Casimir A. Kulikowski Professor Rutgers University Department of Computer Science Hill Center - Busch Campus Piscataway. NJ 08854 (732) 445-2006 FAX -0537 kulikows@cs.rutgers.edu

Intelligent systems and machine learning in molecular biology

My major areas of research are artificial intelligence. medical informatics. and bioinformatics. In AI. my concentration is on expert problem solving and knowledge representation. pattern recognition. clustering. distributed problem solving and planning. multimodal interfaces and image interpretation. In medical informatics I am working on models for guidelines. on methods of medical decision support. biomedical imaging and predictive data mining. In bioinformatics I am working on structural domain parsing from protein sequence data. scaling. dimensionality reduction. and clustering methods for genomics and proteomics. and drug design.

Selected Publications

Vashist A, Kulikowski CA, Muchnik I. (2007) Ortholog clustering on a multipartite graph.
IEEE/ACM Trans Comput Biol Bioinform. 4(1):17-27.

Hagerty CG, Pickens DS, Chang J, Kulikowski CA, Sonnenberg FA. (2006) Prediction in annotation based guideline encoding. AMIA Annu Symp Proc. 314-8.

Maojo V, Kulikowski CA. (2006) Reflections on biomedical informatics: from cybernetics to genomic medicine and nanomedicine. Stud Health Technol Inform. 124:19-24.

Sonnenberg FA, Hagerty CG, Acharya J, Pickens DS, Kulikowski CA. (2005) Vocabulary requirements for implementing clinical guidelines in an electronic medical record: a case study. AMIA Annu Symp Proc. 709-13.

Kulikowski CA. Stefanelli M. (2004) Medinfo 2004--an opportunity to shape the future of medical informatics together. Methods Inf Med. 43(2):122-3.

Maojo V. Kulikowski CA. (2003) Bioinformatics and medical informatics: collaborations on the road to genomic medicine? J Am Med Inform Assoc. 10(6):515-22.

Kulikowski CA. Muchnik I. Vashist A.. Anghelescu A. Yun H J. Linton E. Messing J. (2001). Multialignment of paralogs for functional annotation: application to the rice genome. Proc. 5th Annual Conf on Computational Genomics . Baltimore. 18.

Kulikowski CA Muchnik I Yun HJ Dayanik AA Zhang D Song Y Montelione GT. (2001). Protein structural domain parsing by consensus reasoning over multiple knowledge sources and methods. Proc. World Congress on Health and Medical Informatics (Medinfo) . 965-969. London.

Chang S Kulikowski CA Dunn SM Levy S (2001). Biomedical Image Skeletonization: A novel method applied to fibrin network structures. Proc. World Congress on Health and Medical Informatics (Medinfo) . 901-905 London.

Ammenwerth E Knaup P Maier C Mludek V Singer R Skonetzki S Wolff A Huax R Kulikowski C (2001). Digital libraries and recent medical informatics research P findings from the IMIA yearbook of medical informatics. Methods of Information in Medicine 40: 163-7.

Xing EP Wolf DM Dubchack I Spengler S Zorn M Muchnik I Kulikowski CA. (2001). Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: A Dynamic programming algorithm for multiple alignment segmentation J. Theor. Biol 212:129-139.

Kulikowski. C.A.. (2000) Artificial Intelligence in Medicine: History. Evolution. and Prospects. in Handbook of Biomedical Engineering (J. Bronzino. ed.). 2nd Edition. pp. 181.1-181.19. CRC and IEEE Press. Boca Raton. FL.