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WASHINGTON, June 14, 2018 /PRNewswire/ -- Demonstrating the power of student data scientists and researchers, Deloitte and the National Institutes of Health's (NIH) National Library of Medicine (NLM) celebrated two student-led research teams that made significant new virus and antibiotic resistance discoveries. These student teams, from San Diego State University (SDSU) and Kingsborough Community College of The City University of New York (KCC CUNY), used novel computational techniques to identify patterns in DNA data, provided by the NLM National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).
At KCC CUNY, students learned to perform bio-surveillance on public metagenomic datasets, identifying fungal and other micro-eukaryotic, bacterial, archaeal, and viral sequences within these datasets. The students analyzed HIV, HPV and Lyssavirus datasets, among others. Their findings reinforced the fundamentals of computational biology utilizing Next Generation Sequencing (NGS) technology, a critical tool in determining metagenomics data sets. Further plans are underway to developing this as a research opportunity for all interested CUNY students and beyond.
SDSU students enrolled in the Microbial Metagenomics Discovery Challenge learned how to use the "cross assembly" program that sorts through the DNA and RNA present in a sample, separates out the known microbes, and locates the genetic signatures of a virus. Led by Professor Edwards, students applied those skills by hunting for new viruses—as well as looking for the genetic hallmarks of antibiotic resistance—in real datasets of DNA. The SDSU winning team examined viruses present in California mosquitoes, how often those viruses were carried by California mosquitoes and their threats to humans.
"To make more medical breakthroughs happen, more students and young researchers need to be getting their hands dirty in these biomedical datasets," said Dr. Juergen Klenk, principal, Deloitte Consulting LLP and federal health precision medicine leader. "The next generation of researchers are digital natives, familiar with data science and crowdsourcing. This discovery challenge offers an innovative model for biomedical research of the future.
"It also demonstrates how to incentivize a vast community with an open data philosophy and a prize-based competition, to effectively advance research that could not be performed with traditional models due to the sheer size of the dataset. In this challenge, a simple crowdsourcing mechanism generated many valuable, viable ideas, and we are excited about the ones that surfaced to the top."
"Viral discovery is critical for understanding how viruses evolved inside of us and in other ecosystems, and what they mean for human and ecosystem health. This course and support from Deloitte has helped to inspire a new generation of scientists to find the next crAssphage," said Dr. Robert Edwards, professor of computer science, San Diego State University.
"Student engagement is the key to their academic success and Deloitte's support has helped them to achieve that," said Dr. Dmitry Brogun, professor of biological sciences, Kingsborough Community and Brooklyn College, City University of New York.
In the Microbial Metagenomics Discovery Challenge, professors from KCC CUNY and SDSU designed an undergraduate course to teach students computational methods and then set the students loose on the largest repository of DNA sequencing data to apply what they learned and make new discoveries. More than 60 students participated in the challenge and formed teams that combed through the SRA over the past three months.
The SRA makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms. Students summarized their findings in short videos, and the most important discoveries will be published.
The winning teams received a $5,000 prize sponsored by Deloitte presented at the NLM Data Science Innovation Conference. A committee of judges from participating universities selected the winners based on the importance of their discoveries and the quality of their presentations.
"There are so many important lifesaving and life-improving discoveries and breakthroughs just waiting to be found in immense amounts of data," said Klenk. "Prizes and challenges are a great way to mobilize talent and fresh thinking. Prize designs succeed where many efforts fail because they activate a crowd of solvers from diverse perspectives and give them access to tools and data."
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