User talk:Kdahlquist

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Hi Dr. Dahlquist, how did you first become interested in biology and what made you want to become a professor? Emmatyrnauer (talk) 20:34, 31 August 2017 (PDT)

My parents exposed me to science from an early age. I did a CTY summer camp in biology when I was in junior high school. However, what really sealed the deal was the AP Biology course I took in high school. I really loved that course. I had wanted to become a teacher ever since I started school because I loved school and loved my teachers. As I went up in grade level, I always wanted to be that year's teacher. So, when I got to college I wanted to become a professor. — Kdahlquist (talk) 20:16, 9 September 2017 (PDT)

Hi Dr. Dahlquist, I saw that you like to read science fiction. Do you have a favorite book in that genre? Mbalducc (talk) 14:39, 1 September 2017 (PDT)

I have many favorite books. I highly recommend the Beggars in Spain trilogy by Nancy Kress (Beggars in Spain, Beggars and Choosers, and Beggar's Ride), the Jump 225 trilogy by David Edelman, with whom I went to elementary school (Infoquake, Multireal, and Geosynchron), the Xenogenesis trlogy by Octavia Butler (Dawn, Adulthood Rites, Imago), The Sparrow and Children of God by Mary Doria Russell (Jesuits in space!), the classic Ender's Game series by Orson Scott Card, and, of course, The Hitchhiker's Guide to the Galaxy by Douglas Adams, whom I was fortunate enough to meet in Oxford when I studied abroad there in 1991. — Kdahlquist (talk) 20:24, 9 September 2017 (PDT)

Hey Dr. Dahlquist! My question in regarding how you got interested and involved in the computational aspect of biology and what about this aspect of your research do you most enjoy? Qlanners (talk) 11:21, 2 September 2017 (PDT)

I got interested in bioinformatics when I started my postdoc in 2000, the year that the rough draft of the human genome project came out. I had always been interested in cellular pathways, but when I started graduate school, the genome wasn't finished and you could spend 2 years cloning and sequencing a single gene. Then people would create models of how cellular processes worked based on just a single gene, which seemed silly to me, since there where thousands of genes (we didn't even now how many at that time). Once the genome was completed and technologies like DNA microarrays could be used to measure gene expression for all the genes in the genome at once, I wanted to work in that field. Since everything was so new, we had to develop our own software for analysis, which is when I got involved in bioinformatics. We will be retracing some of my steps this semester. — Kdahlquist (talk) 20:28, 9 September 2017 (PDT)

Hi Dr. Dahlquist! I noticed you had needlework as one of you interests on your wiki page. What kind of things do you sew/embroider? Simonwro120 (talk) 16:53, 3 September 2017 (PDT)

Ever since my son was born, I don't have time anymore :( I like counted cross-stitch and needlepoint, and generally work on more abstract designs, such as Celtic knotwork. I have also crocheted some hyperbolic planes, and sewed a medieval dress when I belonged to the Society for Creative Anachronism when I was in college. — Kdahlquist (talk) 20:33, 9 September 2017 (PDT)

Hello Dr. Dahlquist! What most excites you about studying genes? Zvanysse (talk) 16:58, 3 September 2017 (PDT)

I'm not so much interested in studying individual genes as how they work together in networks to coordinate all cellular activities. I see it as a puzzle to be worked out. When we are successful, we should be able to create a mathematical model that can accurately predict what the cell does, given a set of inputs. To me, that would mean that we really understand how cells work. — Kdahlquist (talk) 20:38, 9 September 2017 (PDT)

Hi Dr. Dahlquist, At what point did you realize that you would need software like GRNmap in order to support the scale of the projects that you were doing? Cazinge (talk) 22:48, 4 September 2017 (PDT)

I wanted to start modeling, even before I came to LMU. The summer I was hired and before I formally started my position in Fall 2005, I connected with Dr. Erika Camacho who was then in the LMU Mathematics Department to go to an interdisciplinary curriculum development workshop. We began the modeling project togehter, co-mentoring a student name Nathan Wanner that year. Dr. Camacho left LMU to take a job at Arizona State in 2007 and Dr. Fitzpatrick kindly took over the collaboration. Dr. Dionisio and I had also been collaborating since I joined LMU. In 2014, I brought the two collaborations together to create GRNmap out of the code that had been worked on since the early days with Dr. Camacho. — Kdahlquist (talk) 20:42, 9 September 2017 (PDT)

Hello Dr. Dahlquist! My question is, I noticed you were a teacher for the study abroad program at Oxford. What was your favorite and least favorite part about teaching outside the United States? Bhamilton18 (talk) 13:09, 4 September 2017 (PDT)

Actually, I wasn't a teacher, but a student when I studied abroad in Oxford. It was a fantastic experience (I got to meet Douglas Adams, as I mentioned above, among other things). The educational system in England is quite different than in in the U.S. In college, students focus on a single topic. I studied the philosophy of science while I was there, which was hard for me since I had no formal training in philosophy. I had to write a paper a week and read it aloud to my tutor to receive feedback, so it wasn't like the classes we have here. One semester was a little too short to get used to it. I am very glad I got the chance to do it, though. — Kdahlquist (talk) 20:46, 9 September 2017 (PDT)

Hello Dr. Dahlquist! I understand that your family is a big part of your life and that you try to separate your work and home lives, but do you often enlighten your family about the work you do? Are they as interested in biology and science as you? Johnllopez616 (talk) 15:56, 4 September 2017 (PDT)

My husband knows all about my work life--I am very grateful to him for the support he lends me by listening to me "debrief" about my day. He's an engineer, so we share a more technical background. My son is a little too young still to understand exactly what I do, but he's definitely interested. He always wants to meet my students. I haven't taken him into the lab much (too dangerous), but he's definitely interested in what I do. I hope to include him more and more as he gets older. — Kdahlquist (talk) 20:49, 9 September 2017 (PDT)

Hi Dr. Dahlquist, what is your favorite research project you've done/participated in so far? Cwong34 (talk) 16:47, 4 September 2017 (PDT)

I'm doing it right now! When I got a faculty position, I was finally able to design my own research projects myself and studying gene regulatory networks in yeast using genomics, bioinformatics, and mathematical biology has been my favorite so far. I am so fortunate to have a job where I can do this! — Kdahlquist (talk) 20:52, 9 September 2017 (PDT)

Hello Dr. Dahlquist, I attended the seminar about GRNmap and GRNsight and was curious as to any new research or projects you have been working on since then. Secondly, where do you think the GRNmap/sight will be within the next year? Thanks! Aporras1 (talk) 17:58, 4 September 2017 (PDT)

I haven't started any entirely new research projects, but have been working on extending both GRNmap and GRNsight. Last year for GRNmap, the coding team completed a substantial refactor of the code, removing global variables and allowing the model to run when there are missing data points. The GRNmap data analysis team made a lot of progress on developing ways to interpret the modeling results. The GRNsight team worked on making the viewport and graph area larger, enabling zooming and scrolling, as well as allowing the user to change the normalization factor for the edge weights so that graphs could be compared on the same scale. Dr. Dionisio, Dr. Fitzpatrick, and I are working on an NSF grant together to fund the next phase of the project. We plan to work on quantifying the uncertainty of the modeling results and creating novel ways to visualize the uncertainty with GRNsight. — Kdahlquist (talk) 20:56, 9 September 2017 (PDT)

Hi Dr. Dahlquist! When you applied to college, did you apply under Biology? If not, when did you realize that Biology was the field you wanted to spend the rest of your life doing? Ebachour (talk) 18:45, 4 September 2017 (PDT)

I went to Pomona College as an undergrad and they didn't make you choose a major on the application. I said that I was interested in biology and philosophy, so they assigned me to a philosophy advisor during orientation. That ended up being a problem because he didn't tell me to take general chemistry and instead told me to take a philosophy course that was at the same time. I pretty quickly realized that I wanted to major in biology, not philosophy, but I was behind in chemistry. So, I ended up having to take it over the summer between my freshman and sophomore years. I fell in love with biology in AP Biology in high school, but I didn't declare it right away because I wanted to explore my options, not realizing that I would get behind. It all worked out in the end, though. — Kdahlquist (talk) 21:00, 9 September 2017 (PDT)

Hello Dr. Dahlquist, I noticed on your user page that you listed dance as one of your hobbies. What are some of your favorite dances? (I learned some Greek folk dancing growing up and would like to learn to salsa.) Kwrigh35 (talk) 20:31, 4 September 2017 (PDT)

I like all kinds of dance. I did tap dancing in elementary school and flag team and color guard in junior high and high school. When I studied abroad in England, I learned Scottish Country Dancing, which is really fun. I also did Sacred Circle Dancing (a type of folk dancing, which includes some Greek folk dances) when I was in grad school at UC Santa Cruz. I don't get to do much now, but hope to bring it back into my life in the future. — Kdahlquist (talk) 21:03, 9 September 2017 (PDT)

Hi Dr. Dahlquist! What has been the most important thing you have learned regarding computational biology? Hhinsch (talk) 23:36, 4 September 2017 (PDT)

It's not necessarily a "thing", but a process--the importance of keeping excellent records (source code, notebooks, data) for reproducible research. It is what we are teaching in this class. — Kdahlquist (talk) 21:07, 9 September 2017 (PDT)

Hello Dr. Dahlquist! My question is, how were you able to incorporate so many different areas of study into your research and how did you come to collaborate with those professors at LMU? Dbashour (talk) 12:48, 5 September 2017 (PDT)

Part of being a good scientist is learning or creating the tools needed to answer the questions she is interested in. To answer the questions I have about gene regulatory networks, I have had to learn aspects of computational and mathematical biology. In the case of Dr. Camacho, mentioned above, with whom I started the math modeling project, I just looked her up on the LMU websire and cold e-mailed her to ask if she was interested in working with me. When she left LMU, Dr. Fitzpatrick stepped in to replace her in the project because we were all part of an NSF grant together, but he and I hit it off really well and have continued the collaboration well beyond that initial grant. As for Dr. Dionisio, when I first came to LMU, other faculty told us both that we needed to meet. Once we did and talked about our mutual interests, we immediately thought we should start collaborating. The rest, as they say, is history. — Kdahlquist (talk) 21:15, 9 September 2017 (PDT)

Hello Dr. Dahlquist, my question would be: what would you say the hardest part of studying biology is? ArashLari (talk) 14:46, 5 September 2017 (PDT)

I would say that it is getting a handle on the vocabulary. Each sub-field of biology also has it's own nuanced vocabulary. When I switched fields when I started my postdoc, I had to learn a whole new vocabulary. It was a little bit easier since I did have a PhD, but I had to read papers with a dictionary again when I started my postdoc. — Kdahlquist (talk) 21:17, 9 September 2017 (PDT)

Hi Dr. Dahlquist. One of my best friends goes to Pomona College. The other goes to UCSC. I thought that was a funny coincidence. Which schooling experience did you enjoy more? Nicolekalcic (talk) 22:05, 6 September 2017 (PDT)

It's like comparing apples and oranges. Undergraduate and graduate school are nothing like each other. The emphasis during graduate school is on research, not classes, and it's a really different experience. I liked the classes I had at Pomona more, but I didn't really take that many classes in grad school. Santa Cruz has been my favorite place to live in the world, and I really enjoyed doing research full time (hence becoming a professor...). — Kdahlquist (talk) 21:21, 9 September 2017 (PDT)
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