User talk:Kam D. Dahlquist: Difference between revisions
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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. | |||
''— [[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. | |||
''— [[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. | |||
''— [[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. ''— [[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. | |||
''— [[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 | 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 | ||
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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) | 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. ''— [[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) | |||
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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. ''— [[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. ''— [[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. ''— [[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. ''— [[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! ''— [[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. ''— [[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. | |||
''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 18:49, 21 September 2011 (EDT)'' | |||
Revision as of 15:49, 21 September 2011
I was wondering how you became so interested in Bioinformatics? 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. — Kam D. Dahlquist 18:17, 31 August 2011 (EDT)
Hey Dr. Dahlquist, I was wondering if there was ever a career you wanted to pursue outside of science? *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. — Kam D. Dahlquist 18:43, 31 August 2011 (EDT)
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? - Isaiah M. Castaneda 18:59, 31 August 2011 (EDT)
- One of the things I am really proud of is the 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. — Kam D. Dahlquist 19:41, 31 August 2011 (EDT)
What was your favorite part of your undergraduate years? 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. — Kam D. Dahlquist 19:44, 31 August 2011 (EDT)
Hey Dr. Dahlquist, I was wondering what recent scientific advancement are you most excited about for the future? 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! — Kam D. Dahlquist 11:31, 7 September 2011 (EDT)
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. Chris H. Rhodes 19:44, 11 September 2011 (EDT)
Dr. Dahlquist, I was wondering what part of bioninformatics you like working with the most? 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. — Kam D. Dahlquist 14:25, 14 September 2011 (EDT)
Hi Dr. Dahlquist, what was your favorite part of your graduate work? 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 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.
— Kam D. Dahlquist 18:49, 21 September 2011 (EDT)
