Electrical Engineer Named MIT Technology Review Innovator Under 35
Yatish Turakhia, an assistant professor of electrical and computer engineering at the University of California San Diego Jacobs School of Engineering, has been named an MIT Technology Review Innovator Under 35. He was recognized in the Computing category for developing software tools to track and map the SARS-CoV-2 virus and future pathogens.
The tools, called UShER and RIPPLES, efficiently and accurately track new variants of the virus on what’s known as a phylogenetic tree– a visual history or map of an organism’s genetic changes and variations over time and geography– and sensitively detect and track recombinant strains of the virus. They enabled researchers and public health officials around the world to more accurately track the viral genome of SARS-CoV-2, mapping new variants onto the phylogenetic tree as they develop, and tracking the evolutionary and transmission dynamics of the virus.
The tools were developed by Turakhia as a postdoctoral researcher with Professors Rusell Corbett-Detig and David Haussler at UC Santa Cruz, and were later improved and expanded at UC San Diego by Turakhia’s lab members. UShER was also separately packaged into a web interface by Angie Hinrichs, a senior software architect with the UCSC Genome Browser team, which led to its wider adoption.
“Our global understanding of how covid spreads would have been severely compromised without Yatish’s work,” said David Haussler to MIT Technology Review. Haussler is the scientific director of the UCSC Genomics Institute. “The product of his algorithm, which nobody else could make, is a global picture of how the virus spread in full genetic detail around the entire globe.”
Most recently, Turakhia and a team of two undergraduate researchers at the Jacobs School of Engineering at UC San Diego packaged some of this data into a web interface called RiVeT. This interface provides information on the origin of recombinants – genetically different versions of the virus that joined to create hybrid strains – discovered through RIPPLES. It also links to other visuals of the same recombinants, such as the Taxonium, to help researchers and curators more easily track the relationship and spread of virus strains. RiVeT makes the data from UShER and RIPPLES more useful and easily accessible, and provides weekly updates on the recombinants discovered through RIPPLES.
While all of the data used in these tools had been based on clinical samples, Turakhia’s team is now developing ways for their tracking tools to work with wastewater data. He received funding from an Amazon Research Award and the Center for Disease Control (CDC) to apply these genomic surveillance software tools to wastewater monitoring.
“For a variety of reasons, people are not doing Covid-19 clinical sequencing at the same rate that we saw even a year ago,” said Turakhia. “The variants continue to evolve, and most of the evidence that’s in circulation is coming from wastewater data. This is much cheaper than clinical data, and can give you a population-level analysis. However, it’s much harder to do wastewater monitoring. My group is working with other researchers, including at UC San Diego and Scripps Research, to see how we can combine our software mapping and recombinant detection tools to make wastewater surveillance a lot more potent for SARS-CoV-2 and other pathogens going forward.”
Turakhia said being included as an Innovator Under 35 was an exciting honor personally, but also a welcomed recognition for this research area.
“It’s great that MIT Technology Review has recognized the importance of genomic surveillance,” he said. “They’ve placed it alongside other very relevant topics like climate change and AI, which of course have and deserve a lot of public attention. But I think genomic surveillance is also an important field that will help us combat future pandemics and outbreaks, and save lives as a result.”
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