9. RECOMB 2005: Cambridge, MA, USA

• Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan:
  Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. 1-13
  
• Ariel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman:
  Towards an Integrated Protein-Protein Interaction Network. 14-30
  
• Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir:
  The Factor Graph Network Model for Biological Systems. 31-47
  
• Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski:
  Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution. 48-65
  
• Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes:
  Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. 66-82
  
• Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini:
  Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis. 83-100
  
• Dmitri A. Papatsenko, Mike Levine:
  A Regulatory Network Controlling Drosophila Development. 101-101
  
• Susan Lindquist, Ernest Fraenkel, Tiago Outeiro, Aaron Gitler, Julie Su, Anil Cashikar, Smitha Jagadish:
  Yeast Cells as a Discovery Platform for Neurodegenerative Disease. 102-102
  
• Kuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung, Wen-Lian Hsu:
  RIBRA-An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem. 103-117
  
• Marshall W. Bern, Jindong Chen, Hao Chi Wong:
  Avoiding Local Optima in Single Particle Reconstruction. 118-132
  
• Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson, Ron Y. Pinter, Zohar Yakhini:
  A High-Throughput Approach for Associating microRNAs with Their Activity Conditions. 133-151
  
• Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang:
  RNA-RNA Interaction Prediction and Antisense RNA Target Search. 152-171
  
• Vineet Bafna, Haixu Tang, Shaojie Zhang:
  Consensus Folding of Unaligned RNA Sequences Revisited. 172-187
  
• Charles DeLisi:
  Discovery and Annotation of Genetic Modules. 188-188
  
• Kim R. Rasmussen, Jens Stoye, Eugene W. Myers:
  Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. 189-203
  
• Sing-Hoi Sze, Yue Lu, Qingwu Yang:
  A Polynomial Time Solvable Formulation of Multiple Sequence Alignment. 204-216
  
• Dan Gusfield, Vikas Bansal:
  A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. 217-232
  
• Daniel H. Huson, Tobias H. Klöpper, Pete J. Lockhart, Mike A. Steel:
  Reconstruction of Reticulate Networks from Gene Trees. 233-249
  
• Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot:
  A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. 250-264
  
• Trinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung:
  Constructing a Smallest Refining Galled Phylogenetic Network. 265-280
  
• Wolfgang Baumeister:
  Mapping Molecular Landscapes Inside Cells. 281-282
  
• David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor:
  Information Theoretic Approaches to Whole Genome Phylogenies. 283-295
  
• Benny Chor, Tamir Tuller:
  Maximum Likelihood of Evolutionary Trees Is Hard. 296-310
  
• Teresa M. Przytycka, George Davis, Nan Song, Dannie Durand:
  Graph Theoretical Insights into Evolution of Multidomain Proteins. 311-325
  
• Ari Frank, Stephen Tanner, Pavel A. Pevzner:
  Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry. 326-341
  
• Yunhu Wan, Ting Chen:
  A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search. 342-356
  
• Marshall W. Bern, David Goldberg:
  EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning. 357-372
  
• Eric S. Lander:
  Biology as Information. 373-373
  
• Samuel S. Gross, Michael R. Brent:
  Using Multiple Alignments to Improve Gene Prediction. 374-388
  
• Sören Sonnenburg, Gunnar Rätsch, Christin Schäfer:
  Learning Interpretable SVMs for Biological Sequence Classification. 389-407
  
• Yan Liu, Jaime G. Carbonell, Peter Weigele, Vanathi Gopalakrishnan:
  Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition. 408-422
  
• Jinbo Xu:
  Rapid Protein Side-Chain Packing via Tree Decomposition. 423-439
  
• Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson:
  Recognition of Binding Patterns Common to a Set of Protein Structures. 440-455
  
• Chen Yanover, Tomer Hertz:
  Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions. 456-471
  
• Jonathan King, Cammie Haase-Pettingell, Ryan Simkovsky, Peter Weigele:
  Amino Acid Sequence Control of the Folding of the Parallel beta-Helix, the Simplest beta-Sheet Fold. 472-473
  
• Nicholas Chia, Ralf Bundschuh:
  A Practical Approach to Significance Assessment in Alignment with Gaps. 474-488
  
• Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman:
  Alignment of Optical Maps. 489-504
  
• James J. Collins:
  Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology. 505-505
  
• Chen-Hsiang Yeang, Tommi Jaakkola:
  Modeling the Combinatorial Functions of Multiple Transcription Factors. 506-521
  
• Tommy Kaplan, Nir Friedman, Hanah Margalit:
  Predicting Transcription Factor Binding Sites Using Structural Knowledge. 522-537
  
• Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina S. Leslie:
  Motif Discovery Through Predictive Modeling of Gene Regulation. 538-552
  
• Eran Halperin, Elad Hazan:
  HAPLOFREQ - Estimating Haplotype Frequencies E.ciently. 553-568
  
• Vineet Bafna, Vikas Bansal:
  Improved Recombination Lower Bounds for Haplotype Data. 569-584
  
• Zhihong Ding, Vladimir Filkov, Dan Gusfield:
  A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. 585-600
  
• David Altshuler:
  Human Genome Sequence Variation and the Inherited Basis of Common Disease. 601-602
  
• David Sankoff, Matthew Mazowita:
  Stability of Rearrangement Measures in the Comparison of Genome Sequences. 603-614
  
• Anne Bergeron, Julia Mixtacki, Jens Stoye:
  On Sorting by Translocations. 615-629
  

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