User:Kam D. Dahlquist

Contact Info

Kam D. Dahlquist, Ph.D.
Associate Professor
Department of Biology
Loyola Marymount University
1 LMU Drive, MS8220
Los Angeles, CA 90045 

• Email me through OpenWetWare
• Dahlquist Lab OpenWetware site

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

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

1. Demir E, Cary MP, 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 AC, 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, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, 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 KH, Rzhetsky A, Schachter V, Sobral BS, 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 PD, Sander C, and Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep;28(9):935-42. DOI:10.1038/nbt.1666 |
2. Ogando DG, Dahlquist KD, Alizadeh M, Kunchithapautham K, Li J, Yu N, LaVail MM, Rohrer B, Vollrath D, and Danciger M. Candidate genes for chromosomes 6 and 10 quantitative trait loci for age-related retinal degeneration in mice. Mol Vis. 2010 Jun 5;16:1004-18.

3. 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 Abstract

4. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, and Pico AR. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007 Jun 24;8:217. DOI:10.1186/1471-2105-8-217 |
5. Dahlquist KD. Using GenMAPP and MAPPFinder to view microarray data on biological pathways and identify global trends in the data. Curr Protoc Bioinformatics. 2004 May;Chapter 7:Unit 7.5. DOI:10.1002/0471250953.bi0705s05 |
6. Segal MR, Dahlquist KD, and Conklin BR. Regression approaches for microarray data analysis. J Comput Biol. 2003;10(6):961-80. DOI:10.1089/106652703322756177 |
7. Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, and Conklin BR. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 2003;4(1):R7. DOI:10.1186/gb-2003-4-1-r7 |
8. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, and Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet. 2002 May;31(1):19-20. DOI:10.1038/ng0502-19 |
9. Dahlquist KD and Puglisi JD. Interaction of translation initiation factor IF1 with the E. coli ribosomal A site. J Mol Biol. 2000 May 26;299(1):1-15. DOI:10.1006/jmbi.2000.3672 |
10. Recht MI, Douthwaite S, Dahlquist KD, and Puglisi JD. Effect of mutations in the A site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction. J Mol Biol. 1999 Feb 12;286(1):33-43. DOI:10.1006/jmbi.1998.2446 |
11. Recht MI, Fourmy D, Blanchard SC, Dahlquist KD, and Puglisi JD. RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. J Mol Biol. 1996 Oct 4;262(4):421-36. DOI:10.1006/jmbi.1996.0526 |
12. Dahlquist K and Puglisi JD. Investigating the structure and function of translation initiation factor 1 in Escherichia coli. Nucleic Acids Symp Ser. 1995(33):170-1.

Useful links

• Introductory tutorial
• OpenWetWare help pages