Dahlquist:Publications

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Current revision (16:09, 2 September 2011) (view source)
(commented out biblio tagged stuff and pasted in actual publication list)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
{{Template:Dahlquist}}
{{Template:Dahlquist}}
-
<biblio>
+
=== Peer-reviewed Research ===
-
#Paper1 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 [http://portal.acm.org/citation.cfm?id=1383648&jmp=cit&coll=portal&dl=ACM&CFID=74660743&CFTOKEN=75759974# Abstract]
+
 
-
#Paper2 pmid=17588266
+
* 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]
-
#Paper3 pmid=18428731
+
* 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]
-
#Paper4 pmid=14980020
+
* 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]
-
#Paper5 pmid=12540299
+
* 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]
-
#Paper6 pmid=11984561
+
* 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]
-
#Paper7 pmid=10860719
+
* 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]
-
#Paper8 pmid=9931247
+
* 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]
-
#Paper9 pmid=8893854
+
* 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]
-
#Paper10 pmid=8643361
+
* 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]
-
</biblio>
+
* 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]
 +
 
 +
=== 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]
 +
* 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]
 +
* 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]
 +
* 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.
 +
 
 +
<!--<biblio>
 +
#Paper1 pmid=20829833
 +
#Paper2 pmid=20577653
 +
#Paper3 Dionisio, JDN and Dahlquist, KD ''Improving the Computer Science in Bioinformatics Through Open Source Pedagogy'' ACM SIGCSE Bulletin 2008 Jun; 40(2) 115-9. doi:10.1145/1383602.1383648 [http://portal.acm.org/citation.cfm?id=1383648&jmp=cit&coll=portal&dl=ACM&CFID=74660743&CFTOKEN=75759974# Abstract]
 +
#Paper4 pmid=17588266
 +
#Paper5 pmid=18428731
 +
#Paper6 pmid=14980020
 +
#Paper7 pmid=12540299
 +
#Paper8 pmid=11984561
 +
#Paper9 pmid=10860719
 +
#Paper10 pmid=9931247
 +
#Paper11 pmid=8893854
 +
#Paper12 pmid=8643361
 +
</biblio>-->

Current revision

Image:HeaderBlueBig.gif Home        Research        Protocols        Notebook        People        Publications        Courses        Contact       


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.


Personal tools