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Peer-Reviewed Publication on Cancer Cells

Mark is an 18 year-old high school senior from Walnut Creek, CA.
High School
Las Lomas High School
Student review
I loved the Polygence experience, and I thoroughly enjoyed my time spent with my mentor, Michel. Whether it was explaining a difficult concept that I had not fully understood from a research paper or walking me through coding difficulties, he has helped me take my first steps into the realm of professional science. Though this program, I was able to have a hands-on experience learning about the research process. Not only was I able to go through the motions of publishing a paper (a skill that is extremely valuable for an aspiring scientific researcher like myself), but I was able to delve into a biological concept in great detail while picking up useful computational skills. For me, the most valuable part of my Polygence experience was the ability to gain professional-like experience in a field I plan to pursue in the future.

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Project description

Protein synthesis is a process central to all life on Earth, including mammalian cells. During this process, ribosomes attach to mRNA strands and translate them into proteins using amino acids. Under stress, ribosomes can stall. Ribosome profiling, a technique that creates a snapshot of active ribosomes in a cell by sequencing ribosome-protected mRNA fragments, captures a snapshot of ribosomes along transcripts and can detect such stalling events. For his project, Mark used a computational approach to research ribosome stalling trends in ribosome profiling and mRNA sequencing data from amino acid-starved pancreatic cancer cells, aiming to explore whether the pattern of ribosome distribution along transcripts under normal conditions can predict the degree of ribosome stalling under stress. He hypothesized that ribosomes would stall more along “elongation-limited” transcripts that have fewer ribosome footprints near the start and stop codons than “initiation-limited” transcripts that have a large fraction of footprints at the start codon. Indeed, Mark found his hypothesis to be true, but observed no relationship between read (a DNA sequence from one fragment a fragment of DNA) density near start and stop codons and disparities between mRNA sequencing reads and ribosome profiling reads. This research identifies an important relationship between read distribution and propensity for ribosomes to stall.

Project outcome

His peer-reviewed article was accepted and published by the Journal of Emerging Investigators.

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Doctor of Philosophy
Computational Genomics, Organic
Biology, Biochemistry, Genetics, Organic Chemistry