1.  Signal Transduction Model Based Functional Module Detection Algorithm for Protein-Protein Interaction Networks, Woochang Hwang, Young-rae Cho, Aidong Zhang and Murali Ramanathan (State University of New York at Buffalo).
2.  Protein Folding Trajectories: Summarization, Event Detection and Consensus Partial Folding Pathway Identification, Hui Yang, Srinivasan Parthasarathy and Duygu Ucar  (Ohio State University).  

1.  Designing and Mining Pathogen Genome Databases: Targets for Drugs, Vaccines and Diagnostics, David Roos, Merriam Professor of Biology & Director, Penn Genomics Institute, University of  Pennsylvania.

1.  Automatic Layout and Visualization of Biclusters, Gregory A. Grothaus, Adeel Mufti and T. M. Murali (Virginia Polytechnic Institute and State University).  

1.  Deciphering Gene Regulatory Networks by in silico approaches, Sridhar Hannenhalli, Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania.
2. Biological processes are controlled at various levels in the cell and while these mechanisms are poorly understood, transcriptional control is widely recognized as an important component and a better understanding of which will provide an efficient means for the therapeutic intervention in disease processes. We have been focusing on various computational problems pertaining to transcriptional regulation, namely, (1) representation and identification of transcription factor binding sites, (2) PolII promoter prediction, (3) Predicting interaction among transcription factors, (4) Transcriptional modeling, i.e. identifying arrangements of TFs that co-regulate a set of transcripts. I will present a brief overview of the computational approaches and challenges as well as a number of applications including transcriptional regulation in memory storage, heart failure, and osteoarthritis.

1.  ExMotif: Efficient Structured Motif Extraction, Yongqiang Zhang and Mohammed Zaki (Rensselaer Polytechnic Institute).
2.  Efficient Search using Hybrid EM for Motif Refinement, Chandan Reddy, Yao-Chung Weng and Hsiao-Dong Chiang (Cornell University).  

1.  Protein Classification using Summaries of Profile-Based Frequency Matrices, Keith Marsolo and Srinivasan Parthasarathy (Ohio State University).