放大人类基因组

帕克·希克斯22岁，a 生物学 主要, 本科时对编程有业余兴趣, 自学了一门编程语言, then applied for a National Science Foundation research opportunity at the University of Colorado over the summer. 在那里, he created a model that helps genome researchers create high-resolution data from low-resolution data. 这项研究随后发表在行业领先的杂志上， 生物信息学对于一个大学生来说，这是一项不寻常的成就.

“这是非常, very uncommon at any university for an undergraduate to be a first author, 意思是主要负责工作和写作的人,康考迪亚大学教授萨拉·卡拉姆说, 谁是希克斯其他项目的学术顾问. 同时在顶级期刊上发表文章的情况就更少见了. 这在康科迪亚很罕见，在其他地方也很罕见.”

Hicks employed methods used in enhancing photo resolutions to enhance data about chromosomal structures, 希望能找到具有生物学意义的区域.

“The information [we gain] could be used to identify a new gene for something, 它可能位于基因组的哪个位置, 和 what sorts of interactions could be occurring between genes that affect the expression of one,他说.

Acquiring high-resolution data is computationally 和 chronologically expensive, 这意味着它需要大量的处理能力和时间. But it is much more useful to “zoom in really close 和 see the intricate details of that picture,他说.

Hicks’ model takes low-resolution data 和 predicts what a high-resolution image would look like based on what the model has “learned” about how high-resolution data should look.

It was deep waters for someone who had just started programming. Hicks had spent much of his time at Concordia among sea urchins, 鲨鱼和螃蟹的校园经理 海洋实验室. 后来他觉得海洋生物学不是他的强项.

“It’s pretty stressful to have an entire lab’s worth of animal health on your h和s,他说. “你有责任喂养它们, 保持水的化学性质稳定, 确保所有人都还活着, 清洗所有的, 设备维护.”

He loved the animals, especially the horn shark 和 swell shark. “你在的时候，它们就会浮出水面, 和 you could scratch their nose a little bit 和 hold them if you wanted to,他说. “They’re only coming up to you because you have food usually, but it’s still cute.”

被职业所吸引 计算机科学 和 数学, he liked the idea of an interdisciplinary approach to those subjects 和 生物学, 所以他自学了如何用Python编程, 一种广泛使用的程序设计语言, 同时在赌博十大平台排行上生物和化学课.

“My goals were to get good enough at it to use in my research in 生物学,他说. When an opportunity came up to do summer research at the University of Colorado, 他申请了这个项目，但没想到会被录取.

“这些课程竞争非常激烈, 和 I didn’t necessarily think I would get in because I taught myself how to program 和 didn’t have much experience in the field of bioinformatics,他说. “But this was a chance to do big research at a large institution.”

令他吃惊的是, 他被邀请参加, 和 he moved to the Colorado Springs campus to work with Assistant Professor of Computer Science Oluwatosin Oluwadare. 他开始每天工作12个小时, 一周工作六天, on a problem he had never encountered before: how to make low-resolution “images” of the genome sharper by training the computer model on high-resolution data, essentially teaching it to take bad images 和 turn them into good ones.

“I had no idea what any of this stuff was at the beginning of the summer,他说.

He started by studying scientific literature about existing models used to enhance the resolutions, 以及这些方法背后的生物学原理. Then he developed his own model 和 collected a training data set 和 a test data set. Most of his time was spent troubleshooting programming issues 和 fixing errors in the code. 最后，他有了一个训练有素的模特.

Karam explains that Hicks’ model takes in low-resolution “chunks” of data about the genome, 分析信息, 和 repeatedly applies a filter to pull out areas of high concentration versus low concentration. 数据经历了一个反复锐化的循环, re-adding数据, then sharpening again with the goal of making the data as high-resolution 和 accurate as possible.

“The biggest challenge in the beginning was coding because I was relatively new, 这是非常复杂的东西,希克斯说. “It took me the entire three months to become fully proficient in coding these things.”

He 和 his summer advisor decided to submit the model for publication, 这是另一种“全新且非常困难的体验”,希克斯说.

它被一个计算机科学会议拒绝了，但是 生物信息学 journal sent back a list of comments with an open door to re-submit. Hicks 和 his advisor performed more testing 和 gathered 和 processed new data sets to answer the reviewer’s questions.

“We had to analyze our results four different ways to make sure the model accurately predicts what’s actually going on in the biological system,希克斯说.

他们的研究随后被接受并发表. That helped him get into his preferred graduate school, he says.

They teach us to think about science 和 really question why we’re doing what we’re doing, 以及为什么这些都很重要.

他说:“他们知道我有工作要审查。. “I’m excited to continue to do cool things like learning new methods of doing these things, 出版, 继续发展我作为科学家的技能.”

Concordia, Hicks says, prepared him well to think in a comprehensive 和 creative way.

“Our 生物学 department here [at Concordia] is outst和ing compared to other institutions I’ve experienced,他说. “They teach us to think about science 和 really question why we’re doing what we’re doing, 以及为什么这一切都很重要.”

Karam says Hicks has an uncommon ability to see connections between different fields, 将一个领域的某一方面应用到另一个领域. “I’ve not seen another student have quite that trajectory of being able to chart a path that wasn’t laid out,卡拉姆说。. “Seeing the connections between computers 和 生物学 和 saying, ’Ah, 这里有一些东西,’然后实现它.”

Hicks will attend the PhD program of the University of Colorado Anschutz Medical Campus for Human Medical Genetics 和 Genomics.