| 2006 | Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. | Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald |
| 2006 | Bistable switching and excitable behaviour in the activation of Src at mitosis. | Hendrik Fu, Werner Dubitzky, C. Stephen Downes, Mary Jo Kurth |
| 2006 | MotifCut: regulatory motifs finding with maximum density subgraphs. | Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, Serafim Batzoglou |
| 2006 | Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. | Barrett C. Foat, Alexandre V. Morozov, Harmen J. Bussemaker |
| 2006 | Semi-supervised LC/MS alignment for differential proteomics. | Bernd Fischer, Jonas Grossmann, Volker Roth, Wilhelm Gruissem, Sacha Baginsky, Joachim M. Buhmann |
| 2006 | Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. | Adrien Faur, Aurlien Naldi, Claudine Chaouiya, Denis Thieffry |
| 2006 | Dense subgraph computation via stochastic search: application to detect transcriptional modules. | Logan Everett, Li-San Wang, Sridhar Hannenhalli |
| 2006 | Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. | Elena J. Edelman, Alessandro Porrello, Justin Guinney, Bala Balakumaran, Andrea Bild, Phillip G. Febbo, Sayan Mukherjee |
| 2006 | Untitled record | Timothy M. D. Ebbels, Bernard F. Buxton, David T. Jones |
| 2006 | CONTRAfold: RNA secondary structure prediction without physics-based models. | Chuong B. Do, Daniel A. Woods, Serafim Batzoglou |
| 2006 | A probabilistic approach to protein backbone tracing in electron density maps. | Frank DiMaio, Jude W. Shavlik, George N. Phillips |
| 2006 | Comparative footprinting of DNA-binding proteins. | Bruno Contreras-Moreira, Julio Collado-Vides |
| 2006 | A top-level ontology of functions and its application in the Open Biomedical Ontologies. | Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich Herre, Janet Kelso |
| 2006 | ISMB 2006. | Philip E. Bourne, Sren Brunak |
| 2006 | AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. | Giovanni Bottegoni, Walter Rocchia, Maurizio Recanatini, Andrea Cavalli |
| 2006 | Integrating structured biological data by Kernel Maximum Mean Discrepancy. | Karsten M. Borgwardt, Arthur Gretton, Malte J. Rasch, Hans-Peter Kriegel, Bernhard Schlkopf, Alexander J. Smola |
| 2006 | A model-based approach for mining membrane protein crystallization trials. | Sitaram Asur, Pichai Raman, Matthew Eric Otey, Srinivasan Parthasarathy |
| 2006 | The iRMSD: a local measure of sequence alignment accuracy using structural information. | Fabrice Armougom, Sbastien Moretti, Vladimir Keduas, Cdric Notredame |
| 2006 | ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. | Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, Minoru Kanehisa |
| 2006 | DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. | Iris Antes, Shirley W. I. Siu, Thomas Lengauer |
| 2006 | Automatic clustering of orthologs and inparalogs shared by multiple proteomes. | Andrey Alexeyenko, Ivica Tamas, Gang Liu, Erik L. L. Sonnhammer |
| 2005 | Reversal distance for partially ordered genomes. | Chunfang Zheng, Aleksander Lenert, David Sankoff |
| 2005 | Classifying noisy protein sequence data: a case study of immunoglobulin light chains. | Chenggang Yu, Nela Zavaljevski, Fred J. Stevens, Kelly Yackovich, Jaques Reifman |
| 2005 | Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry data. | Jiangsheng Yu, Xue-wen Chen |
| 2005 | Automatic detection of subsystem/pathway variants in genome analysis. | Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik |