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| 2005 | A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search. Yunhu Wan, Ting Chen |
| 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 | A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot |
| 2005 | A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. Zhihong Ding, Vladimir Filkov, Dan Gusfield |
| 2005 | A Polynomial Time Solvable Formulation of Multiple Sequence Alignment. Sing-Hoi Sze, Yue Lu, Qingwu Yang |
| 2005 | A Practical Approach to Significance Assessment in Alignment with Gaps. Nicholas Chia, Ralf Bundschuh |
| 2005 | A Regulatory Network Controlling Drosophila Development. Dmitri A. Papatsenko, Mike Levine |
| 2005 | Alignment of Optical Maps. Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman |
| 2005 | Amino Acid Sequence Control of the Folding of the Parallel beta-Helix, the Simplest beta-Sheet Fold. Jonathan King, Cammie Haase-Pettingell, Ryan Simkovsky, Peter Weigele |
| 2005 | Avoiding Local Optima in Single Particle Reconstruction. Marshall W. Bern, Jindong Chen, Hao Chi Wong |
| 2005 | Biology as Information. Eric S. Lander |
| 2005 | Consensus Folding of Unaligned RNA Sequences Revisited. Vineet Bafna, Haixu Tang, Shaojie Zhang |
| 2005 | Constructing a Smallest Refining Galled Phylogenetic Network. Trinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung |
| 2005 | Discovery and Annotation of Genetic Modules. Charles DeLisi |
| 2005 | Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan |
| 2005 | Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis. Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini |
| 2005 | Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. Kim R. Rasmussen, Jens Stoye, Eugene W. Myers |
| 2005 | EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning. Marshall W. Bern, David Goldberg |
| 2005 | Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology. James J. Collins |
| 2005 | Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes |
| 2005 | Graph Theoretical Insights into Evolution of Multidomain Proteins. Teresa M. Przytycka, George B. Davis, Nan Song, Dannie Durand |
| 2005 | HAPLOFREQ - Estimating Haplotype Frequencies E.ciently. Eran Halperin, Elad Hazan |
| 2005 | Human Genome Sequence Variation and the Inherited Basis of Common Disease. David Altshuler |
| 2005 | Improved Recombination Lower Bounds for Haplotype Data. Vineet Bafna, Vikas Bansal |
| 2005 | Information Theoretic Approaches to Whole Genome Phylogenies. David Burstein, Igor Ulitsky, Tamir Tuller, Benny Chor |
| 2005 | Learning Interpretable SVMs for Biological Sequence Classification. Sören Sonnenburg, Gunnar Rätsch, Christin Schäfer |
| 2005 | Mapping Molecular Landscapes Inside Cells. Wolfgang Baumeister |
| 2005 | Maximum Likelihood of Evolutionary Trees Is Hard. Benny Chor, Tamir Tuller |
| 2005 | Modeling the Combinatorial Functions of Multiple Transcription Factors. Chen-Hsiang Yeang, Tommi S. Jaakkola |
| 2005 | Motif Discovery Through Predictive Modeling of Gene Regulation. Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina S. Leslie |
| 2005 | On Sorting by Translocations. Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2005 | Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution. Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski |
| 2005 | Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry. Ari Frank, Stephen Tanner, Pavel A. Pevzner |
| 2005 | Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions. Chen Yanover, Tomer Hertz |
| 2005 | Predicting Transcription Factor Binding Sites Using Structural Knowledge. Tommy Kaplan, Nir Friedman, Hanah Margalit |
| 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 | RNA-RNA Interaction Prediction and Antisense RNA Target Search. Can Alkan, Emre Karakoç, Joseph H. Nadeau, Süleyman Cenk Sahinalp, Kaizhong Zhang |
| 2005 | Rapid Protein Side-Chain Packing via Tree Decomposition. Jinbo Xu |
| 2005 | Recognition of Binding Patterns Common to a Set of Protein Structures. Maxim Shatsky, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson |
| 2005 | Reconstruction of Reticulate Networks from Gene Trees. Daniel H. Huson, Tobias H. Klöpper, Peter J. Lockhart, Mike A. Steel |
| 2005 | Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings Satoru Miyano, Jill P. Mesirov, Simon Kasif, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman |
| 2005 | Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition. Yan Liu, Jaime G. Carbonell, Peter Weigele, Vanathi Gopalakrishnan |
| 2005 | Stability of Rearrangement Measures in the Comparison of Genome Sequences. David Sankoff, Matthew Mazowita |
| 2005 | The Factor Graph Network Model for Biological Systems. Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir |
| 2005 | Towards an Integrated Protein-Protein Interaction Network. Ariel Jaimovich, Gal Elidan, Hanah Margalit, Nir Friedman |
| 2005 | Using Multiple Alignments to Improve Gene Prediction. Samuel S. Gross, Michael R. Brent |
| 2005 | Yeast Cells as a Discovery Platform for Neurodegenerative Disease. Susan Lindquist, Ernest Fraenkel, Tiago Outeiro, Aaron Gitler, Julie Su, Anil Cashikar, Smitha Jagadish |