Abstract is missing.
- QNet: A Tool for Querying Protein Interaction NetworksBanu Dost, Tomer Shlomi, Nitin Gupta 0002, Eytan Ruppin, Vineet Bafna, Roded Sharan. 1-15 [doi]
- Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood TopologyRohit Singh, Jinbo Xu, Bonnie Berger. 16-31 [doi]
- Reconstructing the Topology of Protein ComplexesAllister Bernard, David S. Vaughn, Alexander J. Hartemink. 32-46 [doi]
- Network Legos: Building Blocks of Cellular Wiring DiagramsT. M. Murali, Corban G. Rivera. 47-61 [doi]
- An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and ::::in silico:::: Gene Perturbation ExperimentsAbhishek Garg, Ioannis Xenarios, Luis Mendoza, Giovanni De Micheli. 62-76 [doi]
- A Feature-Based Approach to Modeling Protein-DNA InteractionsEilon Sharon, Eran Segal. 77-91 [doi]
- Network Motif Discovery Using Subgraph Enumeration and Symmetry-BreakingJoshua A. Grochow, Manolis Kellis. 92-106 [doi]
- Nucleosome Occupancy Information Improves ::::de novo:::: Motif DiscoveryLeelavati Narlikar, Raluca Gordân, Alexander J. Hartemink. 107-121 [doi]
- Framework for Identifying Common Aberrations in DNA Copy Number DataAmir Ben-Dor, Doron Lipson, Anya Tsalenko, Mark Reimers, Lars O. Baumbusch, Michael T. Barrett, John N. Weinstein, Anne-Lise Børresen-Dale, Zohar Yakhini. 122-136 [doi]
- Estimating Genome-Wide Copy Number Using Allele Specific Mixture ModelsWenyi Wang, Benilton Carvalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry. 137-150 [doi]
- GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH DataYanxin Shi, Fan Guo, Wei Wu, Eric P. Xing. 151-165 [doi]
- Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic ReactionsHiroyuki Kuwahara, Chris J. Myers. 166-180 [doi]
- Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide BindingNoah Zaitlen, Manuel Reyes-Gomez, David Heckerman, Nebojsa Jojic. 181-195 [doi]
- Reconstructing the Phylogeny of Mobile ElementsSean O Rourke, Noah Zaitlen, Nebojsa Jojic, Eleazar Eskin. 196-210 [doi]
- Beyond Galled Trees - Decomposition and Computation of Galled NetworksDaniel H. Huson, Tobias H. Klöpper. 211-225 [doi]
- Variational Upper Bounds for Probabilistic Phylogenetic ModelsYdo Wexler, Dan Geiger. 226-237 [doi]
- Heuristics for the Gene-Duplication Problem: A ::::Theta:::: ( ::::n:::: ) Speed-Up for the Local SearchMukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, André Wehe. 238-252 [doi]
- Support Vector Training of Protein Alignment ModelsChun-Nam John Yu, Thorsten Joachims, Ron Elber, Jaroslaw Pillardy. 253-267 [doi]
- Tools for Simulating and Analyzing RNA Folding KineticsXinyu Tang, Shawna L. Thomas, Lydia Tapia, Nancy M. Amato. 268-282 [doi]
- Multiple Sequence Alignment Based on Profile Alignment of Intermediate SequencesYue Lu, Sing-Hoi Sze. 283-295 [doi]
- Connectedness Profiles in Protein Networks for the Analysis of Gene Expression DataJoël R. Pradines, Vlado Dancík, Alan Ruttenberg, Victor Farutin. 296-310 [doi]
- Multivariate Segmentation in the Analysis of Transcription Tiling Array DataAntonio Piccolboni. 311-324 [doi]
- A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein MeasurementsAnitha Kannan, Andrew Emili, Brendan J. Frey. 325-338 [doi]
- Rearrangements in Genomes with Centromeres Part I: TranslocationsMichal Ozery-Flato, Ron Shamir. 339-353 [doi]
- Identification of Deletion Polymorphisms from HaplotypesErik Corona, Benjamin J. Raphael, Eleazar Eskin. 354-365 [doi]
- Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief PropagationHetunandan Kamisetty, Eric P. Xing, Christopher James Langmead. 366-380 [doi]
- Minimizing and Learning Energy Functions for Side-Chain PredictionChen Yanover, Ora Schueler-Furman, Yair Weiss. 381-395 [doi]
- Protein Conformational Flexibility Analysis with Noisy DataAnshul Nigham, David Hsu. 396-411 [doi]
- Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like MoleculesYuval Inbar, Dina Schneidman-Duhovny, Oranit Dror, Ruth Nussinov, Haim J. Wolfson. 412-429 [doi]
- Design of Compact, Universal DNA Microarrays for Protein Binding Microarray ExperimentsAnthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger, Martha L. Bulyk. 430-443 [doi]
- Improved Ranking Functions for Protein and Modification-Site IdentificationsMarshall W. Bern, David Goldberg. 444-458 [doi]
- Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography ConditionsAaron A. Klammer, Xianhua Yi, Michael J. MacCoss, William Stafford Noble. 459-472 [doi]
- A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry DataOle Schulz-Trieglaff, Rene Hussong, Clemens Gröpl, Andreas Hildebrandt, Knut Reinert. 473-487 [doi]
- Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient AlgorithmsYufeng Wu. 488-502 [doi]
- An Efficient and Accurate Graph-Based Approach to Detect Population SubstructureSrinath Sridhar, Satish Rao, Eran Halperin. 503-517 [doi]
- RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination BreakpointsWah-Heng Lee, Wing-Kin Sung. 518-532 [doi]
- Comparative Analysis of Spatial Patterns of Gene Expression in ::::Drosophila melanogaster:::: Imaginal DiscsCyrus L. Harmon, Parvez Ahammad, Ann Hammonds, Richard Weiszmann, Susan E. Celniker, Shankar Sastry, Gerald M. Rubin. 533-547 [doi]