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Publications in Phylogenomic Methods and Analyses

Phylogenomic inference and key methods

  • Sjölander, K., "Phylogenomic inference of protein molecular function: advances and challenges," Bioinformatics 2004 (20)2:170-179. Oxford University Press access.
  • Sjölander, K , "Phylogenetic inference in protein superfamilies: Analysis of SH2 domains," Proceedings of the Conference Intelligent Systems for Molecular Biology 1998 6:165-74. PubMed abstract. (Presents the BETE algorithm for protein subfamily identification)
  • Brown D, Krishnamurthy N, Dale J, Christopher W, and Sjölander K, "Subfamily HMMs in Functional Genomics", Proceedings of the Pacific Symposium on Biocomputing, 2005. PSB proceedings.
  • Krogh, A., Brown, M., Mian, S., Sjölander, K. and Haussler, D., "Hidden Markov Models in Computational Biology: Applications to Protein Modeling," Journal of Molecular Biology 1994 Feb 4;235(5):1501-31
  • Sjölander, K., Karplus, K., Brown, M.P., Hughey, R., Krogh, A., Mian, I.S., Haussler D., "Dirichlet Mixtures: A Method for Improved Detection of Weak but Significant Protein Sequence Homology," Computing Applications in the Biosciences (CABIOS ) 1996 Aug;12(4):327-45. Oxford Journals Online abstract. Postscript version. PDF version.
  • Karplus, K, Sjölander K , Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C., "Predicting protein structure using hidden Markov models," Proteins: Structure, Function and Genetics, Suppl 1:134-139. 1997. Invited paper for special issue covering the second Critical Assessment for Protein Structure Prediction (CASP) competition. PubMed abstract.

    Structural and phylogenomic analyses of protein families

  • Venter, C. et al, "The sequence of the human genome," Science, 2001 Feb 16;291(5507):1304-51. (My contributions: the algorithms used for the Panther HMM library construction and functional classification of the human genome. (1) FlowerPower clustering and alignment of homologs; (2) Bayesian Evolutionary Tree Estimation and subfamily identification; (3) Subfamily HMM construction.) Science Online access.
  • Kleffmann, T., Russenberger, D., von Zychlinski, A., Christopher, W., Sjölander, K., Gruissem, W., and Baginsky, S. "The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions," Current Biology 2004 Mar 9;14(5):354-62. PubMed Abstract.
  • Magnani, E., Sjölander, K. , and Hake S., "From endonucleases to transcription factors: evolution of the AP2 DNA-binding domain in plants", Plant Cell, 2004 Sep;16(9):2265-77.PubMed Abstract.
  • Rowland O, Ludwig AA, Merrick CJ, Baillieul F, Tracy FE, Durrant WE, Fritz-Laylin L, Nekrasov V, Sjölander K, Yoshioka H, Jones JD. ''Functional Analysis of Avr9/Cf-9 Rapidly Elicited Genes Identifies a Protein Kinase, ACIK1, That Is Essential for Full Cf-9-Dependent Disease Resistance in Tomato'', Plant Cell. Jan;17(1):295-310. 2004 PubMed Abstract.
  • Rebecca Middleton, Kimmen Sjölander, Nandini Krishnamurthy, Jonathan Foley, and Patricia Zambryski, "Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion", Proceedings of the National Academy of Sciences 2005 Feb 1;102(5):1685-90.
  • Stephen T. Chisholm, Douglas Dahlbeck, Nandini Krishnamurthy, Brad Day, Kimmen Sjölander, and Brian J. Staskawicz, "Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2", Proceedings of the National Academy of Sciences, February 8, 2005, vol. 102, no. 6, 2087-2092.
  • Lillian Fritz-Laylin, Nandini Krishamurthy, Mahmut Tor, Kimmen Sjölander and Jonathan Jones. "Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis", Plant Physiology, June 2005, Vol. 138, pp. 611-623.
  • von Zychlinski A, Kleffmann T, Krishnamurthy N, Sjölander K, Baginsky S, Gruissem W., "Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions", Mol Cell Proteomics. PubMed entry. 2005 May 20 (Epub ahead of print).



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