Zooming in on the Human Genome

Parker Hicks ’22, a biology major, took a side interest in coding as an undergraduate, taught himself a programming language, 然后在夏天申请了国家科学基金会在科罗拉多大学的研究机会. There, 他创建了一个模型，帮助基因组研究人员从低分辨率数据中生成高分辨率数据. The work was then published in the industry-leading journal, Bioinformatics, an unusual accomplishment for an undergraduate student.

“It’s very, 本科生成为第一作者在任何大学都很少见, meaning the one who primarily did the work and the writing,” says Concordia professor Sarah Karam, who was Hicks’ academic advisor on other projects. “To also be in a top journal is less common still. This is rare at Concordia and pretty rare at other places, too.”

希克斯采用了提高照片分辨率的方法来增强有关染色体结构的数据, with the hope of finding regions of biological significance.

“(我们获得的)信息可以用来识别某种新基因, where that might be located within the genome, 以及影响其中一种表达的基因之间会发生什么样的相互作用,” he says.

获取高分辨率数据在计算上和时间上都很昂贵, meaning it takes a lot of processing power and time. 但是，“放大到非常近的距离，看到那张图片的复杂细节”会有用得多,” he says.

希克斯的模型采用低分辨率数据，并根据模型对高分辨率数据的“了解”来预测高分辨率图像的样子.

对于一个刚刚开始编程的人来说，这是一个难题. 希克斯在康科迪亚的大部分时间都和海胆在一起, sharks and crabs as manager of the on-campus marine lab. Then he decided marine biology wasn’t his forte.

他说:“要处理整个实验室的动物健康问题，压力相当大。. “You’re responsible for feeding them, keeping the water chemistry stable, checking to make sure everything’s still alive, cleaning everything, maintaining the equipment.”

他喜欢动物，尤其是角鲨和浪鲨. “They would come up to the surface when you were around, 如果你想的话，你可以抓一下他们的鼻子，抱着他们,” he says. “它们通常只是因为你有食物才会靠近你，但它们仍然很可爱.”

Drawn to a career in computer science and mathematics, 他喜欢用跨学科的方法来研究这些学科和生物学, so he taught himself how to write in Python, a widely-used programming language, while taking classes in biology and chemistry at Concordia.

他说:“我的目标是在这方面做得足够好，以便用于我的生物学研究。. 当有机会去科罗拉多大学做暑期研究时, he applied to the program but didn’t think he would be accepted.

“These programs are very competitive, 我并不认为我能被录取，因为我是自学编程的，在生物信息学领域没有太多经验,” he says. “但这是一个在大型机构进行大型研究的机会.”

To his surprise, he was invited to participate, 他搬到了科罗拉多斯普林斯校区，和计算机科学助理教授奥卢瓦托辛·奥卢瓦达雷一起工作. He began working 12 hours a day, six days a week, 在一个他从未遇到过的问题上:如何通过训练高分辨率数据的计算机模型，使低分辨率的基因组“图像”更清晰, 本质上是教它把不好的图像变成好的图像.

“夏天刚开始的时候，我对这些东西一无所知，”他说.

他首先研究了用于提高分辨率的现有模型的科学文献, and the biology behind those methods. 然后他开发了自己的模型，并收集了一个训练数据集和一个测试数据集. 他的大部分时间都花在解决编程问题和修复代码中的错误上. Eventually, he had a well-trained model.

卡拉姆解释说，希克斯的模型采用了关于基因组的低分辨率“大块”数据, analyzes the information, 反复使用过滤器将高浓度区域和低浓度区域分离出来. The data undergoes a cycle of repeated sharpening, re-adding data, 然后再次锐化，目的是使数据尽可能高分辨率和准确.

“一开始最大的挑战是编程，因为我是新手, and this is pretty complex stuff,” Hicks says. “我花了整整三个月的时间才完全精通这些东西的编码.”

他和他的暑期导师决定将这个模型提交出版, another “entirely new and pretty difficult experience,” Hicks says.

It was rejected by a computer science conference, but the Bioinformatics 《十大正规赌平台平台》寄回了一份评论列表，并为重新提交敞开了大门. 希克斯和他的导师进行了更多的测试，并收集和处理了新的数据集，以回答审稿人的问题.

“我们必须以四种不同的方式分析我们的结果，以确保模型准确地预测生物系统中实际发生的事情,” Hicks says.

Their research was then accepted and published. 他说，这帮助他进入了自己心仪的研究生院.

它们教会我们思考科学，并真正质疑我们为什么在做我们正在做的事情, and why any of this matters.

“They knew I had work under review,” he says. “我很高兴能继续做一些很酷的事情，比如学习做这些事情的新方法, publishing, and continuing to develop my skills as a scientist.”

希克斯说，菲律宾十大网赌网站让他能够以全面和创造性的方式进行思考.

“与我所经历过的其他机构相比，我们(在康科迪亚)的生物系非常出色,” he says. “他们教会我们思考科学，并真正质疑我们为什么要做我们正在做的事情, and why any of this matters at all.”

卡拉姆说，希克斯有一种不同寻常的能力，能看到不同领域之间的联系, take an aspect from one arena and apply it in another. “我还没有见过其他学生有这样的轨迹，能够绘制出一条没有规划好的道路,” Karam says. “看到计算机和生物学之间的联系，然后说, ’Ah, there’s something there,’ and making it happen.”

希克斯将参加科罗拉多大学安舒茨医学院的人类医学遗传学和基因组学博士课程.