14. ISMB 2006: Fortaleza, Brazil (Supplement of Bioinformatics)

• Philip E. Bourne, Søren Brunak:
  ISMB 2006. 1-2
  
• ISMB 2006 Organization. 3-7
  

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

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