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Women-led undergraduate research in bioinformatics breaks new ground in genomic data mining

High performance systems Dec 23, 2020

The National Center for Genome Analysis Support (NCGAS), from its home in UITS Research Technologies (a Pervasive Technology Institute center) fosters women-led talent in bioinformatics through a partnership with the Center for Excellence in Women and Technology (CEW&T).

Christine Campbell, an IU Bloomington undergraduate at the Luddy School of Informatics, Computing, and Engineering participated in CEW&T’s 2020 summer Research Experience for Undergraduates (REU) program. The program strives to immerse young scientists in current research efforts; Campbell’s REU project focused on data mining and information modeling for genome analysis.

Christine Campbell, Indiana University, Bloomington

Attending the program remotely due to the COVID-19 pandemic, Campbell said the experience gave her a quality, hands-on experience with genomic informatics. “When I saw this opportunity, I thought it would be a great chance to get more experience in the field, because so much of it involves computing,” said Campbell, who is pursuing a minor in bioinformatics. 

Campbell participated in a year-long seminar hosted by CEW&T learning R-Studio and Linux command lines, which developed skills for her summer REU project studying the genomes of microbes. Found in methane-rich hydrocarbon seeps deep in the ocean, these microbes use methane as a form of energy instead of sugar, oxygen, or light. “It’s really interesting, but we don’t know everything about the genomes of the microbes,” said Campbell. “There is a lot of data, with multiple layers of research,” said Campbell. “The NCGAS team was really good at breaking down information about using the software and learning how to use the different programs,” she continued.  

Mining genomic data from samples collected in the Gulf of Mexico and comparing them to other samples led to the archives of the National Center for Biotechnology Innovation (NCBI). By studying a novel metabolism, Campbell hopes to find new insights into the genomic functions of energy production. “Two specific genes I was able to find were very similar between hydrocarbon seeps and from polluted sediment samples from the Gulf of Mexico. Looking into their gene functions, you can see parallels with other species, even humans,” explained Campbell, who says she has an interest in studying genomic components of cancer or Parkinson’s disease in the future.

Campbell, along with her research group, was recognized by the American Society for Microbiology Microbe Conferences in 2020. “These young researchers are improving access to data by learning data mining, in addition to participating in microbiology research,” said Bhavya Papudeshi, the Bioinformatics Analyst at NCGAS who served as Campbell’s mentor.  

NCGAS Sn. Scientist Tom Doak added, “We are pleased to support early career researchers who show dedicated interest in the field. Since 2018 we have worked with CEW&T to further our mission of equity and excellence in research. The 2020 REU cohort is another outstanding example of this partnership, and we look forward to welcoming next year’s participants.” 

Overall, Campbell says the experience helped her acclimate to the research expectations and technology of bioinformatics, and got her comfortable with the idea of pursuing a career in the field. “You see all of these people working on research projects and using this really advanced technology and it’s a little intimidating at first,” said Campbell. “But then you realize that no one really has all the answers, and that’s why we’re here working together,” she said. 

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