User:Kam D. Dahlquist

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*[[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]]
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*[[BIOL398-01/S10 | BIOL 398-01 Bioinformatics Laboratory OpenWetWare site]]
 
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*[[BIOL367/F10 | BIOL 367 Biological Databases OpenWetWare site]]
 
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*[[BIOL398-01/S11 | BIOL 398-01 Biomathematical Modeling OpenWetWare site]]
 
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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.
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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).
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=== Office Hours Spring 2011 ===
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== Courses Taught ==
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MW 1:00 PM - 3:00 PM
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* See complete list on [[Dahlquist:Courses | this page]].
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* Links to OpenWetWare sites:
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**[[BIOL398-03/S13 | BIOL 398-03 Biomathematical Modeling OpenWetWare site]] (Spring 2013)
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**[[BIOL368/F11 | BIOL 368 Bioinformatics Laboratory OpenWetWare site]] (Fall 2011)
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**[[BIOL398-01/S11 | BIOL 398-01 Biomathematical Modeling OpenWetWare site]] (Spring 2011)
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**[[BIOL367/F10 | BIOL 367 Biological Databases OpenWetWare site]] (Fall 2010)
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**[[BIOL398-01/S10 | BIOL 398-01 Bioinformatics Laboratory OpenWetWare site]] (Spring 2010)
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=== Office Hours Spring 2013 ===
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Mondays and Wednesdays 12:00-2:00 PM and by appointment
Office: Seaver 218
Office: Seaver 218
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==Publications==
==Publications==
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=== Peer-reviewed Research ===
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* 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]
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* 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]
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* 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]
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* 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. [http://www.ncbi.nlm.nih.gov/pubmed/17588266 Abstract][http://www.biomedcentral.com/1471-2105/8/217 Full Text]
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* 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.[http://www.ncbi.nlm.nih.gov/pubmed/12540299 Abstract][http://genomebiology.com/content/4/1/R7 Full Text]
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* Segal, M.R., Dahlquist, K.D., & Conklin, B.R. (2003) Regression Approaches for Microarray Data Analysis. ''Journal of Computational Biology'' 10: 961-980. [http://www.ncbi.nlm.nih.gov/pubmed/14980020 Abstract][http://www.liebertonline.com/doi/pdf/10.1089/106652703322756177 Full Text]
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* 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. [http://www.nature.com/ng/journal/v31/n1/full/ng0502-19.html Full Text]
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* 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. [http://www.ncbi.nlm.nih.gov/pubmed/10860719 Abstract][http://www.sciencedirect.com/science/article/pii/S0022283600936726 Full Text]
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* 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. [http://www.ncbi.nlm.nih.gov/pubmed/9931247 Abstract][http://www.sciencedirect.com/science/article/pii/S0022283698924469 Full Text]
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* Recht, M.I., Fourmy, D., Blanchard, S.C., Dahlquist, K.D., & Puglisi, J.D.  (1996)  RNA Sequence Determinants for Aminoglycoside Binding to an A-site rRNA Model Oligonucleotide.  Journal of Molecular Biology  262:  421-436. [http://www.ncbi.nlm.nih.gov/pubmed/8893854 Abstract][http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WK7-45MG2FS-3T-1&_cdi=6899&_user=945462&_pii=S0022283696905264&_origin=&_coverDate=10%2F04%2F1996&_sk=997379995&view=c&wchp=dGLbVlW-zSkzS&md5=5afbe9391114d5a8a1b5e581462b7002&ie=/sdarticle.pdf Full Text]
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=== 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. [http://www.biomedcentral.com/1471-2105/11?issue=S12 Proceedings Home Page]
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* 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]
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* 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. [http://books.google.com/books?id=v5JPZXo9ql0C&lpg=PP1&dq=The%20Ribosome%3A%20Structure%2C%20Function%2C%20Antibiotics%2C%20and%20Cellular%20Interactions&pg=PP6#v=onepage&q=The%20Ribosome:%20Structure,%20Function,%20Antibiotics,%20and%20Cellular%20Interactions&f=false Google Books]
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* 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.
==Useful links==
==Useful links==
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[[Help|OpenWetWare help pages]]
*[[Help|OpenWetWare help pages]]

Revision as of 19:03, 21 January 2013

Contents

Contact Info

Kam D. Dahlquist, Ph.D.
Associate Professor
Department of Biology
Loyola Marymount University
1 LMU Drive, MS8220
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

Office Hours Spring 2013

Mondays and Wednesdays 12:00-2:00 PM and by appointment

Office: Seaver 218

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 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
  4. Identifying Soil Bacteria and Biochemical Pathways in the Ballona Wetlands for the Bioremediation of Organic Pollutants

Publications

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. Abstract 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. AbstractFull 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. 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. AbstractFull Text
  • 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.AbstractFull Text
  • Segal, M.R., Dahlquist, K.D., & Conklin, B.R. (2003) Regression Approaches for Microarray Data Analysis. Journal of Computational Biology 10: 961-980. AbstractFull Text
  • 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. Full Text
  • 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. AbstractFull Text
  • 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. AbstractFull Text
  • Recht, M.I., Fourmy, D., Blanchard, S.C., Dahlquist, K.D., & Puglisi, J.D. (1996) RNA Sequence Determinants for Aminoglycoside Binding to an A-site rRNA Model Oligonucleotide. Journal of Molecular Biology 262: 421-436. AbstractFull Text

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. 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. Google Books
  • 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.

Useful links

Personal tools