As a graduate student, I was always amazed by—and a little skeptical of—any software that promised to help my data woes. I’m still curious to know what goes on behind the scenes, so to speak, when a website manages to take my search terms and raw data and turn them into pretty graphs and new correlations. Watch this space to find out about the “behind the scenes” people and ideas that shape NextBio.
We’re excited to bring you “Life @ NextBio”, a series which spotlights our curators, engineers, advisors, and others as they talk about life and work at NextBio. This week, meet Aisha Furqan, associate scientist in Curation, recent graduate from the Biological Sciences Department at Cal Poly Pomona, and enthusiastic NextBio user.
NB: How did you start working at NextBio and what do you do here?
I found out about NextBio through—believe it or not—a Craigslist ad! I had recently moved to Cupertino with my husband and was looking for a job. I started out as an intern in February 2010 and was eventually hired as an associate scientist. I did switch to Genentech for a short while but came back to NextBio because I love it here so much.
NB: What do you do in the scientific curation team?
I work on genome-wide association studies (GWAS). I gather papers from various journals and publications and I look at the data that they’ve provided. I gather that data and curate it. Just like a librarian would look at new books to decide what section they’re relevant to and cross-reference them, I look at the data and study it, methodically sort it.
So, for instance, if there’s a genome-wide association study about variants associated with Alzheimer’s disease, there are some repositories that store such data, but they’re not very easily searchable. So I look through all the raw data, the supplemental data, how they designed their experiments, and what genes they studied. I make sure it’s all in order, and then add tags for the disease, the experimental design, which SNPs were identified, and so on.
NB: Does curation ever feel dull or repetitive?
Absolutely not, because every paper is different! Yeah, all the papers look alike, and I’m definitely very familiar with the style and structure of GWAS papers now. But at the same time, when I get a new paper almost every 2-4 hours or so—that’s my big motivation. If I finish this I get to read another new paper, I can find out what’s going on, what all the researchers are doing. It’s not like I spend days on end reading about a single research topic. I get to learn about the latest research in so many fields: Alzheimer’s, height, diabetes. And every paper is different. I never know what I’m going to find out next!
NB: Using NextBio’s platform helped you complete the research for your Master’s degree. How did that come about?
When I started here as an intern last February, I had finished the coursework for my Master’s degree but my experiments never materialized. Things were always up in the air, experiments were failing and so on. At NextBio, we’d just started working on the Body Atlas, so I was working on a project to validate the app. That’s where it started to cook up.
I started simply with validating NextBio, which really convinced me that it works too. I tested 5 really well-studied genes: CEACAM6, PAX8, SFTPC, a spectrin gene, and apolipoprotein E. So I looked at how many studies have been done on them and what the findings were. For each of these studies, I got results from Body Atlas, Disease Atlas, Pharmaco Atlas, and Knockdown Atlas. For each of those, I acquired our top 5 results and validated each one individually. I verified the content in all four atlases, made sure that what we had was what was reported in the literature, checked citations, and so on. For my thesis research, I also compared my NextBio results with things like Google searches, GeneCards, WikiGenes, and iHOP.
So we were pretty sure that the Atlases worked for these well-known genes. For my thesis, I wanted to look at genes that hadn’t been studied. Everybody knows about genes that are studied. How do you find information about genes that aren’t? Where do you even start looking?
Aisha’s NextBio research led her to identifying potential functions for not just one, but five previously uncharacterized genes (one of which she’d love to call “AishaRocks” if she could). Check back with us to read more about her research soon!SHARE