. Therefore, one of the main goals of my research is to develop methods that can efficiently distinguish meaningful data of biological significance from the background noise, leading to more precise and accurate analysis of biological systems. Ultimately, these efforts aim to improve our understanding of the complex evolutionary history of bacterial populations, spurring further research and pushing the boundaries of current knowledge.
Q: What is one of the most rewarding aspects of your research?
A: One of the most rewarding aspects of my research is the sense of satisfaction and happiness I feel when I am able to solve a challenging problem or overcome a significant obstacle. It's an incredibly fulfilling feeling to know that my work has led to a deeper understanding of complex biological systems and has pushed the boundaries of current knowledge. The excitement and sense of achievement I feel when I develop a new computational method that performs better than existing methods is unmatched. Being able to develop and apply cutting-edge techniques to solve important biological questions is a thrilling experience. The potential for my research to make a real-world impact is truly rewarding.
Q: Who are your mentors and how have they helped you in your research and academics?
A: I have been fortunate to have several mentors who have provided invaluable guidance and support throughout my academic and research journey. Dr. Tarun Kanti Mandal, my undergraduate professor at Haldia Institute of Technology, introduced me to the fascinating field of bioinformatics, which sparked my passion for research.
During my graduate studies at UNT, I had the privilege of working under the supervision of Dr. Rajeev Azad who played the crucial role in providing me with the scientific and technical expertise necessary to tackle complex biological problems. Dr. Azad has been a constant pillar of strength while being immensely patient, even during the most challenging hours. Their mentorship helped me to develop a strong foundation in my field, and they provided me with the opportunities and resources necessary to succeed in my research.
I have also had the privilege of working with several collaborators and colleagues who have contributed to my growth as a scientist, pushing me to think creatively and critically about my research. Overall, the mentorship and guidance I have received from my mentors and colleagues have been instrumental in my academic and research success.
Q: Why did you choose UNT for your studies?
A: I chose UNT for several reasons. First, the university has a strong reputation in my field of study, and I was impressed by the faculty and their research interests. Second, UNT offers a range of resources and opportunities to support students, specifically in the form of teaching and research assistantships, travel scholarships to conferences and various student organizations. I was particularly drawn to the opportunity to work in the university's state-of-the-art research facilities.
UNT's location in Denton, Texas is ideal for me. It's close enough to major cities like Dallas and Fort Worth, but it has a more relaxed and friendly atmosphere that I appreciate. This university seemed like the perfect fit for me both academically and personally, and I have had a wonderful and wholesome time being a part of the UNT community.
Q: What is one of the most important things you have learned while at UNT?
A: During my time at UNT, I have had the opportunity to learn and grow in many ways. One of the most important things I have learned is the value of both independent research and collaboration. On one hand, UNT has presented me with challenging research problems that have allowed me to develop as an independent researcher, honing my critical thinking and problem-solving skills. On the other hand, I have also learned the importance of collaboration and teamwork in achieving research goals. Through working with my peers and mentors, I have come to appreciate the diverse perspectives and skill sets that can be brought together to solve complex problems. Overall, UNT has played an instrumental role in shaping my academic and personal growth, both as an independent researcher and a collaborative team member.
Q: Is there anything else you'd like to share with us?
A: UNT has been such a huge part of my life and I feel incredibly blessed to have been a part of it. It has given me the chance to grow as a researcher and become a bioinformatics scientist. I have had the opportunity to collaborate with some brilliant minds and engage in fascinating discussions, which has broadened my perspective and deepened my understanding of my field. From this community of amazing colleagues, I have found some of my closest friends. I've made so many unforgettable memories with them that are just as important to me as any academic achievements. To put it simply, some of the best years of my life were spent at UNT!
For more information about Dr. Azad's research lab, visit: https://bioinformatics.unt.edu/faculty/azad-lab-bioinformatics-and-compu...