| 2008 | Summary of the BioLINK Special Interest Group Session on the Future of Scientific Publishing. | Scott Markel |
| 2008 | Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. | Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial |
| 2008 | Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature. | Hongfang Liu, Manabu Torii, Guixian Xu, Zhang-Zhi Hu, Johannes Goll |
| 2008 | Classification and feature selection algorithms for multi-class CGH data. | Jun Liu, Sanjay Ranka, Tamer Kahveci |
| 2008 | Estimating true evolutionary distances under the DCJ model. | Yu Lin, Bernard M. E. Moret |
| 2008 | Alignment and classification of time series gene expression in clinical studies. | Tien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph |
| 2008 | Designing succinct structural alphabets. | Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li |
| 2008 | GenoQuery: a new querying module for functional annotation in a genomic warehouse. | Frdric Lemoine, Bernard Labedan, Christine Froidevaux |
| 2008 | Annotation-based inference of transporter function. | Thomas J. Lee, Ian T. Paulsen, Peter D. Karp |
| 2008 | A robust framework for detecting structural variations in a genome. | Seunghak Lee, Elango Cheran, Michael Brudno |
| 2008 | Combinatorial influence of environmental parameters on transcription factor activity. | Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders |
| 2008 | Detection of IUPAC and IUPAC-like chemical names. | Roman Klinger, Corinna Kolrik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich |
| 2008 | Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. | Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss, William Stafford Noble |
| 2008 | Assessing the functional structure of genomic data. | Curtis Huttenhower, Olga G. Troyanskaya |
| 2008 | Integrating high dimensional bi-directional parsing models for gene mention tagging. | Chun-Nan Hsu, Yu-Ming Chang, Cheng-Ju Kuo, Yu-Shi Lin, Han-Shen Huang, I-Fang Chung |
| 2008 | Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation. | Dimitar Hristovski, Andrej Kastrin, Borut Peterlin, Thomas C. Rindflesch |
| 2008 | Differential variability analysis of gene expression and its application to human diseases. | Joshua Wing Kei Ho, Maurizio Stefani, Cristobal G. dos Remedios, Michael A. Charleston |
| 2008 | Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. | Iman Hajirasouliha, Fereydoun Hormozdiari, Sleyman Cenk Sahinalp, Inan Birol |
| 2008 | Algorithm for backrub motions in protein design. | Ivelin Georgiev, Daniel A. Keedy, Jane S. Richardson, David C. Richardson, Bruce Randall Donald |
| 2008 | A computational framework to empower probabilistic protein design. | Menachem Fromer, Chen Yanover |
| 2008 | Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP. | Andrew D. Fox, William A. Baumgartner Jr., Helen L. Johnson, Lawrence E. Hunter, Donna K. Slonim |
| 2008 | A max-margin model for efficient simultaneous alignment and folding of RNA sequences. | Chuong B. Do, Chuan-Sheng Foo, Serafim Batzoglou |
| 2008 | Identifying functional modules in protein-protein interaction networks: an integrated exact approach. | Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Mller |
| 2008 | Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...). | Robert Denroche, Ramana Madupu, Shibu Yooseph, Granger G. Sutton, Hagit Shatkay |
| 2008 | Inferring differentiation pathways from gene expression. | Ivan G. Costa, Stefan Roepcke, Christoph Hafemeister, Alexander Schliep |