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Pursuing computational biology research, hoping to change the way we fight cancer

 

As a freshman, Simran Kadadi was looking for a research angle that was connected to biology, yet would complement her computer science background. She didn’t know it would eventually lead to work in a computational biology lab, an award for her work and ultimately a plan for the future.

 

Simran Kadadi, a junior majoring in computer science honors with a specialization in both the machine intelligence and algorithmic foundations track

Simran Kadadi, a junior majoring in computer science honors with a specialization in both the machine intelligence and algorithmic foundations track, wanted to connect her background in computer science with biology. In her freshman year, she approached Majid Kazemian, assistant professor of computer science and biochemistry, with an interest in computational biology research. 

“I was interested in pursuing research connected to biology that would complement my computer science background,” said Kadadi. She added, “Professor Kazemian recommended courses that would prepare me for bioinformatics research, specifically he recommended his class on computational genomics to further determine my interest. This class opened my eyes to the diversity in computer science, and I was excited to find a fit in this profession.”

 

Computational biology research

Currently, Kadadi works as an undergraduate research student in the Kazemian Lab. The lab focuses on studying gene regulation in viral associated cancers, autoimmune disorders, and infectious diseases. They utilize biological assays and computational models to identify novel biological pathways, new host-pathogen interactions and regulatory RNAs that could trigger disease. 

Kadadi’s research focuses on Epstein Barr Virus (EBV) associated cancers. 

“My favorite part of my academic undergraduate experience at Purdue CS is using my computer science background to tackle real-world problems that affect real people,” said Kadadi.

In 2020, an estimated 19.3 million new cancer cases were diagnosed worldwide. EBV infects approximately 95% of all adults and is responsible for approximately 1% of all cancers. Kadadi’s goal was to examine the nature of the interactions and the role of EBV using single-cell RNA sequencing (scRNA-seq). Many B-cell origin lymphomas have been associated with EBV, making it an area of significant interest in the cancer research community.

Kadadi investigated the cellular response of EBV infection at the single-cell level in nasopharyngeal cancer (NPC) patients by sourcing datasets, filtering the low-quality cells, and identifying variable features within the data. She analyzed the data by applying various dimension reduction techniques to drive biological interpretations. She used the uniform manifold approximation and projection algorithm (UMAP), a neighbor graph-based approach to identify the cell identities, to visualize the high dimensional data in a 2D map. 

Along with two other Purdue computer science majors, Kadadi received honorable mention for her work in the 2022 Computing Research Association (CRA) Outstanding Undergraduate Researcher Award competition.

“I want to have an effect on real problems that affect real people,” she said. Kadadi added, “I’m learning about the ability to push the boundaries of what we know of the human body and the field of genomics. It helped me take my interest in biology and uncover a lifelong passion for exploration and discovery in computer science.”

 

Belonging

When Kadadi began her research as a sophomore, she felt welcomed by Professor Kazemian and Bingyu Yan, a PhD student and mentor.

“They guided me through the research process and encouraged me to ask questions, make mistakes, and learn to be meticulous with my work,” said Kadadi. She added, “This positive culture of learning at the Kazemian Lab inspired me to take a leap with my journey in computational biology, and I am so glad I did. My research with the lab has helped me find meaning in my coursework and grow as a computer scientist.”

 

Leadership

Kadadi also volunteers her time with the Department of Computer Science’s Undergraduate Student Board (USB). The USB is a student-run organization that is dedicated to improving the student experience within computer and data science majors at Purdue University.

“My favorite accomplishment at Purdue has been my activism and leadership with the USB,” said Kadadi. “This club has helped me stay connected and take initiative within the computer science and data science community at Purdue.”

 

Computer science for the future

When asked how she envisions her future in the computer science profession, Kadadi first looks at the advances made in the past and considers the possibilities to come.

“Advances in computer science over the last century have revolutionized the way we perceive the world around us. Computer science dissects the art of nature and makes it binary. It allows us to view the world through a detail-oriented lens,” said Kadadi. “

She explained data and computer science simplifies the incomprehensible into quantifiable patterns. “Computers have allowed us to store and analyze hundreds of terabytes of genomic data, a treasure trove of unexplored information,” said Kadadi

Specifically with Kadadi’s research she conceded the pathways that can lead to cancer are unprecedentedly intricate. Moreover, she explained that the growing data set makes it exigent to parse through this dataset and achieve conclusive results in cancer research. 

“In my lifetime, I would like to tackle this complex mechanism and help kickstart the engine leading us to find ways to treat this growing database as a roadmap to success,” said Kadadi.

Kadadi would like to lead in this paradigm shift to an increasingly data-driven treatment strategy that can take input from one’s own genetic information and morph into concrete solutions. Machine Learning has the immense potential to allow doctors to directly compare patient outcomes with similar genetic profiles. 

“As I pursue my plans for further academic study, I hope to lead a future where computational genomics paves the way for future treatment plans,” said Kadadi.

 

 

About the Department of Computer Science at Purdue University

Founded in 1962, the Department of Computer Science was created to be an innovative base of knowledge in the emerging field of computing as the first degree-awarding program in the United States. The department continues to advance the computer science industry through research. US News & Reports ranks Purdue CS #20 and #18 overall in graduate and undergraduate programs respectively, ninth in both software engineering and cybersecurity, 14th in programming languages, 13th in computing systems, and 24th in artificial intelligence. Graduates of the program are able to solve complex and challenging problems in many fields. Our consistent success in an ever-changing landscape is reflected in the record undergraduate enrollment, increased faculty hiring, innovative research projects, and the creation of new academic programs. The increasing centrality of computer science in academic disciplines and society, and new research activities - centered around data science, artificial intelligence, programming languages, theoretical computer science, machine learning, and cybersecurity - are the future focus of the department. cs.purdue.edu

 

Writer: Emily Kinsell, emily@purdue.edu

Sources: Simran Kadadi, skadadi@purdue.edu

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