List of Publications

Faramarz Valafar

 

*      Jon W. Huss III, Camilo Orozco, James Goodale, Chunlei Wu, Serge Batalov, Tim J. Vickers, Faramarz Valafar, Andrew I. Su. A Gene Wiki for Community Annotation of Gene Function. PLoS Biology, 2008, 6(7): e175 http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060175, Impact Factor at time of submission: 14.101

*      J. Wegrzyn, T. Drudge, F. Valafar, and V. Hook. Bioinformatic Analyses of Mammalian 5’-UTR Sequence Properties of mRNAs Predicts Alternative Translation Initiation Sites. BMC Bioinformatics, 2008, 9:232.  http://www.biomedcentral.com/1471-2105/9/232, Impact Factor at time of submission: 4.958

*      G. Hernandez, F. Valafar, W. E. Stumph.  Insect Small Nuclear RNA Gene Promoters Evolve Rapidly yet Retain Conserved Features Involved in Determining Promoter Activity and RNA Polymerase Specificity. Nucleic Acid Research. 35(1): 21-34 2007, Oxford University Press. http://nar.oxfordjournals.org/cgi/content/abstract/35/1/21, Impact Factor at time of submission: 7.552  

*      A. Salim, F. Valafar. Reconstruction of Gene Regulatory Networks from Temporal Microarray Data Using Order Estimation Criteria and Artificial Neural Networks, IEEE World Congress on Computational Intelligence, and International Joint Conference on Neural Networks (IJCNN’06), Vancouver, Canada, July 16-21 2006, 4588-4593. http://www-rohan.sdsu.edu/~faramarz/papers/Salim-Valafar-WCCI2006.pdf

*      L. G. Guerrero, E. Kleinman, M. Quinsay, F. Valafar, F. Gonzales, P. Paolini.  Calcium Pathway Gene Expression Changes Produced by Rosiglitazone in Neonatal Rat Cardiocyte. CSUPERB (California State University Program for Education and Research in Biotechnology) Annual Meeting, San Jose, CA, January 13-15, 2006, 115.

*      L. G. Guerrero, P. Paolini, J. Jiménez, E. Kleinman, M. Quinsay, A. Salim, F. Valafar, G. Gonzales. Gene Profiling of Cardiyocytes in Response to Treatment with an Antibiotic Drug. NIH ABRCMS Annual Symposium, Atlanta, GA November 2-5, 2005.

*      F. Valafar, R. Harris, A. M. Ausin, J. S. Angulo, and T. Impelluso. Scalability of VSTM: A Memory Model and Inter-Processor Communication Perspective. Proceedings of the International Conference on Parallel Distributed Processing Techniques and Applications 2004 (PDPTA’04), Las Vegas, Nevada, June 21-24 2004, 1352-1358.

*      Harris R., A. M. Ausin, J. S. Angulo, F. Valafar, and T. Impelluso. VSTM: Virtual Stress Testing Machine.  Proceedings of the 2004 International Conference on Parallel Distributed Processing Techniques and Applications (PDPTA’04), Las Vegas, Nevada, June 21-24 2004, 1345-1351.

*      Havre, S. L., M. Singhal, B. Gopalan, D. A. Payne, K. R. Klicker, G. R. Keibel, K. J. Auberry, E. G. Stephan, G. Chin, A. L. Corrigan, K. R. Klicker, H. J. Sofia, F. Valafar, and H. Valafar.  Integrating Evolving Tools for Proteomics Research.  Proceedings of the 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’04), Las Vegas, Nevada, June 21-24 2004, 105-110.

*      Peters, C.A. and F. Valafar. Comparison of Three Nonparametric Density Estimation Techniques Using Bayes' Classifier Applied to Microarray Data Analysis. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2003 (METMBS’03), Las Vegas, Nevada, June 23-26 2003, 119-125. (http://www-rohan.sdsu.edu/~faramarz/papers/ME281-Peters-Valafar.pdf)

*      Arora, I. and F. Valafar. Grouping of Partially Methylated Alditol Acetates from GC-EIMS Spectra Using Principal Component Analysis, Non-Parametric Density Estimation and K-Nearest Neighbor Classification. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2003 (METMBS’03), Las Vegas, Nevada, June 23-26 2003, 172-178. (http://www-rohan.sdsu.edu/~faramarz/papers/ME279-Arora-Valafar.pdf)

*      Xu, H. F. Valafar, and M. Vuskovic. Prediction of Sickle Cell Anemia Patient's Response to Hydroxyurea Treatment Using ARTMAP. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2003 (METMBS’03), Las Vegas, Nevada, June 23-26 2003, 502-508. (http://www-rohan.sdsu.edu/~faramarz/papers/ME280-xu-valafar-vuskovic.pdf)

*      Valafar, F.  2002. Invited article: Pattern Recognition Techniques in Microarray Data Analysis: A Survey.  Special Issue Annals of New York Academy of Sciences, Techniques in Bioinformatics and Medical Informatics.  Volume 980, December 2002, 41-64. (http://www-rohan.sdsu.edu/~faramarz/papers/valafar-survey.pdf)   

*      Valafar H., J. H. Prestegard, and F. Valafar 2002.  Datamining Protein Structure Databanks for Crystallization patterns of Proteins. Special Issue Annals of New York Academy of Sciences, Techniques in Bioinformatics and Medical Informatics.    Volume 980, December 2002, 13-22. (http://www-rohan.sdsu.edu/~faramarz/papers/protein-struct-mining.pdf)

*      Li M., B. Wang, Z. Momeni, and F. Valafar. 2002. Pattern Recognition Techniques in Microarray Data Analysis.  Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2002 (METMBS’02), Las Vegas, Nevada, June 24-27 2002, 610-616. (http://rohan.sdsu.edu/~faramarz/papers/prma.pdf). 

*      Valafar, F.  2002. Neural Network Applications in Biological Sequencing. Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2002 (METMBS’02), Las Vegas, Nevada, June 24-27 2002, 617-619 & 623-626. (http://rohan.sdsu.edu/~faramarz/papers/NNreport.pdf)

*      Valafar H. and F. Valafar 2002.  Data Mining and Knowledge Discovery in Proton Nuclear Magnetic Resonance (1H-NMR) Spectra using Frequency Information Transformation (FIT).  Journal of Knowledge Based Systems. Special issue on Knowledge Discovery and Data Mining.  Elsevier publications.  15 (2002) 251-259.

*      Valafar H. and F. Valafar 2001. Knowledge Discovery in 1H-NMR Spectra of Complex Carbohydrates using Frequency Information Transformation (FIT).  Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2001 (METMBS’01), Las Vegas, Nevada, June 25-28 2001.  CSREA press.

*      Valafar H., F. Valafar, and J. Prestegard 2001.  One and Two Dimensional Statistical Data-Mining of Protein Databank for Crystallization Patterns of Proteins.  Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2001 (METMBS’01), Las Vegas, Nevada, June 25-28 2001.  CSREA press.

*      Valafar H., F. Valafar, Alan Darvill, Peter Albersheim, Abdullah Kutlar, Christy Woods, and John Hardin, 2000.  Predicting the effectiveness of Hydroxyurea in Individual Sickle Cell Anemia Patients.  Journal of Artificial Intelligence in Medicine.  18 (2): 133-148 February 2000. (http://rohan.sdsu.edu/~faramarz/papers/SICKLEPAPER.REV16.pdf).

*      Valafar F. and O. Ersoy 2000.  Parallel Probabilistic Self Organizing Hierarchical Neural Networks (PPSHNN).  Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2000 (METMBS’00), Las Vegas, Nevada, June 26-29 2000, pp. 609-614.  CSREA press.

*      Valafar F. 2000.  A Web-based Medical Database with Distributed Data Banks and Distributed Search Engines.  Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2000 (METMBS’00), Las Vegas, Nevada, June 26-29 2000, pp. 665-668.  CSREA press.

*      Valafar F. 2000.  A Parallel Implementation of PPSHNN.  Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2000 (METMBS’00), Las Vegas, Nevada, June 26-29 2000, pp. 699-702.  CSREA press.

*      Valafar F. 2000.  Image segmentation using PPSHNN.  Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2000 (METMBS’00), Las Vegas, Nevada, June 26-29 2000, pp. 737-738.  CSREA press.

*      Valafar H., F. Valafar 2000.  Reduction in the complexity of 1D 1H-NMR spectra by the use of Frequency to Information Transformation.  Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences 2000 (METMBS’00), Las Vegas, Nevada, June 26-29 2000, pp. 207-212.  CSREA press.

*      Valafar F., H. Valafar 1999.  CCRC-Net: An Internet-Based Spectral Database for Complex Carbohydrates, Using Artificial Neural Networks Search Engines.  Trends in Analytical Chemistry, 18 (8) 508-512 August 1999.  (http://www.elsevier.com/homepage/saa/trac/column/ccrc-net.htm)

*      Valafar H., F. Valafar, Identification of 1H-NMR Spectra of N-Linked Oligosaccharides Using Artificial Neural Networks.  21st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Atlanta, Georgia, October 13-16, 1999, proceedings 2, pp. 932 0589-1019.

*      Valafar H., F. Valafar, Prediction of a Patient's Response to Hydroxyurea Treatment Using Artificial Neural Networks. 21st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Atlanta, Georgia, October 13-16, 1999, proceedings 1, pp. 388 0589-1019.

*      Valafar F., H. Valafar, W. S. York.  Identification of 1H-NMR Spectra of Xyloglucan Oligosaccharide: A Comparative Study of Artificial Neural Networks and Bayesian Classification Using Nonparametric Density Estimation. International Conference on Artificial Intelligence 1999 (IC-AI'99), Las Vegas, Nevada, June 28-July 1, 1999.

*      Valafar F., H. Valafar. A Comparative study of Artificial Neural Networks Using Reinforcement learning and Multidimensional Bayesian Classification Using Parzen Density Estimation for Identification of GC-EIMS Spectra of Partially Methylated Alditol Acetates on the World Wide Web. International Conference on Artificial Intelligence 1999 (IC-AI'99), Las Vegas, Nevada, June 28-July 1, 1999.

*      Valafar H., F. Valafar, O. Ersoy. Parallel, Self Organizing, Consensus Neural Networks. International Joint Conference on Neural Networks 1999 (IJCNN’99), Washington D.C., July 10-16, 1999, pp. 1225-1228.

*      Valafar H., F. Valafar, Prediction of a Patient's Response to a Drug Using Artificial Neural Networks. International Joint Conference on Neural Networks 1999 (IJCNN’99), Washington D.C., July 10-16, 1999, pp. 3694-3697.

*      Roushanzamir S., H. Valafar, F. Valafar.  A Comparative Study of Linear and Quadratic Discriminant Classifier Techniques for Variable Selection: A Case Study in Predicting the Effectiveness of Hydroxyurea Treatment of Sickle Cell Anemia. International Joint Conference on Neural Networks 1999 (IJCNN’99), Washington D.C., July 10-16, 1999, pp. 3627-3631.

*      Valafar H., O. Ersoy, F. Valafar 1998.  Parallel Implementation of Distributed Global Optimization (DGO).  Proceedings of the international conference on Parallel Distributed Processing Techniques and Applications 1998 (PDPTA ’98), Las Vegas, Nevada, June 1998, pp. 1782-1787.

*      Valafar H., F. Valafar, L. C. Morris, R. Cherniak 1998.  Artificial Neural Networks in Chemotype Analysis of Cryptococcus neoformans.  Accepted for publication in the proceedings of IEEE International Biomedical Engineering Days 1998 (IBED '98), Istanbul, Turkey, May 20-22 1998, pp. 42-44.

*      Cherniak R., H. Valafar, L. C. Morris, and F. Valafar 1998. Cryptococcus neoformans Chemotyping by Quantitative Analysis of 1H-NMR Spectra of Glucuronoxylomannans Using a Computer Based Artificial Neural Network.  American Society for Microbiology (ASM) Journal of Clinical and Vaccine Immunology, March 1998 5(2): 146-159.

*      Cherniak R., H. Valafar, L. C. Morris, and F. Valafar 1997. Cryptococcus neoformans Chemotyping by Quantitative Analysis of 1H-NMR Spectra of Glucuronoxylomannans Using a Computer Based Neural Network.  American Society for Microbiology (ASM).  97th General Meeting, Miami, Florida, May 4-8, F39 page 266.

*      Valafar, F. and O. K. Ersoy.  1996.  PNS modules for the synthesis of parallel self-organizing hier­archical neural networks.  International Journal of Circuits, Systems, and Signal Processing 15(1): 23-50.

*      Valafar, H., F. Valafar, and O. K. Ersoy.  1996.  Distributed Global Optimization (DGO).  Pro­ceedings of the International Conference on Neural Networks (IEEE-ICNN ’96): Washington, DC, June 2-6, 530a-536.

*      Cherniak R., H. Valafar, L. C. Morris, and F. Valafar 1996.  Invited Talk Titled: Chemotyping of Cryptococcus Neoformans by Analysis of Glucuronoxylomannan.  3rd International Conference on Cryptococcus and Cryptococcosis. Institut Pasteur, Paris, France, September 22-26, 1996.  Paper VII.1 page 129.

*      Valafar, F. and O. K. Ersoy.  1995.  A parallel implementation of backpropagation neural network on MasPar MP-1.  Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA ‘95), Athens, GA, November 3-5, pp. 158-166.

*      Valafar, F., H. Valafar, O. K. Ersoy, and R. J. Schwartz.  1995.  Comparative studies of two neural network architectures for modeling of human speech production.  Proceedings of the Interna­tional Conference on Neural Networks (IEEE-ICNN ’95), Perth, Australia, November 27-De­cember 1, Vol. 4, pp. 2056-2061.

*      Valafar, F. and O. K. Ersoy.  1995.  A Parallel Piecewise-Linear Division of Complex Classifica­tion Space Using PNS Modules.  Technical Report, Purdue University, West Lafayette, IN, Feb­ruary.

*      Valafar, F. and O. K. Ersoy.  1994.  PNS modules for the synthesis of parallel self-organizing hier­archical neural networks.  IEEE International Conference on Circuits and Systems (IEEE-ISCAS ‘94), London, England, May 30-June 2, pp. 335-338 0271-4310.

*      Valafar, F. and O. K. Ersoy.  1994. Parallel Probabilistic Self-Organizing Hierarchical Neural Networks (PPSHNN).  Technical Report, Purdue University, West Lafayette, IN, February.

*      Valafar, F.  1994.  Parallel Probabilistic Self-Organizing Hierarchical Neural Networks (PPSHNN).  Doctoral dissertation, Electrical Engineering Department, Purdue University, West Lafayette, IN, Fall 1994.

*      Valafar, F. and O. K. Ersoy.  1993.  PNS modules for the synthesis of parallel self-organizing hier­archical neural networks.  In:  Intelligent Engineering Systems Through Artificial Neural Networks, Volume 3 (C. Dagli, L. L. Burke, B. R. Fernandez, Eds.) ASME Press, New York, pp. 21-26.  [Also presented at the Conference on Artificial Neural Networks in Engi­neering (ANNIE ’93), Saint Louis, MO].

*      Valafar, F. and O. K. Ersoy.  1993.  A Parallel Implementation of Backpropagation Neural Network on MasPar MP-1.  Technical Report EE93-14, Purdue University, West Lafayette, IN, March.

*      Valafar, F., H. Valafar, O. K. Ersoy, and R. J. Schwartz.  1991.  Comparative Studies of Two Neural Network Architectures for Modeling of Human Speech Production.  Technical Report EE91-42, Purdue University, West Lafayette, IN, October.