User talk:Kdahlquist
From LMU BioDB 2013
- If funding and resources were no issue, what is the one research project you would most want to start/be part of? Kgosch (talk) 20:16, 5 September 2013 (PDT)
- I would greatly expand my current project of using differential equations to model the gene regulatory network in a yeast cell to a whole cell model. Right now I collaborating with Dr. Fitzpatrick to model a network of about 20 transcription factors. I would love to scale up the experiments and the model to include all ~200 transcription factors in the cell, and then to include other pathways such as signaling and metabolic pathways in the model. To do all of that would require a lot of computational resources, a lot of experiments, and a lot of personnel to accomplish all of that. — Kdahlquist (talk) 15:40, 10 September 2013 (PDT)
- In today's world, what type of projects are being worked on that specifically mix both computer science and biology Kevinmcgee (talk) 20:23, 3 September 2013 (PDT)
- This is a difficult question to answer because there are so many! This is not an exhaustive list, just some examples that come to me off of the top of my head: predicting 3-D protein structures, anything to do with analyzing whole genome or even "metagenome" data, training computers to "read" the scientific literature to capture the information stored there in a computable form, mathematical modeling of metabolism, gene regulatory networks, evolution, ecosystems, etc., and so on. — Kdahlquist (talk) 16:19, 10 September 2013 (PDT)
- What is your favorite aspect about this class? Slouie (talk) 10:54, 29 August 2013 (PDT)
- My favorite thing is to see students who were feeling nervous or intimidated by computers at the beginning of the class, excelling in their final project in the class. I love to see the students learn and grow and get excited about the research! — Kdahlquist (talk) 16:20, 10 September 2013 (PDT)
- Have you always been interested in computer science, or are you relatively new to it as well? Vkuehn (talk) 11:35, 29 August 2013 (PDT)
- I took a computer science class in high school. We learned Turbo Pascal, and I even took the AP Computer Science exam. However, I didn't do much further with computers until I became a Postdoc in 2000 and went to work on the GenMAPP computer program. We will be using GenMAPP later on in the course. After that, I found computer science to be essential to my work. I don't do any programming myself, though, I work closely with computer scientists like Dr. Dionisio. — Kdahlquist (talk) 16:14, 10 September 2013 (PDT)
- How has your experience with computer science affected your research in biology? Gleis (talk) 16:33, 29 August 2013 (PDT)
- It is essential to my research in biology. Without the tools of computational biology, I would not be able to analyze the data from the experiments in my lab. You will be learning how to do this analysis as part of the research project in the course. — Kdahlquist (talk) 14:02, 5 September 2013 (PDT)
- What is a current research project of yours and does it include a computer science aspect to it? Hilda Delgadillo: HDelgadi (talk) 17:07, 29 August 2013 (PDT)
- The XMLPipeDB project that you will learn about in class is one of my current research projects and definitely includes computer science! I also have a mathematical modeling project with Dr. Fitzpatrick in the Math Department where we are using differential equations to model the gene regulatory network controlling the cold shock response in yeast. I also do "wet lab" experiments with DNA microarrays to generate the data for the math modeling project. You will learn how to analyze that type of data in this class as part of the XMLPipeDB project. — Kdahlquist (talk) 14:54, 10 September 2013 (PDT)
- Do you use computer science/bio informatics in biology disciplines other than molecular or genetic biology? Lena (talk) 17:51, 29 August 2013 (PDT)
- I, myself, don't because all of my research projects involve molecular biology. However, computation has impacted nearly all areas of biology. For example, there are many ecological and evolutionary models out there. — Kdahlquist (talk) 15:58, 10 September 2013 (PDT)
- What was the best research project that you worked on? Mpetredi (talk) 19:39, 29 August 2013 (PDT)mpetredi
- I happen to think that my current projects are my best projects! :) When I became a professor, I finally was able to completely determine the direction of my own researcy. As a graduate student and postdoc I worked on things related to my advisor's research. While I had freedom from within that project to determine the direction, I now have complete freedom to do so. Right now the biomathematical modeling project and the XMLPipeDB projects are closest to my heart. — Kdahlquist (talk) 15:47, 11 September 2013 (PDT)
- How did you select your research topic? Did you know what you wanted to study going into graduate school? Taur.vil (talk) 21:03, 29 August 2013 (PDT)
- I'm not sure if you mean my research topic in grad school or now because they have changed. In grad school, I studied the binding of translation initiation factor IF1 to the rRNA of the small subunit A site. I got interested in the ribosome because RNA biology was just coming to the forefront with the discovery of the catalytic activity of RNA. I found my research advisor, Jody Puglisi, after hearing him talk to the grad seminar and after rotating in his lab. For my field, it is customary to rotate in labs so that you can decide which direction you want to go during your first year instead of having to find an advisor when you are applying. I had also considered doing research in plants since I had done that as an undergrad, but ultimately did not find that as interesting as the project I chose. For my postdoctoral work and current work, I wanted to get involved in genomics and bioinformatics because I had always been interested in understanding the cell as an entire system, but until the human genome project, the tools were not available to study all the genes at one time. Now they are and I'm really excited to be in this field. You will be learning about my current research throughout this course. — Kdahlquist (talk) 14:16, 5 September 2013 (PDT)
- What is one thing you wish you know when you were an undergraduate college student? Laurmagee (talk) 21:32, 29 August 2013 (PDT)
- There are a couple of things that come to mind.
- I wish that I hadn't taken so many classes with first-time instructors. They turned out to be the worst classes that I took in college because the instructors were "learning on the job". I had avoided classes with popular professors because they were always large classes. In retrospect, I wish I had taken those classes instead.
- I wish that someone would have prepped me for what graduate school was really going to be like. I had a very romanticized notion of what it was; it was a difficult adjustment to get my expectations to line up with reality. — Kdahlquist (talk) 09:08, 12 September 2013 (PDT)
- There are a couple of things that come to mind.
- At what point in life did you decide that you wanted to be a biologist? - Dwilliams (talk) 22:20, 29 August 2013 (PDT)
- What made you want to be a biologist? Kmeilak (talk) 23:10, 29 August 2013 (PDT)
- I'll answer Kevin and Dillon's questions together because they are related. My parents got me hooked on science from a young age with things like science camps and books. I remember reading Charlie Brown's Big Book of Questions and Answers when I was in the primary grades and first learning about cells. My AP Biology class my junior year of high school really cemented my love for biology--I just found everything about cells to be so fascinating. I'm still fascinated by cells and the intricate mechanisms by which they work. I love my job because I get to think about this every day. — Kdahlquist (talk) 14:08, 5 September 2013 (PDT)
- What helped you decide to collaborate with Dr. Dionisio to create the Biological Databases class? Ajvree (talk) 23:19, 29 August 2013 (PDT)
- When I first came to LMU, several of my colleagues knew of our mutual interests in bioinformatics/medical informatics and told me that I should be in touch with Dr. Dionisio. From our first conversation, we really hit it off and immediately starting talking about how we could collaborate on a project. The XMLPipeDB project that we will work on in this class was in direct answer to solving a research problem I was having and it was natural for us to start teaching together to help create the project. — Kdahlquist (talk) 10:36, 9 September 2013 (PDT)
- Has it been difficult to implement interdisciplinary courses at LMU such as this class? Ksherbina (talk) 23:47, 29 August 2013 (PDT)
- Dr. Dionisio and I had a relatively easy time when we started team-teaching in Spring 2006. We just had to gain approval from both of our department chairs to teach the first iteration of this class, which was a Master's level class for Computer Science. After the 2008 financial crisis, resources have become more limited and we have been asked to teach this class only every-other-year instead of every year. I imagine that we would have a more difficult time right now getting this class off the ground for the first time. — Kdahlquist (talk) 10:35, 4 September 2013 (PDT)
