Program

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AFP 2006 Program

Day 1
	Opening remarks
	Keynote1	Adam Godzik, Burnham Institute for Medical Research and the	TBA
	Talk 1	Fenglou Mao, Hongwei Wu, and Ying Xu	High-Resolution Functional Assignments of Genes through Mapping KEGG Pathways to Bacterial Genomes
	Talk 2	Hon Nian Chua, Wing-Kin Sung, Limsoon Wong	Guilt by Indirect Functional Association	Slides
	Break
	Keynote 2	Christos Ouzounis, European Bioinformatics Institute	CorrIE: probabilistic proteins sequence annotation based on functional classifications
	Talk 3	Jason Li, S. K. Halgamuge, Sen-Lin Tang	Gene function prediction based on synteny and discriminative learning
	Talk 4	Julie D.Thompson, Odile Lecompte, Arnaud Muller, Emmanuel Perrodou, Andrew Waterhouse, Jim Procter, Geoffrey J. Barton, Frédéric Plewniak, Patrice Koehl, and Olivier Poch	Proteome annotation with MACSIMS (Multiple Alignment of Complete Sequences Information Management System)
	Lunch
	Keynote 3	Steven E. Brenner, University of California, Berkeley	Problems and Proposals in Protein Molecular Function Prediction
	Talk 5	Barbara E. Engelhardt, Michael I. Jordan, Steven E. Brenner	SIFTER: a Model of Molecular Function Evolution to Predict Protein Function
	Talk 6	Sayaka Mizutani, Shawn Cokus, Matteo Pellegrini	An Improved Method for Identifying Functionally Linked Proteins Using Phylogenetic Profiles	Slides
	Break
	talk 7	Kimmen Sjölander, Dan Kirshner, Nandini Krishnamurthy and Duncan Brown	Structural Phylogenomic Analysis: New Methods and Challenges
	talk 8	Ryosuke Watanabe, Edgar Vallejo, Enrique Morett	Inferring Functional Coupling of Genes from Phylogenetic Profiles using the Bond Energy Algorithm	Slides
	Keynote 4	Russ B. Altman,	Clustering Protein Microenvironments for Automated Function Prediction
	poster session

Day 2
	Keynote 5	Anna Tramontano, , La Sapienza	Revisiting Function Prediction at CASP
	Talk 9	Guy Nimrod, Nir Ben-Tal	Identification of DNA-binding Proteins Based on the Projection of Evolutionary Conservation on their Structures: Progress Report	Slides
	Talk 10	Funkhouser T, Laskowski R, Thornton J	Protein Function Prediction by Matching Volumetric Models of Active Sites
	Talk 11	Eunseog Youn, Predrag Radivojac, Brandon Peters, Charles Moad, Randy Heiland, Sean D. Mooney	Supervised Classification of Enzyme Residue Function using Machine Learning Methods
	Break
	Keynote 6	Shoshana Wodak, University of toronto, Canada	Identifying meaningful functional modules in the yeast protein protein interaction network
	Talk 12	Andreas Henschel, Christof Winter, Wan Kyu Kim and Michael Schroeder	Function and Interaction Prediction Using Multiple Motif Descriptors for Classified Domain-Domain interactions and ligand binding sites.
	talk 13	T. M. Murali	Hierarchically Consistent Prediction of Gene Function
	Lunch
	Keynote 7	Terry Gaasterland, Scripps Institute of Oceanography	Function Prediction in the RNA World
	talk 14	Jian Qiu, Martial , Asa Ben-Hur, Jean-Philippe Vert, William Stafford Noble	Kernels for Protein Structures
	talk 15	Ie, Iain Melvin a, Rui Kuang, Jason Weston, William Stafford Noble, Christina Leslie	Multi-Class Protein Classification using Adaptive Codes	Slides
	Break
	Discussion Panel	Keynote Speakers
	Banquet

Day 3
	Keynote 8	Philip Bourne, University of California, San Diego	Novel Ways to Think about Protein Structure and its Impact on Function Prediction
	Talk 16	Lei Xie, Philip E. Bourne	A Robust and Efficient Algorithm for Geometrical Characterizations of Protein Structures and Its applications in Studying Protein-Ligand Interactions	Slides
	Talk 17	Andrea Rossi, Fatima Al-Shahrour, Fred P. Davis, Ursula Pieper, Joaqu�Dopazo, Andrej Sali and Marc A. Marti-Renom	The AnnoLite Program for Rapid and Reliable Comparative Annotation of Protein Structures	Slides
	Break
	Talk 18	Tsai-Tien Tseng, Milton H. Saier Jr.	Voltage-gated Ion Channels and Auxiliary Subunits in the Transport Classification System
	Talk 19	Bill Chang, Glyn Roberts, Jo-Ming Ong, Saman Halgamuge and Nalin Wickramarachchi	Protein Motif Discovery with Particle Swarm Algorithm
	Concluding remarks