User talk:Kam D. Dahlquist: Difference between revisions

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What is your favorite sport to watch? [[User:Zachary T. Goldstein|Zachary T. Goldstein]] 19:29, 30 August 2016 (EDT)


== Answers to Student Questions Spring 2013 ==
: I enjoy watching figure skating (I got to go to the World Championships in 2007 when they were held in LA).  Out of the ''traditional'' sports, I most enjoy basketball.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:42, 30 August 2016 (EDT)''
 
*Hey Dr.Dahlquist, I do not know how I chose 18 for that question on journal 12, I think it must have been a typo or I was overly tired when doing the assignment.  I changed it to 120. Also made correction on my answer to question 4 and shared my matrix and transpose with you on lionshare.
 
Thanks*[[User:Kevin Matthew McKay|Kevin Matthew McKay]] 13:55, 18 April 2013 (EDT)
 
Hi Dr. Dahlquist,
Sorry I didn't post a question here, I misunderstood the directions.
I've noticed that it is really hard to explain scientific idea to those not in the science field. After numerous discussions with my roommates, some of them still do not believe global warming is an issue being worsened by people. They also don't believe it is "as bad as scientists make it out to be". Is it an issue with scientists being unable to explain their knowledge to those not in the field, or is it just too hard to convince people that their long-held beliefs are wrong?
Thanks! (also, I think I've made all the corrections you recommended to my page, but I'm still not sure if I'm doing the template right)
[[User:Salman Ahmad|Salman Ahmad]] 20:18, 7 February 2013 (EST)
 
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Good afternoon,
I responded to your feedback for my week 1 work on my talk page.  Have a good weekend!
[[User:Elizabeth Polidan|Elizabeth Polidan]] 19:53, 2 February 2013 (EST)
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Hey Dr. Dahlquist, did you ever consider medical school?  What made you choose the research path?
[[User:Kevin Matthew McKay|Kevin Matthew McKay]] 20:34, 17 January 2013 (EST)
 
: I didn't consider medical school.  I'm actually pretty squeamish and have fainted at the sight of blood.  My parents instilled in me a love of science by giving me lots of educational opportunities when I was a kid.  I really loved my AP Biology class in high school, which inspired me to become a biology major.  I did undergraduate research in a plant physiology lab, which got me interested in research.  I also had always wanted to be a teacher because I loved my teachers and loved school when I was a kid.  This all came together to choose a profession as a biology professor where I could both teach and do research. 
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:38, 21 January 2013 (EST)''
 
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Hi Dr. Dahlquist, I understand that you have a strong background in biology; what led you to have an interest in biomathematics? How has biomathematics helped you to become a better biologist? Thanks, [[User:Laura Terada|Laura Terada]] 15:31, 17 January 2013 (EST)
 
: I got interested in biomathematics when I was a postdoc at the Gladstone Institute of Cardiovascular Disease/UCSF.  I was working on analyzing data from microarrays and it became really clear that I needed to learn statistics in order to analyze the data properly.  We were also working on visualizing the data on biological pathways.  I got started in modeling because I wanted to have a more quantitative model of the data we were visualizing on pathways.  The biomathematics has helped me become a better biologist because I am able to perform a more robust analysis of quantitative data.  I feel that I have a "leg up" on other biologists who do not do this type of analysis. 
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:43, 21 January 2013 (EST)''
 
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Hi Dr. Dahlquist, I was wondering what research projects your lab at LMU are currently working on?
[[User:James P. McDonald|James P. McDonald]] 21:15, 21 January 2013 (EST)
 
:I have three related research projects:
# Understanding the transcriptional response to cold stress in yeast, ''Saccharomyces cerevisiae''.
# Mathematical modeling of the above (which you guys will work on in this class).
# Developing an open source program called [http://xmlpipedb.cs.lmu.edu/ XMLPipeDB] to create gene databases for analyzing microarray data.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 15:56, 22 January 2013 (EST)''
 
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Hi Dr. Dahlquist, I was wondering what your favorite subject in undergraduate biology was? Also, what is some of the research you did in college, and what are you currently working on? [[User:Kasey E. O&#39;Connor|Kasey E. O&#39;Connor]] 21:31, 21 January 2013 (EST)
 
:I was always interested in how cells worked, so the classes that I took related to that were the equivalent of our Cell Function course, Genetics, and Biochemistry.  I knew that I was interested in molecular biology, but I didn't actually take a course specifically in that until graduate school
 
:In college, I worked in a plant physiology lab that was studying photosystem II in chloroplasts.  My advisor had discovered that some peripheral membrane proteins in photosystem II dissociated from the membrane during heat stress in wheat.  I was studying a strain of the ''Clorella pyrenoidosa'' algae that could survive at high temperatures to see whether these proteins stayed associated with the membrane.  My experiments suggested that they did, but we were not able to prove it definitively because we were having trouble purifying thylakoid membranes from the algae.
 
:My current research projects are listed in the answer to James' question.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:27, 24 January 2013 (EST)''
 
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Hello Dr. Dahlquist,
If you could be any celebrity for a day, who would you be and why?
 
*'''[[User:Matthew E. Jurek|Matthew E. Jurek]] 23:01, 21 January 2013 (EST)''':
 
: Wow, I've never been asked this before!  The first name that came to mind was Meryl Streep.  I really admire her as an actor and would love to be on one of her movie sets experiencing how she does such a great job doing characters like Julia Child or Margaret Thatcher.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:32, 24 January 2013 (EST)''
 
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My burning question
 
Hello Professor Dahlquist,
 
If you had to change careers, what would you choose?
 
Thank you,
[[User:Elizabeth Polidan|Elizabeth Polidan]] 22:33, 21 January 2013 (EST)
 
:It's hard for me to imagine not doing something science-related.  One of my favorite jobs was when I worked at a book store in high school.  I was like a kid in a candy shop.  Sadly, that book store does not exist anymore; nor do many book stores.  I have become more and more interested in politics and government policy, so I could see myself as an investigative journalist, or working on government policy in some area.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:38, 24 January 2013 (EST)''
 
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Hi Dr. Dahlquist,  I was wondering what class you hated the most during undergraduate and why?  [[User:Anthony J. Wavrin|Anthony J. Wavrin]] 00:47, 22 January 2013 (EST)
 
:I would have to say an Intro to Politics class that I took.  The class had a really great reading list, but all we seemed to do was sit around "bs-ing" during class and not really getting into the texts.  I distinctly remember one class where some of the students would say more and more outrageous things to see if the professor would call them out on it, but he never did.  Despite what looked like a great syllabus, I didn't feel like the class lived up to its potential.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:42, 24 January 2013 (EST)''
 
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Dr. Dahlquist:
What is the most enjoyable research that you've done?
Thanks,
[[User:Ashley Rhoades|Ashley Rhoades]] 01:26, 22 January 2013 (EST)
 
:I would have to say that my current research is the most enjoyable.  When I became a professor I was able to finally determine my research direction completely by myself (not influenced by my graduate or postdoc advisor).  That meant that I could finally choose what I was most interested in to work on.  My research projects are listed above in the answer to James' question.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:46, 24 January 2013 (EST)''
 
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Dr. Dahlquist,
 
What are some of the different fields you have worked in within the area of biology? [[User:Paul Magnano|Paul Magnano]] 02:47, 22 January 2013 (EST)
 
:* plant physiology (photosystem II in algae)
:* RNA biochemistry (binding of translation initiation factor IF1 to A site of small subunit of the ribosome)
:* bioinformatics (development of [http://www.genmapp.org GenMAPP] software; development of [http://xmlpipedb.cs.lmu.edu/ XMLPipeDB] software)
:* genomics (global transcriptional response to cold shock in yeast)
:* biomathematics (modeling of transcriptional network controlling the cold shock response in yeast)
:* metagenomics (diversity of soil bacteria in the Ballona Wetlands)
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:58, 24 January 2013 (EST)''
 
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Hi Dr. Dahlquist,
What drew you back to Biology after studying Philosophy?
[[User:Helena M. Olivieri|Helena M. Olivieri]] 01:10, 23 January 2013 (EST)
 
:*I wouldn't say that I ever really left biology.  I got interested in the philosophy of science when I was in high school and just briefly considered majoring in philosophy in my first semester freshman year.  The biology major didn't start until the second semester and as soon as I took my first college biology class, I made my decision to major in biology and do some philosophy on the side.  I ended up taking a few extra courses in philosophy in college and was fortunate to be able to do a specialized tutorial in the philosophy of science when I studied abroad at Oxford my junior year.  I guess I thought I wanted to approach the philosophy of science from the point of view of a practicing scientist.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 20:03, 24 January 2013 (EST)''
 
 
Hi Dr. Dahlquist, I was wondering, after reading the Stewart and Janovy reading, whether or not you have ever thought about switching the specimens you currently do research on, for a completely different animal? 
[[User:Nicholas A. Rohacz|Nicholas A. Rohacz]] 20:11, 23 January 2011 (EST)
 
: When I was an undergraduate, I worked on an single-celled algae species named ''Chlorella pyrenoidosa''.  For two of my rotation projects in graduate school, I worked on the plants ''Ginkgp biloba'' and ''Arabidopsis thaliana''.  For my thesis, I studied ''E. coli''.  During my postdoctoral research, the lab was studying mice, but I was not directly involved with working with the mice myself, although I did take the training when I first started.  I've also worked with the fruit fly, ''Drosophila melanogaster'', for a genetics lab I taught at another school.  It's only when I started my first faculty position that I decided to work on yeast.  Now that you have asked and I've thought about it, if I were to switch organisms, I would probably pick another single-celled one.  I'm most interested at what goes on at the cellular level and it seems simplest to me to work on that with an actual single-celled organism.  They are simpler than cells from multicellular organisms.  They are definitely easier to work with and the work is more straightforward because there is less complexity in these cells in general.  In my Biological Databases class that I teach with Dr. Dionisio in the Fall, the students create gene databases for different microorganisms, so if I was really going to switch organisms, I might pick a bacteria that we worked on for Biological Databases.  In that class we've worked on ''Vibrio cholerae'', ''Plasmodium falciparum'', ''Mycobacterium tuberculosis'', ''Mycobacterium smegmatis'', ''Helicobacter pylori'', ''Salmonella typhimurium'', and, of course, yeast.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 13:23, 24 January 2011 (EST)''
 
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Hey Dr. Dahlquist!! Why did you choose to co-teach a math class instead of merely staying in the field of biology? [[User:Sarah Carratt|Sarah Carratt]] 16:56, 16 January 2011 (EST)
 
: The short answer is that Dr. Fitzpatrick and I do research together and we were both interested in sharing our common interest with students in a class.  As to why I am interested in biomathematics in the first place, the field that I work in has become math-intensive in order to analyze and model the data.  What we are able to do by combining our efforts in biology and mathematics is much greater than what either of us would be able to achieve alone using just biology or mathematics.  Research is becoming more and more interdisciplinary as the problems get larger and larger and require expertise from different areas to solve.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 18:52, 17 January 2011 (EST)''
 
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Hello there Dr. Dahlquist! After reading Janovy, I was wondering if you can recall your earliest memory that might have lead you to the career path you have chosen?
[[User:Carmen E. Castaneda|Carmen E. Castaneda]] 08:36, 16 January 2011 (EST)
 
: I don't know how old I was (sometime early in elementary school), but my parents bought me a book called something like ''Charlie Brown's Big Book of Questions''.  In that book, I learned that all life was made of cells and that a human had trillions of cells in his or her body.  The book also talked about matter being made of atoms and I wondering about the relationship between atoms and cells, like which was bigger or smaller.  My parents were good about fostering my interest in science and in junior high school I participated in a summer CTY program in Biology at a local high school.  Biology was one of my favorite classes in high school, so in college I continued along that track, most interested in how cells work.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:26, 17 January 2011 (EST)''
 
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Hi Dr. Dahlquist! I was wondering why you chose to study cell biology other than any other discipline in the Biology field?[[User:Alondra Vega|Alondra Vega]] 11:57, 16 January 2011 (EST)
 
: If you see my answer to Carmen's question above, I was intrigued by cells from when I was very little.  I would more properly call myself a Molecular Biologist as opposed to a Cell Biologist because what I am particularly studying is gene regulation which falls more into the area of molecular biology.  I am just really interested in how cells work at the molecular level.  I am interested in other fields of biology as they intersect with cellular mechanisms.  Now that DNA sequencing is so cheap, there are lots of opportunities for field and organismal biologists to ask cellular questions.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 20:33, 17 January 2011 (EST)''
 
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Hello Dr. Dahlquist. Perhaps a simple question for you: What do you think is the role of engineering in the field of bio research?
[[User:James C. Clements|James C. Clements]] 00:30, 17 January 2011 (EST)
 
: Biology is becoming increasingly interdisciplinary and is pulling theories and methods from the mathematics, physical sciences, and engineering in order to understand the very large datasets we are not generating in biology.  For example, genomics needs to make sense of the huge amount of information generated when a genome is sequenced, as well as other high-throughput methods that are regularly being used.  Other fields in biology are also generating large data sets such as studies in biodiversity. The fields of mathematical biology and bioinformatics are explicitly pulling from mathematics and computer science and are the ones with which I am most familiar, so I can be more specific about those.  We are going to be learing about gene regulatory networks later in the course; scientists are thinking of them as biological circuits and are applying principles from electrical engineering to understand them and also create them in the lab.  The field of synthetic biology is actively trying to engineer biological circuits.  A lot of the people in this field have pages on this wiki.  Conversely, I think that increasingly, engineers are getting interested in biology as a rich domain of problems to solve.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:58, 17 January 2011 (EST)''
 
 
Dr. Dahlquist, I would like to know the work ethic that it takes to become a prominent scientist or member to the scientific community? [[User:Bobak Seddighzadeh|Bobak Seddighzadeh]] 03:20, 26 January 2010 (EST)Bobak Seddighzadeh
 
: Bobak, scientists work very hard with long hours.  One of the difficult things about being a scientist is finding a balance between work and a personal life.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 21:53, 27 January 2010 (EST)''
 
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Hey Dr. Dahlquist, I was wondering what made you decide to become a professor in Biology?
--[[User:Kristoffer T. Chin|Kristoffer T. Chin]] 15:48, 20 January 2010 (EST)
 
Hi Dr. Dahlquist! I was wondering how you decided to become a professor and what drew you to come work at LMU? [[User:Amanda N. Wavrin|Amanda N. Wavrin]] 21:12, 23 January 2010 (EST)
 
: Kris and Amanda, your questions are related, so I'll answer them together.  I have always loved school since I was a little kid, and I always admired my teachers.  So, I wanted to be a teacher since I was a little kid.  Each year I advanced in school, I wanted to teach that grade, so by the time I got to college, I wanted to be a college professor.  I went to college at Pomona College, which is a liberal arts college smaller than LMU.  I really liked that environment because I'm not just interested in biology, but in other fields such as philosophy, ethics, politics, the arts, etc.  I thought that if I could teach at a liberal arts college, I would have more opportunities to interact with colleagues in those fields in addition to teaching and doing research in biology, which I love.
 
: Finding a faculty position involves an element of luck.  The colleges and universities that have positions open in your field at the time you are ready to look for a job is a little random.  I was lucky there was a position open for someone in my field when I was looking.  When I interviewed at LMU, I was impressed by the collegiality and community shown by the faculty and students.  I liked how faculty were collaborative in their teaching and research.  I enjoyed the time I spent having pizza with the biology students in particular.  I'm very glad that I made the decision to come here.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 22:03, 27 January 2010 (EST)''
 
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Hi Dr. Dahlquist, My question is how did you become so good at using computers and websites such as this? [[User:J&#39;aime C. Moehlman|J&#39;aime C. Moehlman]] 19:17, 20 January 2010 (EST)
 
: J'aime, in a word, practice, practice, practice.  I am motivated to learn new things because it helps me with my research and teaching.  I'm willing to try new things even though it can be uncomfortable at first, especially when I am first learning.  I am not afraid of making a mistake or breaking the computer.  I try to work with people who know more than me and I pay attention to what they do and try it myself.  I first learned how to use MediaWiki about two years ago.  Mostly, I just looked at other people's code and used trial and error to figure out how to do stuff.  Because I have so much experience now, even with something new, I generally know how to figure things out.  As you gain experience, you will be able to learn things faster.  So, be willing to learn and don't be afraid to try something new!  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 22:08, 27 January 2010 (EST)''
 
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What's up, Dr. Dahlquist?  (I had to use a different greeting than the two before me)  Anyway, if you could choose one place in the world to live for a year, where would it be and why?  --[[User:Alex J. George|Alex J. George]] 00:17, 21 January 2010 (EST)
 
: Alex, hmmmm.  My favorite place that I lived in the past was Santa Cruz, where I went to graduate school.  I was sad to leave there after living there for four years.  It was a beautiful place to live, next to the beach and mountains.  Also, it had a lot of book stores, good restaurants, and whole food stores (the real kind that sells grains in bins, not the Whole Foods chain).  Two years ago, my husband and I traveled in Austria because I went to a conference held in Vienna.  I thought that Vienna would be a great European city to live in--great art, great music, great public transportation, great coffee and chocolate, but what we really liked was the lake district around Salzburg.  It seemed like it would just be a very beautiful place to live.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 22:15, 27 January 2010 (EST)''
 
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Good Afternoon Dr. Dahlquist, My question is if you were given the opportuinty to switch careers would you do so? And if you would what would it be and why? *'''[[User:Salomon Garcia Valencia|Salomon Garcia Valencia]] 18:27, 23 January 2010 (EST)''':
 
: Salomon, It's hard for me to imagine a life in which I wasn't doing science.  All the things I could imaging switching to still involve science somehow.  I'm becoming more and more interested in politics and government.  AAAS offers fellowships for scientists to be advisors to the federal government for a year (either working for Congress or the Executive branch) and I might apply to do that sometime.  I'm also interested in investigative journalism, which is going away now that newspapers are dying.  My favorite non-science job I've ever had is working at an independent book store (although those are going away, too).  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 22:20, 27 January 2010 (EST)''
 
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Dr. Dahlquist, what is your philosophy of teaching? How has this philosophy changed (if it has) over the course of your career? [[User:Janelle N. Ruiz|Janelle N. Ruiz]] 03:12, 24 January 2010 (EST)
 
: Janelle, when you apply for a faculty position, you have to write a teaching philosophy.  I add to this statement every year as part of my faculty service report (a yearly report on my teaching/advising, research, and service that I submit to the Chair of the department and Dean), and I updated it quite substantially as part of my application for tenure and promotion to Associate Professor last year.  The take-home message of my teaching philosophy is that science is a process and you learn it by doing it.  When I design a course, I reflect upon what I do as a practicing scientist and how break that down into manageable steps that students can take.  I reflect on what I know (with my head), what skills I have (with my hands), and the personal qualities that I need (with my heart) to do my science.  I try to include authentic research into my courses.  I would say that my philosophy has matured over time so that I have become more student-centered instead of teacher-centered.  I have gained a lot of practical experience that I did not have at the beginning on how to manage the logistics of a course.  I participate in the scholarship of teaching and learning which is a scientific way to approach teaching where I gather data on what and how students learn and use that information to improve my teaching the next time.  This course is very much in keeping with the philosophy that you learn by doing.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 22:37, 27 January 2010 (EST)''
 
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Hello Dr. Dahlquist, I wanted to ask if you hope to center on teach Bioinformatics full time at Loyola if you had a choice. I know that you were a great professor for Cell Function, but i feel as we got into Bioinformatics things got even better and seemed to be a very strong fit. Again, this would be only if it was your choice to fully teach Bioinformatics, or do you prefer teaching both?
[[User:Kevin A Paiz-Ramirez|Kevin A Paiz-Ramirez]] 9:15 pm, 24 jan 2010 (EST)
: Kevin, I like teaching courses at all levels of the curriculum, both lower division, like Cell Function, and upper division, like Biological Databases, Bioinformatics Lab, and Molecular Biology of the Genome.  I also like to teach courses for non-science majors (even though I only got to do that once) and seminars for seniors (I've only done that once as well).  The one thing that I would like to do with Cell Function is to have the opportunity to take students into the computer lab to do some bioinformatics.  There is a lot we could do that would fit with the course, but because of the class size, there's no computer lab I can use.  I would like it even better if we could actually have a lab section for the course so that we could do some lab experiments that went along with the content of the course.  I really like teaching courses where there is some type of lab or practical aspect where we get down to doing real research.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 22:44, 27 January 2010 (EST)''
 
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Hi Dr. Dahlquist, I was wondering what was your first course that made you so interested in Bioinformatics?  Also, what were your strategies in developing your skills?  00:26, 25 January 2010 (EST) [[ User:Ryan N. Willhite|Ryan N. Willhite]]
 
: Ryan, I never took a course in bioinformatics (at least in the way that you probably mean) because those courses did not exist when I was in college or graduate school.  I started teaching bioinformatics workshops myself when I was a postdoctoral researcher.  I got interested in the field because I was interested in how biological pathways worked in a cell.  But when I was in graduate school, people would take two years to clone and sequence a single gene, let alone all the genes in a pathway.  When the human genome project was completed, we finally had the technology to study all the genes at once and I was excited that we could start answering the questions I had about pathways in the cell.  To make the best use of this technology, we needed computer programs to analyze the data, so bioinformatics was a good fit for me.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 22:57, 27 January 2010 (EST)''
 
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Hello, Dr. D. What are you favorite and least favorite aspects of having a career in academia? '''[[User:Angela A. Garibaldi|Angela A. Garibaldi]] 23:47, 25 January 2010 (EST)''':
 
: Angela, my favorite aspect of working in academia is that I get paid to do what I love--learn new things.  My least favorite aspect is that academia is essentially a feudal system that has not changed much since the 1600's when it was invented.  It is set up so that the people at the bottom have very little power and the people at the top have a lot of power, with lots of step functions where the result is all or none (getting your PhD, getting tenure).  Also, there are still very few women at the top (full professors, administrators).  There is a lot of sexism and misogyny that go on that would not be tolerated in other sectors of society.  But still, I think this is the best career for me.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 23:05, 27 January 2010 (EST)''
 
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Besides the areas of your research (including Bioinformatics, ribosome structure, yeast, etc.) what other aspects of Biology interest you the most? [[User:Michael R. Pina|Michael R. Pina]] 11:19, 26 January 2010 (EST)
 
: Michael, that's a tough question, you've named all of my favorite areas of biology! :)  I like learning about evolution because it is the foundation of biology.  I subscribe to both ''Science'' and ''Nature'' and I like to browse the articles to keep abreast of what's current in general in biology, so in some sense, I could say that I like it all.  Things that draw my attention tend to be "big picture" questions that look at things like a system.  That's why biology is so exciting right now because more and more researchers are asking system's level questions.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 23:08, 27 January 2010 (EST)''
 
== Week 4 assignment ==
 
Hi Dr. Dahlquist, I have a question on the assignment for this week.  I am currently having a difficult time understanding Part 2 Activity 2 in calculating for Min and Max Difference.  In the first table, I was able to use the Clustdist tool with one of my alignments with 3 clones.  The page that it took me gave me a screen that looks like this
[[Image:Untitled.JPG|Center|1000px]]
 
The problem I have is now calculating for the min difference and the max difference. I am not sure how i am supposed to select the highest and lowest pairwise scores.  Do it add up all the distance matrix for the x-coordinate of S2V1-3 and then compare that to the other clones and use the smallest sum and highest sum and those would be my min and max difference after multiplication of 285?
 
I am also having a difficult time understanding how to look at the maximum and minimum difference across subjects.  The instructions are a bit unclear
--[[User:Kristoffer T. Chin|Kristoffer T. Chin]] 00:19, 13 February 2010 (EST)
 
 
I was wondering how you became so interested in Bioinformatics? [[User:Zeb Russo|Zeb Russo]] 18:04, 31 August 2011 (EDT)
 
: When I first started grad school, I was interested in signaling pathways.  However, back in 1993, all people could do was to clone and sequence a single gene and study it, so there wasn't any way to actually study the pathway at a systems level.  When I got my degree in 2000 and was looking for a postdoc, DNA microarrays became available and we could study whole genomes.  So, I became involved in bioinformatics so that I could learn about how pathways in the cell worked at a whole system level.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 18:17, 31 August 2011 (EDT)''
 
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Hey Dr. Dahlquist, I was wondering if there was ever a career you wanted to pursue outside of science? *'''[[User:Nicolette S. Harmon|Nicolette S. Harmon]] 18:26, 31 August 2011 (EDT)''':
 
: Lately I've been thinking that if I had to choose a different career, I would be interested in journalism or public policy, especially since journalism seems to be devolving into "infotainment" these days.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 18:43, 31 August 2011 (EDT)''
 
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What are some accomplishments you have achieved so far (career related or not) that you are particularly proud of and what is something that you hope to achieve within the next 10 years? - [[User:Isaiah M. Castaneda|Isaiah M. Castaneda]] 18:59, 31 August 2011 (EDT)
 
: One of the things I am really proud of is the [http://www.genmapp.org GenMAPP software] that I helped develop when I was a postdoc.  It has been used by thousands of people world-wide.  We are going to use it in the third project in the course.  Within the next 10 years, I will be going up for promotion to full professor.  I want to integrate the current biomathematical modeling and bioinformatics software projects I am working on to create a user-friendly simulation tool for students to investigate gene regulatory pathways and networks.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:41, 31 August 2011 (EDT)''
 
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What was your favorite part of your undergraduate years? [[User:Samantha M. Hurndon|Samantha M. Hurndon]] 19:13, 31 August 2011 (EDT)
 
: I think my favorite experience when I was an undergraduate was studying abroad at Oxford University in England.  I joined a bunch of clubs and had a great time traveling around the country.  Two of my favorite classes were "Gender and Science", taught by a woman physics professor, and "Understanding the Earth: Feminist Perspectives", taugth by a woman geology professor.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:44, 31 August 2011 (EDT)''
 
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Hey Dr. Dahlquist, I was wondering what recent scientific advancement are you most excited about for the future? [[User:Chris H. Rhodes|Chris H. Rhodes]] 14:13, 6 September 2011 (EDT)
 
: I've been excited ever since the Human Genome Project was completed in 2000-2003. That project enabled a whole suite of technologies (like DNA microarrays) that allow us to do high-throughput experiments and study cells at a systems level.  I'm very excited about the advancements in using this data to model a cell's activities.  I'm also excited for the prospect that soon it will be cheap enough to sequence individual genomes on a regular basis.  However, I think our ability to capture more and more data is outpacing our ability to understand it.  However, like I said in class, it's a really good time to be a biologist! ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 11:31, 7 September 2011 (EDT)''
 
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Week 2 Journal Question
* Hey Dr. Dahlquist, I had a quick question about the week 2 journal. Would it be alright if I incorporated the answers to the handout questions into my conclusion instead of sticking them in the results section? It seemed to me like a more natural way of presenting the information and I'm kind of having trouble with thinking what else would go into the conclusion. I already made the changes to the page if you wanted to look at it and see if it seems right.[[Chris_Rhodes_Week_2]] Thanks. [[User:Chris H. Rhodes|Chris H. Rhodes]] 19:44, 11 September 2011 (EDT)
 
 
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Dr. Dahlquist, I was wondering what part of bioninformatics you like working with the most? [[User:Alex A. Cardenas|Alex A. Cardenas]]
 
: My favorite part of bioinformatics is really called "systems biology"; it involves studying the pathways and networks in the cell.  My favorite thing is to take DNA microarray data and use it to understand the gene regulatory networks in the cell.  I am involved in a modeling project that is trying to express the network interactions with differential equations.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 14:25, 14 September 2011 (EDT)''
 
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Hi Dr. Dahlquist, what was your favorite part of your graduate work? [[User:Robert W Arnold|Robert W Arnold]] 23:13, 20 September 2011 (EDT)
 
: Hmmm.  I've never been asked that before.  I think my favorite part of my graduate work came out of my biggest frustration.  I was trying to reproduce the results in [http://www.sciencemag.org/content/277/5330/1262.abstract?ijkey=cc68074be3249ee57b012114d1e1268370ae2331&keytype2=tf_ipsecsha this ''Science'' paper], and I wasn't able to. Upon looking closer at the gel in the paper, I realized that they had done the proper controls and that if you accounted for that, my results were indeed similar to theirs.  From that, I made a hypothesis about the role of Initiation Factor 1 binding to the A site of the small subunit of the ribosome to provide kind of a "proofreading" function during translation initiation.  Coming up with that hypothesis was very satisfying after being frustrated for a long time.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 18:49, 21 September 2011 (EDT)''
 
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==week 12 paul magnano==
I uploaded the genelist/GO for 5 clusters on the original assignment, im not sure why you were not able to access it on lionshare. I just re shared it with you please let me know if you cannot access it still. [[User:Paul Magnano|Paul Magnano]] 12:55, 18 April 2013 (EDT)
 
 
== Week 1 Questions Fall 2014 ==
 
Hello Dr. Dahlquist,
Do you believe that you have encountered any resistance from your peers throughout your career due to being a woman in a traditionally male dominated field?
[[User:Nicole Anguiano|Nicole Anguiano]] 01:29, 3 September 2014 (EDT)
 
: I don't think I would use the phrase "resistance from peers" to describe my experiences, but I will say that I have experienced some challenges unique to being a woman in my field.  I would be happy to share more with you about this offline.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 19:13, 3 September 2014 (EDT)''
 
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Hi Dr. Dahlquist,
What is the one thing that is at the top of your bucket list?
[[User:Isabel Gonzaga|Isabel Gonzaga]] 20:09, 28 August 2014 (EDT)
 
: Wow, that's a tough one.  I guess I haven't really thought of what's on my bucket list!  What immediately comes to mind is that there are restaurants that I've always wanted to eat at.  [http://sbe.com/restaurants/locations/thebazaar-beverlyhills/] Bazaar is known for it's molecular gastronomy and I definitely want to go there sometime!
 
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Hello Dr. Dahlquist,
What is your favorite food to eat?
[[User:Chloe Jones|Chloe Jones]] 03:49, 3 September 2014 (EDT)Chloe Jones
 
: It's hard to narrow it down to just one!  I often say that chips and salsa are God's perfect food!  It's a tradition in my family to get food at Hacienda del Rey on Lincoln on Friday nights--I love Mexican food!  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 18:47, 3 September 2014 (EDT)''
-->
 
Hello Dr. Dahlquist,
If you were not a biology professor nor doing research, what career would you see yourself in?<br>
[[User:Natalie Williams|Natalie Williams]] 19:26, 17 January 2015 (EST)
 
: Recently, I've gotten interested in public policy and investigative journalism.  I would like to use my scientific training in data analysis to tackle broader societal questions.  I think investigative journalism is important to holding our elected officials accountable for their actions. ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 20:13, 21 January 2015 (EST)''
 
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Hi Dr. Dahlquist, <br>
What is your favorite book and why? <br>
[[User:Kara M Dismuke|Kara M Dismuke]] 17:03, 18 January 2015 (EST)
 
: It's hard to choose just one!  I'm a big Harry Potter fan, the 5th, 6th, and 7th books are my favorites.  ''Beggars in Spain'' by Nancy Kress (and the two follow-ups in the trilogy, ''Beggars and Choosers'' and ''Beggar's Ride'') is up there--it's about genetically modified people that don't need to sleep and I use it in my seminar class BIOL 585:  Issues in Biotechnology.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 20:15, 21 January 2015 (EST)''
 
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Hi Dr. Dahlquist,
If you had a time machine but had to use it for science, which past research or experiment would you most want to be part of? <br>
[[User:Kristen M. Horstmann|Kristen M. Horstmann]] 17:55, 18 January 2015 (EST)
 
: If I can answer your question this way, I'd love to go back to the beginning of life on earth and see if it really happened the way we currently think--the RNA world.  I'd love to take some samples and bring it back to the present to analyze.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 20:55, 29 January 2015 (EST)''
 
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Hi Dr. Dahlquist,
What do you know now that you wish you knew when you were my age?
[[User:Alyssa N Gomes|Alyssa N Gomes]] 22:37, 18 January 2015 (EST)
 
: Ahhh, so many things!  I guess the big two things that I wish I had known (or believed) in college are:
* I am not my results, i.e., my self worth is not determined by my academic performance.  I took feedback on my work too personally so that if I did badly, I felt bad about myself, which was self-destructive.  We actually learn by making mistakes and critical feedback is extremely valuable.
* Slow and steady wins the race, i.e., treat my academic work like a job, work away at it steadily, instead of procrastinating and making an upcoming deadline force me to work.
 
''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 21:05, 29 January 2015 (EST)''
 
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Hello Dr. Dalquist,<br>
What exciting things do you expect to come out of biomathematics in the coming decade?<br>
([[User:William A. C. Gendron|William A. C. Gendron]] 20:47, 19 January 2015 (EST))
 
: I am excitedly awaiting the day that we have a whole cell model (for yeast or other single-celled organism) that can accurately model and predict the dynamics of all molecules in the cell.  I think it will happen in the next decade.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 21:07, 29 January 2015 (EST)''
 
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Hi Dr. Dahlquist, <br>
If you could take one class at LMU, what would it be?<br>
[[User:Tessa A. Morris|Tessa A. Morris]] 23:00, 19 January 2015 (EST)
 
: That's a hard one, there are actually many classes that I would like to take.  I would love to take a theology class, since I've never actually taken one in my life.  I would also like to re-take Organic Chemistry.  I struggled with it when I took it in college because I just didn't have a framework for it in my brain.  It would be interesting to take it now and see what the students are getting simultaneously with me teaching BIOL 201: Cell Function in the Fall.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 21:11, 29 January 2015 (EST)''
 
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Hello Dr. Dahlquist, <br>
My question for you is as follows: What has been your biggest challenge as a researcher and how did you overcome it? <br>
[[User:Lauren M. Magee|Lauren M. Magee]] 23:06, 19 January 2015 (EST)
 
: I've faced some technical hurdles to get experiments to work at different stages of my career, most recently with getting the DNA microarray technique to work in my laboratory here at LMU when I first started here.  I was able to overcome the challenge because of a couple of things.  First, a bunch of faculty got together to write an equipment grant to the Keck foundation that I was able to use to purchase my own DNA microarray scanner.  That made it easier to do more experiments faster and try to work things out.  Second, I asked advice of a mentor and she pointed me in a direction that I hadn't thought of before and once I tried that, the experiments worked.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 21:16, 29 January 2015 (EST)''
 
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Hi Dr. Dahlquist, Who would you say is (or was) your biggest role model and why? <br>
[[User:Lucia I. Ramirez|Lucia I. Ramirez]] 01:34, 20 January 2015 (EST)
 
: This is an interesting question.  I guess I would say that I could name several people who were and are significant mentors to me, for example, Dr. Martina Ramirez.  She was a faculty member at Pomona College when I was a student there and shepherded me through the grad school application process.  But I guess I haven't thought of my mentors as role models, per se, in that I want to model myself after them.  Weirdly enough, there are some fictional characters that I would consider role models for how I would want to be as a person:  Ambassador Delenn from the ''Babylon 5'' television show and Vicky Turner from the novels ''Beggars and Choosers'' and ''Beggar's Ride'' that I mentioned above.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 21:20, 29 January 2015 (EST)''
 
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Hi, Dr. Dahlquist. What would you say was a critical pivotal point in getting where you are today? <br>
*'''[[User:Karina Alvarez|Karina Alvarez]] 03:06, 20 January 2015 (EST)''':
 
: Choosing to change research directions from what I did in graduate school to what I did as a postdoc.  In grad school I was studing the biochemistry of the riboosome in a very narrow, reductionistic sense.  For my postdoc, I entered the realm of genomics and bioinformatics which is what I still do today.  ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 21:23, 29 January 2015 (EST)''
 
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Dr. Dahlquist, how extensive is your knowledge in epigentics, such as DNA methylation? I'm curious about the subject and have some questions on it. <br>
[[User:Jeffrey Crosson|Jeffrey Crosson]] 2:22, 22 January 2015 (EST)
 
: I know something about the subject, what are your questions? ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 21:24, 29 January 2015 (EST)''

Revision as of 16:42, 30 August 2016

What is your favorite sport to watch? Zachary T. Goldstein 19:29, 30 August 2016 (EDT)

I enjoy watching figure skating (I got to go to the World Championships in 2007 when they were held in LA). Out of the traditional sports, I most enjoy basketball. — Kam D. Dahlquist 19:42, 30 August 2016 (EDT)
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