Publications
Peer-reviewed Research
(*indicates undergraduate co-author)Eaton, C.D., Callendar, H.L., Dahlquist, K.D., LaMar, M.D., Ledder, G., Schugart, R.C. (2019) A “Rule of Five” Framework for Models and Modeling to Unify Mathematicians and Biologists and Improve Student Learning. PRIMUS: Problems, Resources, and Issues in Mathematics Undergraduate Studies, published online 12 March 2019. DOI: 10.1080/10511970.2018.1489318. [Full Text]
Dahlquist, K.D., Dionisio, J.D.N., Libeskand-Hadas, R., Bargagliotti, A.E. (2018) Breaking Boundaries in Computing in Undergraduate Courses, Journal of Research in STEM Education 4: 81-100. [PDF]
Dahlquist, K.D., Dionisio, J.D.N., Fitzpatrick, B.G., Anguiano, N.A.*, Varshneya, A.*, Southwick, B.J.*, Samdarshi, M.* (2016) GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks. PeerJ Computer Science 2:e85. DOI: 10.7717/peerj-cs.85. [Full Text] [PDF]
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. [PubMed][Full Text][PDF] [Supplementary Materials]
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. DOI: 10.1038/nbt.1666. [PubMed] [Full Text] [Corrigendum]
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. [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. DOI: 10.1145/1383602.1383648. [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. DOI: 10.1186/1471-2105-8-217. [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. DOI: 10.1186/gb-2003-4-1-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. DOI: 10.1089/106652703322756177. [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. DOI: 10.1038/ng0502-19. [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. DOI: 10.1006/jmbi.2000.3672. [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. DOI: 10.1006/jmbi.1998.2446. [PubMed] [Full Text] [PDF]
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. DOI: 10.1006/jmbi.1996.0526. [PubMed] [Publisher Site] [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 [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. [PubMed]
Preprints and Under Review
Dahlquist, K.D., Aikens, M.L., Dauer, J.T., Donovan, S.S., Eaton, C.D., Highlander, H.C., Jenkins, K.P., Jungck, J.R., LaMar, M.D., Ledder, G., Mayes, R.L., Schugart, R.C. (2017) An Invitation to Modeling: Building a Community with Shared Explicit Practices, submitted to CBE—Life Sciences Education on 25 August, 2017, under revision. Available at PeerJ Preprints 5:e3215v1 https://doi.org/10.7287/peerj.preprints.3215v1.
Slides and Posters
Slides and posters about GRNsight can be found on the GRNsight Publications or SlideShare page.
Slides and posters about GRNmap can be found on the GRNmap Publications page.
Last modified: 3/13/19