Publications

  • Mattia Pelizzola, Yasua Koga, Alexander Eckerhart Urban, Michael Krauthammer, Sherman Weissman, Ruth Halaban, Annette M. Molinaro. MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Genome Research (2008). To appear.
  • Songhua Xu, James McCusker, Michael Krauthammer. Yale Image Finder (YIF): a new search engine for retrieving biomedical images. Bioinformatics. Advance access July 9 2008
  • Leitner F., Krallinger M., Rodriguez-Penagos C., Hakenberg J., Plake C., Kuo C., Hsu C., Tasi R., Hung H., Lau W., Johnson C., Sætre R., Yoshida K., Chen Y., Kim S., Shin S., Zhang B., Baumgartner W., Hunter L., Haddow B., Matthew M., Wang X., Ruch P., Ehrler F., Özgür F., Erkan G., Radev D., Krauthammer M., Luong T., Hoffmann R., Sander C., Valencia A.: Introducing Meta-Services for Biomedical Information Extraction. Genome Biology (2008). To appear.
  • Morgan A., Lu Z., Wang X., Cohen A., Fluck J., Ruch P., Divoli A., Fundel K., Leaman R., Hakenberg J., Sun C., Liu H., Torres R., Krauthammer M., Lau W., Liu H., Hsu C., Schuemie M., Hirschman L.: Overview of BioCreative II Gene Normalization. Genome Biology, Special Issue on BioCreative Challenge Evaluation (2008). To appear.
  • Luong T, Tran N, Krauthammer M: Context-Aware Mapping of Gene Names using Trigrams. Proceedings of the Second BioCreative Challenge Evaluation Workshop; 2007; Madrid, Spain. 2007:145-148.
  • Tran N., Luong T., Krauthammer M. Mapping Terms to UMLS Concepts of the Same Semantic Type. AMIA Annu Symp. Proc. 2007.
  • Smith A, Cheung K, Krauthammer M, Schultz M, Gerstein M. Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Bioinformatics. 2007 Nov 15;23(22):3073-9. (PMID: 17923450)
  • Nielsen DA, Leidner M, Haynes C, Krauthammer M, Kreek MJ. The BiolAD-DB system : an informatics system for clinical and genetic data. Mol Diagn Ther. 2007;11(1):15-9. (PMID: 17286447)
  • Gelernter J, Panhuysen C, Weiss R, Brady K, Poling J, Krauthammer M, Farrer L, Kranzler HR. Genomewide linkage scan for nicotine dependence: identification of a chromosome 5 risk locus. Biol Psychiatry. 2007 Jan 1;61(1):119-26 (PMID:  17081504)
  • Peak H., Kogan Y, Prem T, Codish S, Krauthammer M. Shallow Semantic Parsing of Randomized Controlled Trial Reports. 2006. AMIA Annu Symp. Proc. 2006: 604-608.  (PMID: 17238412)
  • Cheung K, Pi Q. Tuck D, Krauthammer M. A semantic web approach to biological pathway data reasoning and integration. Journal of Web Semantics. 2006. 4(3): 207-215
  • Kogan Y, Collier N, Pakhomov S, Krauthammer M. Towards Semantic Role Labeling & IE in the Medical Literature. AMIA Annu Symp Proc. 2005; 410-4. (PMID:  16779072)
  • 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 Oct 19:101(42):15148-15153.  (PMID:  15471992)
  • Krauthammer M. and Nenadic G. Term Identification in the Biomedical Literature. J Biomed Inform. 2004. 37(6):512-26. (PMID:  15542023)
  • 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.  (PMID:  14871876)
  • 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. (PMID:  15016385)
  • Johnson SB, Campbell DA, Krauthammer M, Tulipano PK, Medonca EA, Friedman C, Hripcsak G.  A Native XML Database Design for Clinical Document Research. Proc AMIA Symp. 2003;:883.  (PMID:  14728388)
  • 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. (PMID:  12169554)
  • Krauthammer M, Johnson SB, Hripcsak G, Campbell DA, Friedman C.  Representing nested semantic information in a linear string of text using XML. Proc AMIA Symp. 2002; 405-9.  (PMID:  12463856)
  • Krauthammer M, Hripcsak G.  A knowledge model for the interpretation and visualization of NLP-parsed discharged summaries. Proc AMIA Symp. 2001; 339-43. (PMID:  11825207)
  • 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.  (PMID:  11472995)
  • 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.   (PMID:  11163982)
  • 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.  (PMID:  11159331)