Parasitic researchers! Casey Greene joins Real Scientists

IMG_9278This week we’re excited to welcome Casey Greene  (@GreeneScientist) to Real Scientists! Casey earned his Ph.D. for his study of gene-gene interactions in the field of computational genetics from Dartmouth College in 2009 and after a post-doc at Princeton University he started a lab in the Department of Genetics in the Geisel School of Medicine at Dartmouth before moving to Penn in 2015 where he is an Assistant Professor in the Department of Systems Pharmacology and Translational Therapeutics. Starting in August, 2017 he became the director of the Childhood Cancer Data Lab for Alex’s Lemonade Stand Foundation. Casey’s lab is dedicated to developing computational tools that biologists use to gain insights from other labs’ data as easily as from their own. These data represent a rich and underused resource, but they are hard to use because the data are comprised of many different experiments. Casey’s lab develops computational techniques that are robust enough to analyze and interpret this public resource. These algorithms have applications across many disease areas and, perhaps most importantly, to questions of basic biology. In 2016, Casey established the “Research Parasite Awards”.

We asked Casey our usual set of questions and you can read his reponses below.

I’ve always been curious about how things work. That combined with doing things that I enjoy seems to have led me here.    “I’ve been interested in how living things work for a while. I had done research in other areas; however, the one that really shaped my trajectory was a summer working on John McDonald’s lab, which at the time was at the University of Georgia, under the guidance Eric Ganko, who was a student at that time. That was my first time putting my enthusiasm for computing together with genetics and molecular biology. I loved it so much that I’ve been combining the two fields ever since.

An organism is in some ways a collection of genes. And how those genes are expressed controls what cells are doing. The difference between cells in your brain and cells in your skin isn’t the genes; it’s how those genes are expressed. Right now anyone with an internet connection can download about 2 million genome-wide assays of how genes are expressed. This is because that specific field of science has a very strong culture in favor of data sharing. These assays are a unique resource. Each one is a snapshot of a collection of cells in some condition. Our lab develops computational methods to integrate these data to learn what they can tell us about how living systems work. We’re a bit different from most groups that work in this area because we focus primarily on methods that are “unsupervised.” This means that we primarily want to know what patterns are present in data. We’re probably most similar to kids looking through microscopes for the first time and yelling, “Whoa! Come look at this!” We’re trying to build new ways to see how things work. Maybe it’s easiest to think of this as a “datascope” which is akin to a microscope in terms of showing us things that we can’t see with the naked eye. This has applications in areas that are relevant to the human health, such as the study of microbial infections, cancer, or other diseases. But I don’t think this is the main reason that the public should care about our research. We hope that our methods will reveal things that we’d never have predicted to see under our data-scope.

Ultimately, I think the public should care because – in our research – we have no clue what we’ll find, and it’s just exciting to see the world in that way. I think this is true of all research, not just our lab’s. Maybe we spend too much time focusing on the application areas of our research, and too little time focusing on the excitement of seeing the world in a way it’s never been seen before. It’s amazing timing that this opportunity came up when it did, because September is Childhood Cancer Awareness Month. I’ve just started the Childhood Cancer Data Lab with Alex’s Lemonade Stand Foundation. Our mission in the CCDL is to accelerate the pace of finding cures for childhood cancer by empowering scientists and doctors to harnessing the power of big data. We’re currently developing software and harmonized datasets for researchers in the field.

I also like to encourage researchers to use other people’s data (sometimes called “research parasitism”) and to share their own. We started the “Research Parasite Awards” [1] last year to recognize particularly innovative reuses. This year we’ve started the “Research Symbiont Awards” [2] to honor those who are particularly good at sharing.

I’m interested in the future of publishing, the maker movement, and citizen science. In my mind these are all relatively related, and I’ve been involved in a number of exploratory projects in this area over the past year. We’ve characterized the coverage of the SciHub server to understand how the availability of published literature is changing. We’ve written a review paper for an area of research entirely in the open via GitHub, which accepted contributions from anyone who wished to participate. Also, I’ve been involved with a project in the Philadelphia area called “Cognoma,” in which hundreds of individuals from the DataPhilly and Code for Philly communities have come together to build a tool to aid cancer researchers. These activities keep me a bit busy outside of the day-to-day of the job.

My perfect day off? I’d have to describe it as a relatively lazy weekend day. Today is a pretty good example. I’d get up, take the dogs for a walk, do a bit of work, make lunch, watch a movie, maybe a little bit more work (fill out this form, for instance), and generally relax around the house. I guess it’s pretty boring, but boring can be relaxing.

Please welcome Carey to Real Scientists!

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