10. RECOMB 2006: Venice, Italy

• Balaji S. Srinivasan, Antal F. Novak, Jason Flannick, Serafim Batzoglou, Harley H. McAdams:
  Integrated Protein Interaction Networks for 11 Microbes. 1-14
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• Xiaoduan Ye, Alan M. Friedman, Chris Bailey-Kellogg:
  Hypergraph Model of Multi-residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination. 15-29
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• Benny Chor, Tamir Tuller:
  Biological Networks: Comparison, Conservation, and Evolutionary Trees. 30-44
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• Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski:
  Assessing Significance of Connectivity and Conservation in Protein Interaction Networks. 45-59
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• Ling Wang, Marco Ramoni, Paola Sebastiani:
  Clustering Short Gene Expression Profiles. 60-68
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• Naftali Kaminski, Ziv Bar-Joseph:
  A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. 69-82
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• Anne-Claude Gavin:
  Global Interaction Networks Probed by Mass Spectrometry. 83-83
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• David Sankoff:
  Statistical Evaluation of Genome Rearrangement. 84-84
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• Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron:
  An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets. 85-98
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• Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik:
  Protein Function Annotation Based on Ortholog Clusters Extracted from Incomplete Genomes Using Combinatorial Optimization. 99-113
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• Jim C. Huang, Quaid Morris, Brendan J. Frey:
  Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. 114-129
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• Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler:
  RNA Secondary Structure Prediction Via Energy Density Minimization. 130-142
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• Banu Dost, Buhm Han, Shaojie Zhang, Vineet Bafna:
  Structural Alignment of Pseudoknotted RNA. 143-158
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• Michael S. Waterman:
  Stan Ulam and Computational Biology. 159-159
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• Chuong B. Do, Samuel S. Gross, Serafim Batzoglou:
  CONTRAlign: Discriminative Training for Protein Sequence Alignment. 160-174
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• Michael Cameron, Yaniv Bernstein, Hugh E. Williams:
  Clustering Near-Identical Sequences for Fast Homology Search. 175-189
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• Adam C. Siepel, Katherine S. Pollard, David Haussler:
  New Methods for Detecting Lineage-Specific Selection. 190-205
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• Miklós Csürös, István Miklós:
  A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer. 206-220
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• Nicholas D. Pattengale, Bernard M. E. Moret:
  A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric. 221-230
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• Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu:
  Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. 231-245
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• Ajay K. Royyuru, Gabriela Alexe, Daniel E. Platt, Ravi Vijaya Satya, Laxmi Parida, Saharon Rosset, Gyan Bhanot:
  Inferring Common Origins from mtDNA. 246-247
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• Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim:
  Efficient Enumeration of Phylogenetically Informative Substrings. 248-264
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• Sagi Snir, Lior Pachter:
  Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. 265-280
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• Constantinos Daskalakis, Cameron Hill, Alexander Jaffe, Radu Mihaescu, Elchanan Mossel, Satish Rao:
  Maximal Accurate Forests from Distance Matrices. 281-295
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• David Heckerman, Carl Myers Kadie, Jennifer Listgarten:
  Leveraging Information Across HLA Alleles/Supertypes Improves Epitope Prediction. 296-308
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• Sauro Menchetti, Andrea Passerini, Paolo Frasconi, Claudia Andreini, Antonio Rosato:
  Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in Sequence. 309-320
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• Teresa M. Przytycka:
  An Important Connection Between Network Motifs and Parsimony Models. 321-335
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• David Haussler:
  Ultraconserved Elements, Living Fossil Transposons, and Rapid Bursts of Change: Reconstructing the Uneven Evolutionary History of the Human Genome. 336-337
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• Stefanie Scheid, Rainer Spang:
  Permutation Filtering: A Novel Concept for Significance Analysis of Large-Scale Genomic Data. 338-347
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• Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano:
  Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. 348-362
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• Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel A. Pevzner:
  A New Approach to Protein Identification. 363-378
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• Chakra Chennubhotla, Ivet Bahar:
  Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. 379-393
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• Shawna L. Thomas, Xinyu Tang, Lydia Tapia, Nancy M. Amato:
  Simulating Protein Motions with Rigidity Analysis. 394-409
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• Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, Jean-Claude Latombe:
  Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation. 410-424
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• Carl Zimmer:
  An Outsider's View of the Genome. 425
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• Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt:
  Alignment Statistics for Long-Range Correlated Genomic Sequences. 426-440
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• John D. Kececioglu, Eagu Kim:
  Simple and Fast Inverse Alignment. 441-455
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• Roman A. Zubarev:
  Revealing the Proteome Complexity by Mass Spectrometry. 456-457
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• Samuel A. Andersson, Jens Lagergren:
  Motif Yggdrasil: Sampling from a Tree Mixture Model. 458-472
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• Ydo Wexler, Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson:
  A Study of Accessible Motifs and RNA Folding Complexity. 473-487
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• Jinbo Xu, Feng Jiao, Bonnie Berger:
  A Parameterized Algorithm for Protein Structure Alignment. 488-499
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• Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki:
  Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. 500-515
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• Wei Xie, Nikolaos V. Sahinidis:
  A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem. 516-529
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• Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald:
  A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles. 530-545
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• Sarah J. Aerni, Eleazar Eskin:
  10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB). 546-562
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• Martin Bader, Enno Ohlebusch:
  Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. 563-577
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• Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang:
  A Parsimony Approach to Genome-Wide Ortholog Assignment. 578-594
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• Jeremy Darot, Chen-Hsiang Yeang, David Haussler:
  Detecting the Dependent Evolution of Biosequences. 595-609
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