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Peer-reviewed Research

  • Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., and Wanner, N.C. (2015) Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457-1492, published online September 29, 2015. DOI: 10.1007/s11538-015-0092-6. 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. 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.