1. Michael Kertesz, John Rinn, Adam Adler, Howard Chang and Eran Segal. “A Method for High-Throughput Measurement of RNA Secondary Structure"

  2. Ritendra Datta and Marshall Bern. “Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing

  3. Jing Zhang, Xin Gao, Jinbo Xu and Ming Li. “Rapid and Accurate Side Chain Prediction with Local Backbone Information

  4. Jason Flannick, Antal Novak, Chuong B. Do, Balaji S. Srinivasan and Serafim Batzoglou. “Automatic Parameter Learning for Multiple Network Alignment

  5. Andreas Sundquist, Eugene Fratkin, Chuong B. Do and Serafim Batzoglou. “Effect of Genetic Divergence in Identifying Ancestral Origin using HAPAA

  6. Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. “Constructing level-2 phylogenetic networks from triplets

  7. Caroline C. Friedel, Jan Krumsiek and Ralf Zimmer. “Bootstrapping the interactome: unsupervised identification of protein complexes in yeast

  8. Igor Ulitsky, Richard M. Karp and Ron Shamir. “Detecting disease-specific disregulated pathways via analysis of clinical expression profiles

  9. Yu Lin, Yaotao Qiao, Chungong Yu, Shiwei Sun and Dongbo Bu. “A Fragmentation Event Model for Peptide Identification by Mass Spectrometry

  10. Oliver Stegle, Anitha Kannan, Richard Durbin and John Winn. “Accounting for Non-Genetic Factors Improves the Power of eQTL Studies

  11. Yu Zhang, Giltae Song, Tomas Vinar, Eric Green, Adam Siepel and Webb Miller. “Reconstructing the evolutionary history of complex human gene clusters

  12. Christophe Dessimoz, Daniel Margadant and Gaston Gonnet. “Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework

  13. Bin Ma and Xiaoming Sun. “More Efficient Algorithms for Closest String and Substring Problems

  14. Wei Zheng, Alan Friedman and Chris Bailey-Kellogg. “Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins

  15. Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai and Jonathan Eisen. “CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads

  16. Yong Li, Randy Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng and Haixu Tang. “A Bayesian approach to protein inference problem in shotgun proteomics

  17. Tien-ho Lin, Pradipta Ray, Geir K. Sandve, Selen Uguroglu and Eric Xing. “BayCis: A Bayesian hierarchical HMM for cis-regulatory module decoding in metazoan genomes

  18. Yanxin Shi, Itamar Simon, Tom Mitchell and Ziv Bar-Joseph. “A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors

  19. Sriram Sankararaman, Gad Kimmel, Eran Halperin and Michael I. Jordan. “A Switching HMM for Inferring Ancestries in Admixed Populations

  20. Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger Linington, Pieter Dorrestein and Pavel Pevzner. “De Novo Sequencing of Nonribosomal Peptides

  21. Eleazar Eskin. “Increasing Power in Association Studies by using Linkage Disequilibrium Structure and Molecular Function as Prior Information

  22. Mustafa Kirac and Gultekin Ozsoyoglu. “Protein Function Prediction based on Patterns in Biological Networks

  23. Michael Baym, Chris Bakal, Norbert Perrimon and Bonnie Berger. “High-Resolution Modeling of Cellular Signaling Networks

  24. Sivan Bercovici, Dan Geiger, Liran Shlush, Karl Skorecki and Alan Templeton. “Panel Construction for Mapping in Admixed Populations via Expected Mutual Information

  25. Sebastian Boecker, Katharina Jahn, Julia Mixtacki and Jens Stoye. “Computation of Median Gene Clusters

  26. Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim and Eugene Myers. “Automatic Recognition of Cells (ARC) for 3D Images of C. elegans

  27. Gordon Burleigh, Oliver Eulenstein, Mukul Bansal and Andre Wehe. “Locating Multiple Gene Duplications Through Reconciled Trees

  28. Michael Sammeth, Gabriel Valiente and Roderic Guigo. “Bubbles, blobs and galls: Alternative Splicing Events of Dimension k in Splicing Graphs

  29. Michael Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, Michael Waterman and Jasmine Zhou. “An Integrative Network Approach To Map the Transcriptome to the Phenome

  30. Rune Lyngsoe, Yun Song and Jotun Hein. “Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony

  31. Raluca Gordan, Leelavati Narlikar and Alexander Hartemink. “A fast, alignment-free, conservation-based method for transcription factor binding site discovery

  32. Maxim Kalaev, Vineet Bafna and Roded Sharan. “Fast and Accurate Alignment of Multiple Protein Networks

  33. Delbert Dueck, Brendan Frey, Nebojsa Jojic, Vladimir Jojic, Guri Giaever, Andrew Emili, Gabe Musso and Robert Hegele. “Constructing Treatment Portfolios Using Affinity Propagation

  34. Paul Medvedev and Michael Brudno. “Ab Initio Short Read Assembly With Mate Pair Data

  35. John Hawkins and Timothy Bailey. “The Statistical Power of Phylogenetic Motif Models

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