User:Kam D. Dahlquist: Difference between revisions
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=== Peer-reviewed Research === | === 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 | * 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. [Abstract][Full Text][PDF] | |||
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. [Abstract][Full Text][PDF] | * 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][Contact us for reprint] | ||
* 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] | |||
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][Contact us for reprint] | * 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. | ||
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] | [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] | |||
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] | |||
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] | * 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] | ||
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 === | === Reviews, Book Chapters, Conference Proceedings === |
Revision as of 15:22, 31 August 2011
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
- See complete list on this page.
- Links to OpenWetWare sites:
- BIOL 368 Bioinformatics Laboratory OpenWetWare site (Fall 2011)
- BIOL 398-01 Biomathematical Modeling OpenWetWare site (Spring 2011)
- BIOL 367 Biological Databases OpenWetWare site (Fall 2010)
- BIOL 398-01 Bioinformatics Laboratory OpenWetWare site (Spring 2010)
Office Hours Fall 2011
Mondays 12:00-2:00 PM, Tuesdays and Thursdays 10:00-11:00 AM and by appointment
Office: Seaver 218
Education
- 2000, PhD, University of California, Santa Cruz
- 1993, BA, Pomona College
Research interests
- XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources; creating MAPPs and Gene Databases for the GenMAPP software
- The Global Transcriptional Response of Saccharomyces cerevisiae to Cold Shock and Recovery
- Mathematical Modeling of the Transcriptional Network Controlling the Environmental Stress Response in Saccharomyces cerevisiae
- 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. [Abstract][Full Text][PDF]
- 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][Contact us for reprint]
- 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. [Current Protocols]
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]