| 2006 | A Parsimony Approach to Genome-Wide Ortholog Assignment. | Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang |
| 2006 | Alignment of Mass Spectrometry Data by Clique Finding and Optimization. | Daniel P. Fasulo, Anne-Katrin Emde, Lu-Yong Wang, Karin Noy, Nathan Edwards |
| 2006 | Conservation Patterns in | Perry Evans, Greg Donahue, Sridhar Hannenhalli |
| 2006 | Structural Alignment of Pseudoknotted RNA. | Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna |
| 2006 | CONTRAlign: Discriminative Training for Protein Sequence Alignment. | Chuong B. Do, Samuel S. Gross, Serafim Batzoglou |
| 2006 | Finding Maximum Likelihood Indel Scenarios. | Abdoulaye Banir Diallo, Vladimir Makarenkov, Mathieu Blanchette |
| 2006 | Maximal Accurate Forests from Distance Matrices. | Constantinos Daskalakis, Cameron Hill, Alexander Jaffe, Radu Mihaescu, Elchanan Mossel, Satish Rao |
| 2006 | Detecting the Dependent Evolution of Biosequences. | Jeremy Darot, Chen-Hsiang Yeang, David Haussler |
| 2006 | A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer. | Mikls Csrs, Istvn Mikls |
| 2006 | Intron Loss Dynamics in Mammals. | Jasmin Coulombe-Huntington, Jacek Majewski |
| 2006 | Biological Networks: Comparison, Conservation, and Evolutionary Trees. | Benny Chor, Tamir Tuller |
| 2006 | Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation. | Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe |
| 2006 | Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. | Chakra Chennubhotla, Ivet Bahar |
| 2006 | Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. | Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki |
| 2006 | Clustering Near-Identical Sequences for Fast Homology Search. | Michael Cameron, Yaniv Bernstein, Hugh E. Williams |
| 2006 | Inferring Positional Homologs with Common Intervals of Sequences. | Guillaume Blin, Annie Chateau, Cdric Chauve, Yannick Gingras |
| 2006 | Inferring Gene Orders from Gene Maps Using the Breakpoint Distance. | Guillaume Blin, Eric Blais, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk |
| 2006 | Evolution of Tandemly Repeated Sequences Through Duplication and Inversion. | Denis Bertrand, Mathieu Lajoie, Nadia El-Mabrouk, Olivier Gascuel |
| 2006 | Reconstructing Domain Compositions of Ancestral Multi-domain Proteins. | Behshad Behzadi, Martin Vingron |
| 2006 | Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps. | Nilanjana Banerjee, Andrea Califano |
| 2006 | A New Approach to Protein Identification. | Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel A. Pevzner |
| 2006 | Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. | Martin Bader, Enno Ohlebusch |
| 2006 | How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation. | Sbastien Angibaud, Guillaume Fertin, Irena Rusu, Stphane Vialette |
| 2006 | Efficient Enumeration of Phylogenetically Informative Substrings. | Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim |
| 2006 | Motif Yggdrasil: Sampling from a Tree Mixture Model. | Samuel A. Andersson, Jens Lagergren |