Yousuf Khan

By Dr. Rachel Niederer

Yousuf Khan is a second-year graduate student at Stanford University, where he is both a Knight-Hennessy Scholar and an NSF fellow. Currently, Yousuf studies translational recoding in the laboratory of Dr. Axel Brunger. He received his B.Sc. in Cellular Biology and Genetics from the University of Maryland, College Park. During this time, he worked with Dr. Jon Dinman and discovered his love of translational reprogramming. He was inspired to join the Dinman lab after reading a blurb on the website describing recoding, specifically how cells and viruses can dynamically redefine their genomes. He notes, “I think even today that is such a fascinating concept, and even in a protein biophysics lab, I find myself cloning and testing constructs trying to validate novel recoding signals!”

Ribosomal frameshifting is a strategy most commonly associated with viral genomes, however, Yousuf became interested in determining whether any human messages also undergo recoding. He notes, “recoding phenomena in humans is rare and there aren’t any canonical ­–1 frameshift signals.” To identify any potential recoding sites, he developed a bioinformatic program for detecting frameshift signals in humans. He took this work with him to Cambridge, where he worked with Andrew Firth and collaborated with John Atkins while earning his master’s degree as a Churchill Scholar. While he hasn’t validated a bonafide hit just yet, he remains cautiously optimistic.

“Yousuf advises starting graduate students not to underestimate interpersonal relationships with potential lab mates when choosing a lab.”

Given his longstanding interest in RNA and translation, it may be surprising that Yousuf chose to join a structural biology lab focused on neurological phenomena such as SNAREs and vesicle fusion. However, Yousuf stresses that the most important thing is fitting well with the lab, noting that in his experience, “if you’re happy where you work the rest will follow.” He advises starting graduate students not to underestimate interpersonal relationships with potential lab mates when choosing a lab. For example, a “light-hearted friendship” he has with a postdoc has proved invaluable in his work as he can get good advice and feedback whenever he needs it. Another advantage he notes from the Brunger lab is that he is able to investigate multiple questions, and in the process, learn protein biophysics while pursuing his interests in RNA and recoding. 

In addition to his time in the lab, as an undergraduate, Yousuf also served as the president of the Pakistani Student Association while playing on the school tennis team. Some of his favorite memories include “waking up at 8 am for a tennis tournament on a Saturday and then rolling into lab around 1 pm to harvest cells for a luciferase assay.” Currently, as part of his Knight-Hennessy Scholarship, he is involved in a program that helps students develop leadership skills and interact with politicians. In doing so, he’s “learned quite quickly that I have to be able to compact my work into about a three-four sentence simple yet pithy package to leave an impression.” As a result, he’s been able to contribute to proposed legislation related to science funding.

Unfortunately, due to the COVID19 pandemic, Yousuf has been unable to attend an RNA Society Meeting in person. However, his favorite memory at a scientific conference came at the Translational Control Meeting in 2019 when there was a live band playing to close out the event. One of his collaborators dared him to join the band, and soon after he was “up on the stage singing a terrible rendition of ‘Somebody that you used to know.’” He looks forward to creating some equally fun memories at future RNA Society Meetings!

Yousuf’s favorite RNA is HIV-1, specifically the recoding region because “I’ve used it as a control for literally almost every single assay I’ve done, and it functions so reliably that I feel a close bond to it. It’s just a simple slippery site and stem-loop for the most part (at least the local secondary structure), yet so reliable.”

You can follow Yousuf on twitter @TheYousufKhan.