User:Kam D. Dahlquist: Difference between revisions

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[http://www.lmu.edu LMU home page]
==Contact Info==
==Contact Info==


  Kam D. Dahlquist, Ph.D.
  Kam D. Dahlquist, Ph.D.
  Associate Professor
  Professor
  Department of Biology
  Department of Biology
  Loyola Marymount University
  Loyola Marymount University
  1 LMU Drive, MS8220
  1 LMU Drive, MS8888
  Los Angeles, CA 90045  
  Los Angeles, CA 90045  
*[[Special:Emailuser/Kam D. Dahlquist|Email me through OpenWetWare]]
*[[Special:Emailuser/Kam D. Dahlquist|Email me through OpenWetWare]]
*[[Dahlquist | Dahlquist Lab OpenWetware site]]
*[[Dahlquist | Dahlquist Lab OpenWetware site]]


I am the head of the [http://myweb.lmu.edu/kdahlqui Dahlquist Lab] at [http://www.lmu.edu Loyola Marymount University].  I learned about [[OpenWetWare]] through a Google search when I was searching for a protocol online. I've joined because I run a lab with undergraduates at a primarily undergraduate institution and would like to post my protocols and supply lists online for easy access and to share them with the community.  I also host some of my courses on this site (see below).
I am the head of the [http://kdahlquist.github.io/DahlquistLab/index.htm Dahlquist Lab] at [http://www.lmu.edu Loyola Marymount University].  I learned about [[OpenWetWare]] through a Google search when I was searching for a protocol online. I've joined because I run a lab with undergraduates at a primarily undergraduate institution and would like to post my protocols and supply lists online for easy access and to share them with the community.  I also host some of my courses on this site (see below).


== Courses Taught ==
== Courses Taught ==


* See complete list on [[Dahlquist:Courses | this page]].
* See complete list on [http://kdahlquist.github.io/DahlquistLab/courses.htm this page].
* Links to OpenWetWare sites:
* Links to OpenWetWare sites:
**[[BIOL368/F11 | BIOL 368 Bioinformatics Laboratory OpenWetWare site]] (Fall 2011)
** Bioinformatics Laboratory
**[[BIOL398-01/S11 | BIOL 398-01 Biomathematical Modeling OpenWetWare site]] (Spring 2011)
*** [[BIOL368/S20 | Biology 368:  Bioinformatics Laboratory Spring 2020]]
**[[BIOL367/F10 | BIOL 367 Biological Databases OpenWetWare site]] (Fall 2010)
*** [[BIOL368/F16 | Biology 368:  Bioinformatics Laboratory Fall 2016]]
**[[BIOL398-01/S10 | BIOL 398-01 Bioinformatics Laboratory OpenWetWare site]] (Spring 2010)
*** [[BIOL368/F14 | Biology 368:  Bioinformatics Laboratory Fall 2014]]
=== Office Hours Fall 2011 ===
*** [[BIOL368/F11 | Biology 368:  Bioinformatics Laboratory Fall 2011]]
 
*** [[BIOL398-01/S10 | Biology 398-01: Bioinformatics Laboratory Spring 2010]]
Mondays 12:00-2:00 PM, Tuesdays and Thursdays 10:00-11:00 AM and by appointment
** Biomathematical Modeling
 
*** [[BIOL388/S19 | Biology 388-01:  Biomathematical Modeling/Mathematics 388-01:  Survey of Biomathematics Spring 2019]]
Office: Seaver 218
*** [[BIOL398-05/S17 | Biology 398-05:  Biomathematical Modeling/Mathematics 388-01:  Survey of Biomathematics Spring 2017]]
*** [[BIOL398-04/S15 | Biology 398-04:  Biomathematical Modeling/Mathematics 388-01:  Survey of Biomathematics Spring 2015]]
*** [[BIOL398-03/S13 | Biology 398-03: Biomathematical Modeling/Mathematics 388-01: Survey of Biomathematics Spring 2013]]
*** [[BIOL398-01/S11 | Biology 398-01: Biomathematical Modeling/Mathematics 388-01: Survey of Biomathematics Spring 2011]]
** Biological Databases
*** [[BIOL367/F10 | Biology / Computer Science 367-01/ Honors 398-05: Biological Databases Fall 2010 partial site on this wiki]]


==Education==
==Education==
Line 32: Line 39:
==Research interests==
==Research interests==


# [http://xmlpipedb.cs.lmu.edu XMLPipeDB]:  A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources; creating MAPPs and Gene Databases for the [http://www.GenMAPP.org GenMAPP] software
# [http://xmlpipedb.cs.lmu.edu XMLPipeDB]:  A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources; [[Dahlquist:MAPP Archive|creating MAPPs]] and [[Dahlquist:Gene Databases|Gene Databases]] for the [http://www.GenMAPP.org GenMAPP Classic] software
# The Global Transcriptional Response of ''Saccharomyces cerevisiae'' to Cold Shock and Recovery
# The Global Transcriptional Response of ''Saccharomyces cerevisiae'' to [[Dahlquist:Yeast Cold Shock|Cold Shock]] and Recovery
# Mathematical Modeling of the Transcriptional Network Controlling the Environmental Stress Response in ''Saccharomyces cerevisiae''
# [[Dahlquist:Mathematical Modeling|Mathematical Modeling]] of the [[Dahlquist:Yeast Transcription Factors|Transcriptional Network]] Controlling the Environmental Stress Response in ''Saccharomyces cerevisiae'' using the [http://kdahlquist.github.io/GRNmap/ GRNmap software]
# Identifying Soil Bacteria and Biochemical Pathways in the Ballona Wetlands for the Bioremediation of Organic Pollutants
# [http://dondi.github.io/GRNsight/index.html GRNsight]:  A Web Application for Visualizing Models of Gene Regulatory Networks


==Publications==
==Publications==
<!--
<biblio>
#Paper1 pmid=20829833
#Paper2 pmid=20577653
#Paper3 Dionisio, JDN and Dahlquist, KD ''Improving the Computer Science in Bioinformatics Through Open Source Pedagogy'' SIGCSE Bulletin 2008 Jun; 40(2) 115-9. doi:10.1145/1383602.1383648 [http://portal.acm.org/citation.cfm?id=1383648&jmp=cit&coll=portal&dl=ACM&CFID=74660743&CFTOKEN=75759974# Abstract]
#Paper4 pmid=17588266
#Paper5 pmid=18428731
#Paper6 pmid=14980020
#Paper7 pmid=12540299
#Paper8 pmid=11984561
#Paper9 pmid=10860719
#Paper10 pmid=9931247
#Paper11 pmid=8893854
#Paper12 pmid=8643361
</biblio>
-->
=== Peer-reviewed Research ===
* Demir, E., Cary, M.P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A.C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K.H,, Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K.H., Rzhetsky, A., Schachter, V., Sobral, B.S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Le Novère, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P.D., Sander, C., and Bader, G.D. (2010) The BioPAX Community Standard for Pathway Data Sharing. ''Nature Biotechnology'' 28: 935-942. [http://www.ncbi.nlm.nih.gov/pubmed/20829833 Abstract] [http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html Full Text]
* Ogando, D.G., Dahlquist, K.D., Alizadeh, M., Kunchithapautham, K., Li, J., Yu, N., LaVail, M.M., Rohrer, B., Vollrath, D., and Danciger, M. (2010) Candidate Genes for Chromosomes 6 and 10 Quantitative Trait Loci for Age-related Retinal Degeneration in Mice. ''Molecular Vision'' 16: 1004-1018. [http://www.ncbi.nlm.nih.gov/pubmed/20577653 Abstract][http://www.molvis.org/molvis/v16/a111/ Full Text]
* Dionisio, J.D.N. and Dahlquist, K.D. (2008) Improving the Computer Science in Bioinformatics Through Open Source Pedagogy ''ACM SIGCSE Bulletin'' 40: 115-119. [http://portal.acm.org/citation.cfm?id=1383648&jmp=cit&coll=portal&dl=ACM&CFID=74660743&CFTOKEN=75759974# Abstract]
* Salomonis, N., Hanspers, K., Zambon, A.C., Vranizan, K., Lawlor, S.C., Dahlquist, K.D., Doniger, S.W., Stuart, J.M., Conklin, B.R., Pico, A.R. (2007) GenMAPP 2: New Features and Resources for Pathway Analysis. ''BMC Bioinformatics'' 8: 217. [PubMed][Full Text][PDF]
* Doniger, S.W., Salomonis, N., Dahlquist, K.D., Vranizan, K., Lawlor, S.C., & Conklin, B.R. (2003) MAPPFinder: Using Gene Ontology and GenMAPP to Create a Global Gene-Expression Profile from Microarray Data. ''Genome Biology'' 4: R7.[PubMed][Full Text][PDF]
* Segal, M.R., Dahlquist, K.D., & Conklin, B.R. (2003) Regression Approaches for Microarray Data Analysis. ''Journal of Computational Biology'' 10: 961-980. [PubMed][Full Text][Preprint]
* Dahlquist, K.D., Salomonis, N., Vranizan, K., Lawlor, S.C., & Conklin, B.R. (2002) GenMAPP, A New Tool for Viewing and Analyzing Microarray Data on Biological Pathways. ''Nature Genetics'' 31: 19-20. [PubMed][Full Text][PDF]
* Dahlquist, K.D. & Puglisi, J.D. (2000) Interaction of Translation Initiation Factor IF1 with the E. coli Ribosomal A Site. ''Journal of Molecular Biology'' 299: 1-15. [PubMed][Full Text][PDF]
* Recht, M.I., Douthewaite, S., Dahlquist, K.D., & Puglisi, J.D. (1999) Effect of Mutations in the A Site of 16S rRNA on Aminoglycoside Antibiotic-Ribosome Interaction. ''Journal of Molecular Biology'' 286: 33-43. [PubMed][Full Text][PDF]
=== Reviews, Book Chapters, Conference Proceedings ===
* Dahlquist, K.D., editor (2010) Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010. ''BMC Bioinformatics'' 11(Suppl 12): S1-S13. [Proceedings Home Page]
* Dahlquist, K.D. (2004) Using GenMAPP and MAPPFinder to View Microarray Data on Biological Pathways and Identify Global Trends in the Data. In ''Current Protocols in Bioinformatics'' (Baxevanis, A.D., Davison, D.B., Page, R., Stein, L., Stormo, G., eds.), John Wiley & Sons, Inc., New York, N.Y., pp. 7.5.1-7.5.26. [http://www.ncbi.nlm.nih.gov/pubmed/18428731 Abstract]
* Puglisi, J.D., Blanchard, S.C., Dahlquist, K.D., Eason, R.G., Fourmy, D., Lynch, S.R., Recht, M.I., & Yoshizawa, S. (1999) Aminoglycoside Antibiotics and Decoding. In ''The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions'' (Garrett, R.A., Douthewaite, S.R., Liljas, A., Matheson, A.T., Moore, P.B., & Noller, H.F., eds.), pp. 419-429. ASM Press, Washington, D.C
* Dahlquist, K. & Puglisi, J.D. (1995) Investigating the Structure and Function of Translation Initiation Factor 1 in Escherichia coli. ''Nucleic Acids Symposium Series'' 33: 170-171. [PubMed]


==Useful links==
Please go to the [http://kdahlquist.github.io/DahlquistLab/publications.htm Dahlquist Lab Publications page] to view a complete list of publications.  Kam Dahlquist's Google Scholar profile is [http://scholar.google.com/citations?user=LYLGfN0AAAAJ&hl=en here].
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[[Help|OpenWetWare help pages]]

Latest revision as of 19:56, 4 May 2020

LMU home page

Contact Info

Kam D. Dahlquist, Ph.D.
Professor
Department of Biology
Loyola Marymount University
1 LMU Drive, MS8888
Los Angeles, CA 90045

I am the head of the Dahlquist Lab at Loyola Marymount University. I learned about OpenWetWare through a Google search when I was searching for a protocol online. I've joined because I run a lab with undergraduates at a primarily undergraduate institution and would like to post my protocols and supply lists online for easy access and to share them with the community. I also host some of my courses on this site (see below).

Courses Taught

Education

  • 2000, PhD, University of California, Santa Cruz
  • 1993, BA, Pomona College

Research interests

  1. XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources; creating MAPPs and Gene Databases for the GenMAPP Classic software
  2. The Global Transcriptional Response of Saccharomyces cerevisiae to Cold Shock and Recovery
  3. Mathematical Modeling of the Transcriptional Network Controlling the Environmental Stress Response in Saccharomyces cerevisiae using the GRNmap software
  4. GRNsight: A Web Application for Visualizing Models of Gene Regulatory Networks

Publications

Please go to the Dahlquist Lab Publications page to view a complete list of publications. Kam Dahlquist's Google Scholar profile is here.

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