SSAO Bridges and Bytes – Spring 2016: Julia (Warnke) Sommer, mentors, thoughts, prayers, and more…

In this issue:

Three Minutes with Julia (Warnke) Sommer

sommerJulia (Warnke) Sommer became a Scott Scholar in 2007. She is from Omaha and a graduate of Omaha Christian Academy (OCA). She holds a BS in Bioinformatics and Mathematics with minors in Chemistry and Computer Science. She lives with her husband Nathan in Aksarben Village and is a PhD Student at UNMC’s Pathology and Microbiology Department

I spent the summer after my freshman year with an atomic-force microscopy device, researching α-synuclein – a protein related to Parkinson’s Disease – in a UNMC biology lab. At the end of my freshman year, the bioinformatics program had an internship for people looking into research through the NIH INBRE program. I had really loved my bioinformatics classes that year, I applied. It was a natural fit for me.

Dean Ali got me interested in Graph Theory and Next-Generation Sequencing for sequencing the human genome. He served as my mentor in the summer research program, and then he started a project on Next-Generation Sequencing to develop software that stitches the genome back together. I officially joined the lab in 2012 and am still focused on next generation sequencing and how it extends into other areas. (As an undergrad, Julia won UNO’s campus-wide Senior Vice Chancellor’s Outstanding Undergraduate Student Award in 2011).

Right now, I’m working with the Henry Doorly Zoo on lemur conservation in Madagascar. We use mitochondrial DNA data from lemurs and are trying to figure-out how they adapt to different regions. This gets into the metagenomics of lemurs but is basically a study of all the organisms in the environment through the microbiome in their gut.

UNO’s Biology Department is looking at the bacteriophage data around lakes of Nebraska, another project I’m working on. I’m helping piece together the genome of these places.

I’ve published 7 papers so far. The lemur and lake projects are too early for publication, but there are other papers that deal with the sequence assembly data. One of the conference papers did get extended into a journal paper. (See a full list of Julia’s Publications)

My goal is to be a professor to mix research, teaching, and other classic things. I’d like to do a post-doc where I can learn more about research, either at UNMC or some other places. My main goal would definitely be to continue in bioinformatics.

Your data has to be good – it can’t be a black box. We have to be careful about the results in the labs because they might be used for medical research or applications. You have to understand what was done so we can apply and develop algorithms to produce results that make sense.

It’s crucial to integrate with domain specific knowledge. We have collaborators around different areas so we can develop algorithms. In many cases, that’s working directly with the biologists. Different features affect the algorithm, and one of the things we learned for all the projects, is we have had to look deeper at the data. Different assemblers work different on these different data types. They’d have to be adjusted to produce better results.

The PKI and Scott Scholar communities has always been wonderful to be a part of. A lot of professors were really supporting and encouraging, and it was nice to go to classes. I had a fun time learning and being with other students, and we were always learning and participating together. I enjoyed all the events around Scott Hall, including the dinners with the Scott’s. I remember this game we made-up called pole ball. We used to have the two poles as the goals. It was like soccer except the poles were the goals.

When I’m not spending time with my husband, I’m involved in some random events at UNMC. A friend and I are developing a dance for UNMC international students. Last summer, I traveled to South Korea for a nine-day trip for a UNO/IST-Yeungnam University joint biomedical workshop with the UNO bioinformatics lab members. In undergrad, I did track and field – triple jump my freshman year. I also did Math Club and was in the Honor’s program.

Find something that you’re really interested in, something that you really love. Something you want to pursue and understand better.

Scott Scholar Mentoring Program

pkiAs most of you know, 2015-16 was the first year for the Scott Scholar Mentoring Program which matches incoming Scott Scholar freshmen with Scott Scholar alumni both in the Omaha area and throughout the country and world. The final in-person event for the mentoring program this year was well-attended BBQ held at PKI on April 15th.

At the BBQ, we did a lightning round of where every mentor works so the community could better get to know each other, in addition to assessing how to improve the program for next year (this fall).

While we know it is a success, there are always kinks to work out when starting a new program. If you are interested in becoming a mentor for the 2016-17 academic year, please email Sheila Karpf. And thanks to all of the mentors for participating this year, in addition to Leah Ellis at PKI for her continued assistance in making the program a success.

This year’s mentors: please submit your survey by Friday, April 22nd. Also, any out-of-Omaha mentors, please contact your protégé before the end of the semester. Finals Week is May 2-5.

Internships Needed

At the mentoring event this month, we learned that several computer science and computer engineering Scott Scholar freshmen applied for summer internships but we’re declined since they are too young.

If you know of internships in these or other areas, particularly for this summer, please email them to Sheila Karpf and she will pass along to the students.

We will be working on a more comprehensive list of potential internships for Scott Scholars soon, so look for info in the next Bridges and Bytes.

Quick Bytes 

  • Your support, thoughts, and prayers are requested across the Scott Scholar Community:
    • Kenneth Ross’s wife, Elicia, passed away in February. An emotional memorial service attended by a few Scott Scholars was held on April 9 in Bellevue. You can donate to the Elicia Ross Memorial Fund to support their daughter Lydia’s education by visiting any Wells Fargo branch or mailing a check to Wells Fargo Bank with the name of the memorial fund written clearly on the check, at this branch address 4707 S 96th St, Omaha, NE 68127
    • Lucy Nash, daughter of Matt and Stacy Nash, spent her first few weeks in the NICU but is thankfully doing better – read about Lucy’s first few weeks
  • Kate (Dempsey) Cooper is now Assistant Professor, Big Data at PKI’s School of Interdisciplinary Informatics
  • Sean West is a PhD Bioinformatics student at UNO

Have anything you’d like to contribute – thoughts, ideas, comments, content? Contact Kyle Hoback.

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