Michael Oliver Krauthammer MD, PhD

Associate Professor of Pathology

Research Interests

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

Research Summary

I conduct research in computational biology and bioinformatics to analyze functional and clinical data linked to human diseases, with a particular focus on skin cancer and mechanisms of substance abuse. Text-mining algorithms are used for extracting molecular and phenotypic data from the research literature to generate models of molecular and clinical processes. Such models guide the identification of disease-related genes or pathways from high-throughput functional data. An important area of research is the mapping of genetic information to molecular interaction networks for pinpointing disease genes in human multifactorial disorders.

Extensive Research Description

Research in biomedical informatics/computational biology. Analyzing molecular networks to identify disease pathways / drug effector pathways for toxicity prediction. Using natural language processing (NLP) techniques to extract problem-specific information from scientific articles or medical reports.

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 19101(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 Feb37(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 2220(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. 200218 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. 200117 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 Dec16(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 23259(1-2):245-52.
  • Gelernter, J., et al. (2007). Genomewide linkage scan for nicotine dependence: identification of a chromosome 5 risk locus. Biol. Psychiatry 61(1):119-26.
  • Cheung, K., Qi, P., Tuck, D., and Krauthammer, M. (2006). A semantic web approach to biological pathway data reasoning and integration. Web Semantics: Science, Services and Agents on the World Wide Web 4(3):207-215.

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