Journal articles

(*) corresponding author
  • Bilal E, Dutkowski J (co-first author), Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, et al. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Computational Biology, In press.
  • Dutkowski J*, Kramer M, Surma, MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T* . A gene ontology inferred from molecular networks. Nature Biotechnology. Advance online publication December 16, 2012 (doi:10.1038/nbt.2463). Pubmed Journal
  • Dutkowski J*, Ideker T*. Protein networks as logic functions in development and cancer. PLoS Computational Biology. 2011. 7(9): e1002180. Pubmed Journal
  • Ideker T*, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power, Cell. 2011. 144(6):860-863. PubMed Journal
  • Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C*. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors, Immunity. 2011. 35(3):413-25. PubMed Journal
  • Bandyopadhyay S, Mehta M, Kuo D, Sung M, Chuang R, Jaehnig E, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum, H, Shokat K, Kolodner RD, Huh W, Aebersold R, Keogh MC, Krogan NJ, Ideker T*. Rewiring of genetic networks in response to DNA damage. Science. 2010; 330:1385-1389. PubMed Journal
  • Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C*. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 2010 Jul;11(7):635-43. PubMed Journal
  • Woźniak M, Tiuryn J, Dutkowski J*. MODEVO: exploring modularity and evolution of protein interaction networks. Bioinformatics. 2010; 26(14):1790-1. PubMed Journal
  • Dutkowski J*, Tiuryn J. Phylogeny-guided interaction mapping in seven eukaryotes. BMC Bioinformatics. 2009;10:393. PubMed Journal
  • Gambin A*, Szczurek E, Dutkowski J, Bakun M, Dadlez M. Classification of peptide mass fingerprint data by novel no-regret boosting method. Comput Biol Med. 39(5):460-73, 2009. PubMed Journal
  • Dutkowski J*, Tiuryn J. Identification of functional modules from conserved ancestral protein-protein interactions, Bioinformatics 2007 23: i149-i158, proceedings of ISMB/ECCB 2007. PubMed Journal
  • Dutkowski J*, Gambin A*. On consensus biomarker selection, BMC Bioinformatics 2007, 8(Suppl 5):S5. PubMed Journal
  • Gambin A*, Dutkowski J , Karczmarski J, Kluge B, Kowalczyk K, Ostrowski J, Poznański J, Tiuryn J, Bakun M, Dadlez M. Automated reduction and interpretation of multidimensional mass spectra for analysis of complex peptide mixtures, International Journal of Mass Spectrometry, 2007, 260:20-30. Journal