*If funding and resources were no issue, what is the one research project you would most want to start/be part of? [[User:Kgosch|Kgosch]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:40, 10 September 2013 (PDT)''

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*In today's world, what type of projects are being worked on that specifically mix both computer science and biology [[User:Kevinmcgee|Kevinmcgee]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:19, 10 September 2013 (PDT)''

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*What is your favorite aspect about this class? [[User:Slouie|Slouie]] ([[User talk: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! ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:20, 10 September 2013 (PDT)''

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*Have you always been interested in computer science, or are you relatively new to it as well? [[User:Vkuehn|Vkuehn]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 16:14, 10 September 2013 (PDT)''

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*How has your experience with computer science affected your research in biology? [[User:Gleis|Gleis]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:02, 5 September 2013 (PDT)''

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*What is a current research project of yours and does it include a computer science aspect to it? Hilda Delgadillo: [[User:HDelgadi|HDelgadi]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:54, 10 September 2013 (PDT)''

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*Do you use computer science/bio informatics in biology disciplines other than molecular or genetic biology? [[User:Lena|Lena]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:58, 10 September 2013 (PDT)''

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*What was the best research project that you worked on? [[User:Mpetredi|Mpetredi]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:47, 11 September 2013 (PDT)''

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* How did you select your research topic? Did you know what you wanted to study going into graduate school? [[User:Taur.vil|Taur.vil]] ([[User talk: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. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:16, 5 September 2013 (PDT)''

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*What is one thing you wish you know when you were an undergraduate college student? [[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 21:32, 29 August 2013 (PDT)

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