Michael Krauthammer

Associate Professor of Pathology

My research is in biomedical informatics/computational biology. Analyzing Omics data to unravel the molecular basis of disease (focus:skin cancer), and to identify diagnostic and predictive biomarkers. Using natural language processing (NLP) techniques to extract problem-specific information from scientific articles or medical reports.

Department of Pathology

Yale University School of Medicine
P.O. Box 208023
310 Cedar Street, LH 219
New Haven, CT 06520-8023

Office: (203) 737-1233


Fax: (203) 785-3644

email: michael.krauthammer@yale.edu


  • MD, Medical Faculty, University of Zurich, Switzerland, 1995
  • PhD (Biomedical Informatics) Columbia University, NY, 2003


  • Molecular interaction networks: computational analysis, pathway discovery, knowledge representation.
  • Statistical modeling and analysis. Text mining in biology: term identification, information extraction.

Selected Publications:

  • Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A. Molecular Triangulation: Bridging Linkage and Molecular-Network Information for Identifying Candidate Genes in Alzheimer’s Disease. Proc Natl Acad Sci USA. 2004.2004 Oct 19;101(42):15148-53.
  • Krauthammer M. and Nenadic G. Term Identification in the Biomedical Literature. J Biomed Inform. 2004 Dec; 37(6):512-526.
  • Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboue PA, Weng W, Wilbur WJ, Hatzivassiloglou V, Friedman C. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 2004 Feb;37(1):43-53.
  • Iossifov I, Krauthammer M, Friedman C, Hatzivassiloglou V, Bader JS, White KP, Rzhetsky A. Probabilistic inference of molecular networks from noisy data sources. Bioinformatics. 2004 May 22;20(8):1205-13.
  • Krauthammer M, Kra P, Iossifov I, Gomez SM, Hripcsak G, Hatzivassiloglou V, Friedman C, Rzhetsky A. Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics. 2002;18 Suppl 1:S249-57.
  • Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics. 2001;17 Suppl 1:S74-82.
  • Rzhetsky A, Koike T, Kalachikov S, Gomez SM, Krauthammer M, Kaplan SH, Kra P, Russo JJ, Friedman C. A knowledge model for analysis and simulation of regulatory networks. Bioinformatics. 2000 Dec;16(12):1120-8.
  • Krauthammer M, Rzhetsky A, Morozov P, Friedman C. Using BLAST for identifying gene and protein names in journal articles. Gene. 2000 Dec 23;259(1-2):245-52.

Comments are closed.