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Last update 06/20/05

Ronald Jansen

Publications

  1. Lin, N., Wu, B., Jansen, R., Gerstein, M., Zhao, H.: Information assessment on predicting protein-protein interactions. BMC Bioinformatics 18 (2004) 154. [Pubmed][PDF]

  2. Jansen, R., Gerstein, M.: Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Current Opinion in Microbiology 7 (2004) 535-545. [Pubmed][PDF][Supplementary website]

  3. Xia, Y., Yu, H., Jansen, R.*, Seringhaus, M., Baxter, S., Greenbaum, D., Zhao, H. and Gerstein, M.: Analyzing cellular biochemistry in terms of molecular networks. Annual Review of Biochemistry 73 (2004) 1051-1087. [Pubmed][PDF]

  4. Krebs, W., Tsai, J., Alexandrov, V., Echols, N., Junker, J., Jansen, R. and Gerstein, M.: Studying protein flexibility in a statistical framework: Tools and databases for analyzing structures and approaches for mapping onto sequences. Methods in Enzymology 374 (2003) 544-584. [Pubmed][PDF]

  5. Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N., Chung, S., Emili, A., Snyder, M., Greenblatt, J. and Gerstein, M.: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302 (2003) 449-453. [Pubmed][PDF][Supplementary website]

  6. Jansen, R., Bussemaker, H. and Gerstein, M.: Revisiting the codon adaptation index from a whole-genome perspective: Analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Research 31 (2003). 2242-2251. [Pubmed][PDF]

  7. Lan, N., Jansen, R. and Gerstein, M.: Towards a systematic definition of protein function that scales to the genome level: Defining function in terms of interactions. Proceedings of the IEEE 90 (2002). 1848-1858. [PDF]

  8. Mateos, A., Dopazo, J., Jansen, R., Tu, Y., Gerstein, M. and Stolovitzky, G.: Systematic learning of gene functional classes from DNA array expression data by using multi-layer perceptrons. Genome Research 12 (2002). 1703-1715. [Pubmed][PDF]

  9. Edwards, A., Kus, B., Jansen, R., Greenbaum, D., Greenblatt, J. and Gerstein, M.: Bridging structural biology and genomics: Assessing genome-wide protein-protein interaction datasets using the structures of known protein complexes. Trends in Genetics 18 (2002). 529-536. [Pubmed][PDF]

  10. Jansen, R., Lan, N., Qian, J. and Gerstein, M.: Integration of genomic datasets to predict protein complexes in yeast. Journal of Structural and Functional Genomics 2 (2002) 712-718. [Pubmed][PDF]

  11. Greenbaum, D., Jansen, R.* and Gerstein, M.: Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 18 (2002). 585-596. [Pubmed][PDF]

  12. Kumar, A., Agarwal, S., Heyman, J., Matson, S., Heidtman, M., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R., Liu, Y., Cheung, K., Miller, P., Gerstein, M., Roeder, G.S. and Snyder, M.: Subcellular localization of the yeast proteome. Genes and Development 16 (2002). 707-719. [Pubmed][PDF]

  13. Gerstein, M., Lan, N. and Jansen, R.: Proteomics. Integrating interactomes. Science 295 (2002). 284-287. [Pubmed][PDF]

  14. Jansen, R., Greenbaum, D. and Gerstein, M.: Relating whole-genome expression data with protein-protein interactions. Genome Research 12 (2002). 37-46. [Pubmed][PDF]

  15. Greenbaum, D., Luscombe, N.M., Jansen, R., Qian, J. and Gerstein, M.: Interrelating different types of genomic data, from proteome to secretome. Genome Research 11 (2001). 1463-1468. [Pubmed][PDF]

  16. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., Mitchell, T., Miller, P., Dean, R.A., Gerstein, M. and Snyder, M.: Global analysis of protein activities using proteome chips. Science 293 (2001). 2101-2105. [Pubmed][PDF]

  17. Qian, J., Stenger, B., Wilson, C.A., Lin, J., Jansen, R., Teichmann, S.A., Park, J., Krebs, W.G., Yu, H., Alexandrov, V., Echols, N. and Gerstein, M.: PartsList: A web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Research 29 (2001). 1750-1764. [Pubmed][PDF]

  18. Drawid, A., Jansen, R.* and Gerstein, M.: Genome-wide analysis relating expression level with protein subcellular localization. Trends in Genetics 16 (2000). 426-430. [Pubmed][PDF]

  19. Gerstein, M. and Jansen, R.: The current excitement in bioinformatics-analysis of whole-genome expression data: How does it relate to protein structure and function? Current Opinion in Structural Biology 10 (2000). 574-584. [Pubmed][PDF]

  20. Jansen, R. and Gerstein, M.: Analysis of the yeast transcriptome with structural and functional categories: Characterizing highly expressed proteins. Nucleic Acids Research 28 (2000). 1481-1488. [Pubmed][PDF]

  21. Ross-Macdonald, P., Coelho, P.S., Roemer, T., Agarwal, S., Kumar, A., Jansen, R., Cheung, K.H., Sheehan, A., Symoniatis, D., Umansky, L., Heidtman, M., Nelson, F.K., Iwasaki, H., Hager, K., Gerstein, M., Miller, P., Roeder, G.S. and Snyder, M.: Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402 (1999). 413-418. [Pubmed][PDF]

  22. Gerstein, M., Jansen, R., Johnson, T., Tsai, J. and Krebs, W.: Studying Macromolecular Motions in a Database Framework: From Structure to Sequence. In: Thorpe, M. and Duxbury, P. (Eds.), Rigidity theory and applications, Kluwer Academic/Plenum (1999). 401-442. [PDF]

  23. Jansen, R.: Computational proteomics: Integrating expression data with genome-wide information. Dissertation (2002). Yale University.
* Joint first author

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