D'haeseleer, P. and Scepanovic, R. (1999) Method and apparatus for computing minimum wirelength position (MWP) for cell in cell placement for integrated circuit chip. United States Patent 5,859,781. [link]
D'haeseleer, P. and Boyle, D. B. (1997) Method of cell placement for an integrated circuit chip comprising integrated placement and cell overlap removal. United States Patent 5,619,419. [link]
Scepanovic, R. and D'haeseleer, P. (1997) Optimal pad location method for microelectronic circuit cell placement. United States Patent 5,638,293. [link]
Segre, D., Zucker, J., Katz, J., Lin, X., D'haeseleer, P., Rindone, W., Karchenko, P., Nguyen, D., Wright, M., and Church, G.M. (2003) From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics 7:301-16. [link] [pdf]
Steffen, M., Petti, A., D'haeseleer, P., Aach, J., and Church, G.M. (2002) Automated Modeling of Signal Transduction Networks. BMC Bioinformatics 3:34-44. [link] [pdf]
D'haeseleer, P., Liang, S. , and Somogyi, R. (2000) Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering. Bioinformatics 16(8):707-26. [link] [pdf]
D'haeseleer, P. and Church, G.M. (2003) Estimating and improving protein interaction error rates. To appear in IEEE Computer Society Bioinformatics Conference. [doc]
D'haeseleer, P., Wen, X., Fuhrman, S., and Somogyi, R. (1999) Linear modeling of mRNA expression levels during CNS development and injury. In Pacific Symposium on Biocomputing '99. World Scientific Publishing Co., pp. 41-52. [ps]
D'haeseleer, P., Wen, X., Fuhrman, S., and Somogyi, R. (1998) Mining the gene expression matrix: Inferring gene relationships from large scale gene expression data. In Information Processing in Cells and Tissues. Paton, R.C., and Holcombe, M. Eds. Plenum Publishing, pp. 203-212. [link]
D'haeseleer, P. (1996) An Immunological Approach to Change Detection: Theoretical Results. In Proceedings of the 9th IEEE Computer Security Foundations Workshop. IEEE Computer Society Press. [ps]
D'haeseleer, P., Forrest, S. and Helman, P. (1996) An Immunological Approach to Change Detection: Algorithms, Analysis and Implications. In Proceedings of the IEEE Symposium on Security and Privacy. IEEE Computer Society Press. [ps]
D'haeseleer, P. and Bluming, J. (1994) Effects of Locality in Individual and Population Evolution. In Advances in Genetic Programming, K.E. Kinnear Jr. Ed., Cambridge MA, MIT Press.
D'haeseleer, P. (1994) Context Preserving Crossover in Genetic Programming. In Proceedings of 1st IEEE Conference on Evolutionary Computation. IEEE Press.
D'haeseleer, P. (2000) Reconstructing Gene Networks from Large Scale Gene Expression Data. Ph.D. dissertation, University of New Mexico, Albuquerque, NM.
D'haeseleer, P. and De Backer, W. (1991) Neuraal Netwerk voor Schriftherkenning (Neural Network for Optical Character Recognition). Thesis work RUG, Ghent Belgium.
D'haeseleer, P. and Moreau, P. (1988) Digitaliseren en Verwerken van Video Beelden (Digitizing and Processing of Video Images). Thesis work KIHO, Ghent Belgium.
Fuhrman, S., D'haeseleer, P. and Somogyi, R. (1999) Tracing genetic information flow from gene expression to pathways and molecular networks. In DNA microarrays: The new frontier in gene discovery and gene expression analysis. Short course syllabus, Society for Neuroscience.
D'haeseleer, P., Liang, S. , and Somogyi, R. (1999) Gene Expression Analysis and Genetic Network Modeling. Pacific Symposium on Biocomputing '99, Tutorial session on Gene Expression and Genetic Networks.
Chao, D.L. and D'haeseleer P. (2001) The Distribution of Variable-length Phatic Interjectives on the World Wide Web. Technical Report TR-CS-2001-23, The University of New Mexico, Albuquerque, NM. [link] [ps.gz]
D'haeseleer, P. (1995) A change detection method inspired by the immune system: Theory, algorithms and techniques. Technical Report CS95-06. The University of New Mexico, Albuquerque, NM.
D'haeseleer, P. (1995) Further efficient algorithms for generating antibody strings. Technical Report CS95-03. The University of New Mexico, Albuquerque, NM.
Genetic network inference: From co-expression clustering to reverse engineering. University of New Mexico, Department of Biology. April 2000, Albuquerque, NM.
Gene network inference using additive regulation models. University of New Mexico, Department of Neurosciences. February 2000, Albuquerque, NM.
Inferring gene networks from gene expression data: Data requirements and linear models. Los Alamos National Labs, Theoretical Biology and Biophysics group. December 1999, Los Alamos, NM
Gene network inference using additive regulation models. Short course on microarrays, Society for Neuroscience. October 1999, Miami, FL.
Gene network inference using additive regulation models. Cambridge Healthtech Institute (CHI) conference on Functional Genomics. October 1999, Boston, MA.
Gene network inference using additive regulation models. National Center For Genome Resources. June 1999, Santa Fe, NM.
Additive regulation models for gene network inference. International Busisness Communications (IBC) conference on Gene Expression. May 1999, Berkeley, CA.
Gene network inference. Fred Hutchinson Cancer Research Center/Santa Fe Institute Exchange Meeting: Melding Theoretical and Experimental Biology. May 1999, Seattle, WA.
Gene network inference from large-scale expression data. Monsanto, Plant Genomics and Bioinformatics group. May 1999, St. Louis, MI.
Gene expression data and Continuous models and reverse engineering. Tutorial on Gene Expression and Genetic Networks (joint with Roland Somogyi and Shoudan Liang), Pacific Symposium on Biocomputing (PSB99). January 1999, Mauna Lani, Hawaii, HI.
An immunological approach to distributed network intrusion detection. Recent Advances in Intrusion Detection. September 1998, Louvain-la-Neuve, Belgium.
Gene expression analysis and estimation of information content using Noise-Adjusted PCA. Poster submission, Pacific Symposium on Biocomputing '04.
Linear modeling of mRNA expression levels during CNS development and injury. Pacific Symposium on Biocomputing '99. January 1999, Mauna Lani, Hawaii, HI.
Data requirements for inferring genetic networks from expression data. Poster session, Pacific Symposium on Biocomputing '99. January 1999, Mauna Lani, Hawaii, HI.
Mining the gene expression matrix: Inferring gene relationships from large scale gene expression data. Information Processing in Cells and Tissues. September 1997, Sheffield, UK.
Poster presentation, International Conference on Computational Molecular Biology (RECOMB97). January 1997, Santa Fe, NM.
An immunological approach to change detection: Theoretical results. IEEE Computer Security Foundations Workshop. June 1996, Dromquinna Manor, Kenmare, County Kerry, Ireland.
An immunological approach to change detection: Algorithms, analysis and implications. IEEE Symposium on Security and Privacy. May 1996, Berkeley, CA.
Context preserving crossover in Genetic Programming. 1st IEEE Conference on Evolutionary Computation. June 1994, Orlando, FL.