Reading List

March 27, 2008

I’ve been traveling a lot lately … hence the relative silence. While gone I’ve focused on implementing some computational techniques. Consequently, I’ve fallen behind on reading. Here is a short (not comprehensive) list of some of the interesting papers have been published recently:

  • Li, X., MacArthur, S., Bourgon, R., Nix, D., Pollard, D.A., Iyer, V.N., Hechmer, A., Simirenko, L., Stapleton, M., Hendriks, C.L., Chu, H.C., Ogawa, N., Inwood, W., Sementchenko, V., Beaton, A., Weiszmann, R., Celniker, S.E., Knowles, D.W., Gingeras, T., Speed, T.P., Eisen, M.B., Biggin, M.D. (2008). Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm . PLoS Biology, 6(2), e27. DOI: 10.1371/journal.pbio.0060027
  • Tuch, B.B., Galgoczy, D.J., Hernday, A.D., Li, H., Johnson, A.D. (2008). The Evolution of Combinatorial Gene Regulation in Fungi. PLoS Biology, 6(2), e38. DOI: 10.1371/journal.pbio.0060038
  • Gruber, A.R., Bernhart, S.H., Hofacker, I.L., Washietl, S. (2008). Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics, 9(1), 122. DOI: 10.1186/1471-2105-9-122
  • Margulies, E.H., Birney, E. (2008). Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. Nature Reviews Genetics, 9(4), 303-313. DOI: 10.1038/nrg2185
  • Suthram, S., Beyer, A., Karp, R.M., Eldar, Y., Ideker, T. (2008). eQED: an efficient method for interpreting eQTL associations using protein networks. Molecular Systems Biology, 4 DOI: 10.1038/msb.2008.4
  • Shivaswamy, S., Bhinge, A., Zhao, Y., Jones, S., Hirst, M., Iyer, V.R. (2008). Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation. PLoS Biology, 6(3), e65. DOI: 10.1371/journal.pbio.0060065

Time to get back to the literature, so I should be posting more soon …


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