| 2006 | RNA Secondary Structure Prediction Via Energy Density Minimization. | Can Alkan, Emre Karako, Sleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler |
| 2006 | 10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB). | Sarah J. Aerni, Eleazar Eskin |
| 2006 | Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution. | Zaky Adam, Monique Turmel, Claude Lemieux, David Sankoff |
| 2005 | Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations. | Elena Zotenko, Katia S. Guimares, Raja Jothi, Teresa M. Przytycka |
| 2005 | A High-Throughput Approach for Associating microRNAs with Their Activity Conditions. | Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini |
| 2005 | Computational Characterization and Identification of Core Promoters of MicroRNA Genes in | Xuefeng Zhou, Jianhua Ruan, Guandong Wang, Weixiong Zhang |
| 2005 | Modeling the Combinatorial Functions of Multiple Transcription Factors. | Chen-Hsiang Yeang, Tommi S. Jaakkola |
| 2005 | Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions. | Chen Yanover, Tomer Hertz |
| 2005 | Rapid Protein Side-Chain Packing via Tree Decomposition. | Jinbo Xu |
| 2005 | An Interactive Map of Regulatory Networks of | Weihui Wu, Yongling Song, Shouguang Jin, Su-Shing Chen |
| 2005 | RIBRA-An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem. | Kuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung, Wen-Lian Hsu |
| 2005 | Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements. | Guandong Wang, Weixiong Zhang |
| 2005 | An Interaction-Dependent Model for Transcription Factor Binding. | Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli |
| 2005 | Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties. | Huiquan Wang, Craig J. Benham |
| 2005 | A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search. | Yunhu Wan, Ting Chen |
| 2005 | Alignment of Optical Maps. | Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman |
| 2005 | Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences. | Sing-Hoi Sze, Xiaoyan Zhao |
| 2005 | A Polynomial Time Solvable Formulation of Multiple Sequence Alignment. | Sing-Hoi Sze, Yue Lu, Qingwu Yang |
| 2005 | A Framework for Orthology Assignment from Gene Rearrangement Data. | Krister M. Swenson, Nicholas D. Pattengale, Bernard M. E. Moret |
| 2005 | Comparison of Protein-Protein Interaction Confidence Assignment Schemes. | Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker |
| 2005 | Learning Interpretable SVMs for Biological Sequence Classification. | Sren Sonnenburg, Gunnar Rtsch, Christin Schfer |
| 2005 | Recognition of Binding Patterns Common to a Set of Protein Structures. | Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson |
| 2005 | Very Low Power to Detect Asymmetric Divergence of Duplicated Genes. | Cathal Seoighe, Konrad Scheffler |
| 2005 | Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. | Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan |
| 2005 | Reversals of Fortune. | David Sankoff, Chunfang Zheng, Aleksander Lenert |