| 2008 | TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences Using Suffix Trees. | Benjarath Phoophakdee, Mohammed Javeed Zaki |
| 2008 | A Parametric Joint Model of DNA-Protein Binding, Gene Expression and DNA Sequence Data to Detect Target Genes of a Transcription Factor. | Wei Pan, Peng Wei, Arkady B. Khodursky |
| 2008 | Annotating Pathways of Interaction Networks. | Jayesh Pandey, Mehmet Koyutrk, Wojciech Szpankowski, Ananth Grama |
| 2008 | Analysis of Large-Scale Sequencing of Small RNAs. | Andrew J. Olson, J. Brennecke, A. A. Aravin, G. J. Hannon, Ravi Sachidanandam |
| 2008 | Session Introduction. | Michael F. Ochs, John Quackenbush, Ramana V. Davuluri |
| 2008 | The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis. | Serita M. Nelesen, Kevin Liu, D. Zhao, C. Randal Linder, Tandy J. Warnow |
| 2008 | Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription Factors. | Rachel Patton McCord, Martha L. Bulyk |
| 2008 | Session Introduction. | Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann |
| 2008 | Use of an Evolutionary Model to Provide Evidence for a Wide Heterogenity of Required Affinities Between Transcription Factors and Their Binding Sites in Yeast. | Richard W. Lusk, Michael B. Eisen |
| 2008 | Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular Systems Hemodynamics. | Joost Lumens, Tammo Delhaas, Borut Kirin, Theo Arts |
| 2008 | Analysis of Microrna-Target Interactions by a Target Structure Based Hybridization Model. | Dang D. Long, Chi Yu Chan, Ye Ding |
| 2008 | Prediction of the Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug Design. | Youyong Li, William A. Goddard III |
| 2008 | Session Introduction. | Jung-Chi Liao, Jeff Reinbolt, Roy Kerckhoffs, Anushka Michailova, Peter W. Arzberger |
| 2008 | Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches. | Jae-Hyung Lee, Michael Hamilton, Colin Gleeson, Cornelia Caragea, Peter Zaback, Jeffry D. Sander, Li C. Xue, Feihong Wu, Michael Terribilini, Vasant G. Honavar, Drena Dobbs |
| 2008 | BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition. | Robert Leaman, Graciela Gonzalez |
| 2008 | Local Reliability Measures from Sets of Co-Optimal Multiple Sequence Alignments. | Giddy Landan, Dan Graur |
| 2008 | CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure. | Pei Fen Kuan, Hyonho Chun, Sndz Keles |
| 2008 | Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. | Sun Kim, Meng Li, Hyun-il Henry Paik, Kenneth P. Nephew, Huidong Shi, Robin Kramer, Dong Xu, Tim Hui-Ming Huang |
| 2008 | An Analysis of Information Content Present in Protein-DNA Interactions. | Christopher Kauffman, George Karypis |
| 2008 | Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example. | Yoshinobu Kano, Ngan L. T. Nguyen, Rune Stre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiroh Matsubayashi, Sophia Ananiadou, Jun'ichi Tsujii |
| 2008 | Population Sequencing Using Short Reads: HIV as a Case Study. | Vladimir Jojic, Tomer Hertz, Nebojsa Jojic |
| 2008 | Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes Mellitus. | Haiyan Hu, Xiaoman Shawn Li |
| 2008 | Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. | Jim C. Huang, Brendan J. Frey, Quaid Morris |
| 2008 | Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. | Raluca Gordn, Alexander J. Hartemink |
| 2008 | Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition. | Dariya S. Glazer, Randall J. Radmer, Russ B. Altman |