Table of Contents

• ISMB 2006Philip E. Bourne, Søren Brunak. 1-2 [doi]
• ISMB 2006 Organization3-7 [doi]
• Automatic clustering of orthologs and inparalogs shared by multiple proteomesAndrey Alexeyenko, Ivica Tamas, Gang Liu, Erik L. L. Sonnhammer. 9-15 [doi]
• DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformationsIris Antes, Shirley W. I. Siu, Thomas Lengauer. 16-24 [doi]
• ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chainsKiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, Minoru Kanehisa. 25-34 [doi]
• The iRMSD: a local measure of sequence alignment accuracy using structural informationFabrice Armougom, Sébastien Moretti, Vladimir Keduas, Cédric Notredame. 35-39 [doi]
• A model-based approach for mining membrane protein crystallization trialsSitaram Asur, Pichai Raman, Matthew Eric Otey, Srinivasan Parthasarathy. 40-48 [doi]
• Integrating structured biological data by Kernel Maximum Mean DiscrepancyKarsten M. Borgwardt, Arthur Gretton, Malte J. Rasch, Hans-Peter Kriegel, Bernhard Schölkopf, Alexander J. Smola. 49-57 [doi]
• AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasetsGiovanni Bottegoni, Walter Rocchia, Maurizio Recanatini, Andrea Cavalli. 58-65 [doi]
• A top-level ontology of functions and its application in the Open Biomedical OntologiesPatryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich Herre, Janet Kelso. 66-73 [doi]
• Comparative footprinting of DNA-binding proteinsBruno Contreras-Moreira, Julio Collado-Vides. 74-80 [doi]
• A probabilistic approach to protein backbone tracing in electron density mapsFrank DiMaio, Jude W. Shavlik, George N. Phillips. 81-89 [doi]
• CONTRAfold: RNA secondary structure prediction without physics-based modelsChuong B. Do, Daniel A. Woods, Serafim Batzoglou. 90-98 [doi]
• ::::springScape::::: visualisation of microarray and contextual bioinformatic data using spring embedding and an information landscape Timothy M. D. Ebbels, Bernard F. Buxton, David T. Jones. 99-107 [doi]
• Dense subgraph computation via stochastic search: application to detect transcriptional modulesLogan Everett, Li-San Wang, Sridhar Hannenhalli. 117-123 [doi]
• Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profilesElena Edelman, Alessandro Porrello, Justin Guinney, Bala Balakumaran, Andrea Bild, Phillip G. Febbo, Sayan Mukherjee. 122-116 [doi]
• Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycleAdrien Fauré, Aurélien Naldi, Claudine Chaouiya, Denis Thieffry. 124-131 [doi]
• Semi-supervised LC/MS alignment for differential proteomicsBernd Fischer, Jonas Grossmann, Volker Roth, Wilhelm Gruissem, Sacha Baginsky, Joachim M. Buhmann. 132-140 [doi]
• Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCEBarrett C. Foat, Alexandre V. Morozov, Harmen J. Bussemaker. 141-149 [doi]
• MotifCut: regulatory motifs finding with maximum density subgraphsEugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, Serafim Batzoglou. 156-157 [doi]
• Bistable switching and excitable behaviour in the activation of Src at mitosisHendrik Fuß, Werner Dubitzky, C. Stephen Downes, Mary Jo Kurth. 164-165 [doi]
• Context-specific independence mixture modeling for positional weight matricesBenjamin Georgi, Alexander Schliep. 166-173 [doi]
• Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein designIvelin Georgiev, Ryan H. Lilien, Bruce Randall Donald. 174-183 [doi]
• Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networksOlivier Gevaert, Frank De Smet, Dirk Timmerman, Yves Moreau, Bart De Moor. 184-190 [doi]
• ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteinsErik Granseth, Håkan Viklund, Arne Elofsson. 191-196 [doi]
• Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics dataJana Hertel, Peter F. Stadler. 197-202 [doi]
• Modelling sequential protein folding under kinetic controlFabien P. E. Huard, Charlotte M. Deane, Graham R. Wood. 203-210 [doi]
• BNTagger: improved tagging SNP selection using Bayesian networksPhil Hyoun Lee, Hagit Shatkay. 211-219 [doi]
• Learning MHC I - peptide bindingNebojsa Jojic, Manuel Reyes-Gomez, David Heckerman, Carl Myers Kadie, Ora Schueler-Furman. 227-235 [doi]
• Finding the evidence for protein-protein interactions from PubMed abstractsHyunchul Jang, Jaesoo Lim, Joon-Ho Lim, Soo-Jun Park, Kyu-Chul Lee, Seon Hee Park. 234-226 [doi]
• Comparative genomics reveals unusually long motifs in mammalian genomesNeil C. Jones, Pavel A. Pevzner. 236-242 [doi]
• Distance based algorithms for small biomolecule classification and structural similarity searchEmre Karakoç, Artem Cherkasov, Süleyman Cenk Sahinalp. 243-251 [doi]
• Rapid knot detection and application to protein structure predictionFiras Khatib, Matthew T. Weirauch, Carol A. Rohl. 258-259 [doi]
• Annotating proteins by mining protein interaction networksMustafa Kirac, Gultekin Özsoyoglu, Jiong Yang. 260-270 [doi]
• A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalkGeoffrey Koh, Huey Fern Carol Teong, Marie-Véronique Clément, David Hsu, P. S. Thiagarajan. 271-280 [doi]
• Finding novel genes in bacterial communities isolated from the environmentLutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, Jens Stoye. 281-289 [doi]
• A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loopsGorka Lasso, John F. Antoniw, Jonathan G. L. Mullins. 290-297 [doi]
• Interpreting anonymous DNA samples from mass disasters - probabilistic forensic inference using genetic markersTien-ho Lin, Eugene W. Myers, Eric P. Xing. 298-306 [doi]
• Peptide sequence tag-based blind identification of post-translational modifications with point process modelChunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai. 307-313 [doi]
• Identifying cycling genes by combining sequence homology and expression dataYong Lu, Ronald Rosenfeld, Ziv Bar-Joseph. 314-322 [doi]
• Quantification of transcription factor expression from Arabidopsis imagesDaniel L. Mace, Ji Young Lee, Richard W. Twigg, Juliette Colinas, Philip N. Benfey, Uwe Ohler. 323-331 [doi]
• Mutation parameters from DNA sequence data using graph theoretic measures on lineage treesReuma Magori-Cohen, Yoram Louzoun, Steven H. Kleinstein. 332-340 [doi]
• Indel seeds for homology searchDenise Y. F. Mak, Yevgeniy Gelfand, Gary Benson. 341-349 [doi]
• Efficient identification of DNA hybridization partners in a sequence databaseTobias P. Mann, William Stafford Noble. 350-358 [doi]
• An experimental metagenome data management and analysis systemVictor M. Markowitz, Natalia Ivanova, Krishna Palaniappan, Ernest Szeto, Frank Korzeniewski, Athanasios Lykidis, Iain Anderson, Konstantinos Mavrommatis, Victor Kunin, Hector Garcia Martin, Inna Dubchak, Philip Hugenholtz, Nikos Kyrpides. 359-367 [doi]
• An equilibrium partitioning model connecting gene expression and ::::cis::::-motif contentJoe Mellor, Charles DeLisi. 368-374 [doi]
• Identification of metabolic units induced by environmental signalsJose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, Tatsuya Akutsu. 375-383 [doi]
• Informative priors based on transcription factor structural class improve ::::de novo:::: motif discoveryLeelavati Narlikar, Raluca Gordân, Uwe Ohler, Alexander J. Hartemink. 384-392 [doi]
• Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight ZonePatrick Ng, Niranjan Nagarajan, Neil Jones, Uri Keich. 393-401 [doi]
• Create and assess protein networks through molecular characteristics of individual proteinsYanay Ofran, Guy Yachdav, Eyal Mozes, Ta-tsen Soong, Rajesh Nair, Burkhard Rost. 402-407 [doi]
• BaCelLo: a balanced subcellular localization predictorAndrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio. 415-416 [doi]
• Semi-supervised analysis of gene expression profiles for lineage-specific development in the ::::Caenorhabditis elegans:::: embryoYuan (Alan) Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi Jaakkola, David K. Gifford, Hui Ge. 417-423 [doi]
• Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic treeAlexander Schliep, Sven Rahmann. 424-430 [doi]
• Integrating copy number polymorphisms into array CGH analysis using a robust HMMSohrab P. Shah, Xiang Xuan, Ronald J. deLeeuw, Mehrnoush Khojasteh, Wan L. Lam, Raymond T. Ng, Kevin P. Murphy. 431-439 [doi]
• Relative contributions of structural designability and functional diversity in molecular evolution of duplicatesBoris E. Shakhnovich. 440-445 [doi]
• Integrating image data into biomedical text categorizationHagit Shatkay, Nawei Chen, Dorothea Blostein. 446-453 [doi]
• On counting position weight matrix matches in a sequence, with application to discriminative motif findingSaurabh Sinha. 454-463 [doi]
• An ontology for a Robot ScientistLarisa N. Soldatova, Amanda Clare, Andrew Sparkes, Ross D. King. 464-471 [doi]
• ARTS: accurate recognition of transcription starts in humanSören Sonnenburg, Alexander Zien, Gunnar Rätsch. 472-480 [doi]
• A computational approach toward label-free protein quantification using predicted peptide detectabilityHaixu Tang, Randy J. Arnold, Pedro Alves, Zhiyin Xun, David E. Clemmer, Milos V. Novotny, James P. Reilly, Predrag Radivojac. 481-488 [doi]
• An integrative approach for causal gene identification and gene regulatory pathway inferenceZhidong Tu, Li Wang, Michelle N. Arbeitman, Ting Chen, Fengzhu Sun. 489-496 [doi]
• Computational inference of the molecular logic for synaptic connectivity in ::::C. elegans::::Vinay Varadan, David M. Miller III, Dimitris Anastassiou. 497-506 [doi]
• Novel Unsupervised Feature Filtering of Biological DataRoy Varshavsky, Assaf Gottlieb, Michal Linial, David Horn. 507-513 [doi]
• Constructing Near-Perfect Phylogenies with multiple homoplasy eventsRavi Vijaya Satya, Amar Mukherjee, Gabriela Alexe, Laxmi Parida, Gyan Bhanot. 514-522 [doi]
• SNP Function Portal: a web database for exploring the function implication of SNP allelesPinglang Wang, Manhong Dai, Weijian Xuan, Richard C. McEachin, Anne U. Jackson, Laura J. Scott, Brian D. Athey, Stanley J. Watson, Fan Meng. 523-529 [doi]
• Protein classification using ontology classificationKaty Wolstencroft, Phillip W. Lord, Lydia Tabernero, Andy Brass, Robert Stevens. 530-538 [doi]
• Inferring Functional Pathways from Multi-Perturbation DataNir Yosef, Alon Kaufman, Eytan Ruppin. 539-546 [doi]
• Accessing bioscience images from abstract sentencesHong Yu, Minsuk Lee. 547-556 [doi]
• A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elementsShaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna. 557-565 [doi]