12. ISMB / 3. ECCB 2004: Glasgow, Scotland, UK (Supplement of Bioinformatics)

• Janet M. Thornton, David Gilbert, Catherine Brooksbank:
  ISMB/ECCB 2004. 1-2
  
• Janet M. Thornton, David Gilbert, Catherine Brooksbank:
  ISMB/ECCB 2004 Organization. 3-5
  
• Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka:
  Application of a new probabilistic model for recognizing complex patterns in glycans. 6-14
  
• Chitta Baral, Karen Chancellor, Nam Tran, Nhan Tran, Anna M. Joy, Michael E. Berens:
  A knowledge based approach for representing and reasoning about signaling networks. 15-22
  
• Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld:
  Deconvolving cell cycle expression data with complementary information. 23-30
  
• Gill Bejerano, David Haussler, Mathieu Blanchette:
  Into the heart of darkness: large-scale clustering of human non-coding DNA. 40-48
  
• Marshall W. Bern, David Goldberg, W. Hayes McDonald, John R. Yates III:
  Automatic Quality Assessment of Peptide Tandem Mass Spectra. 49-54
  
• Doron Betel, Ruth Isserlin-Weinberger, Christopher W. V. Hogue:
  Analysis of domain correlations in yeast protein complexes. 55-62
  
• Emidio Capriotti, Piero Fariselli, Rita Casadio:
  A neural-network-based method for predicting protein stability changes upon single point mutations. 63-68
  
• Robert Castelo, Roderic Guigó:
  Splice site identification by idlBNs. 69-76
  
• Shann-Ching Chen, Ivet Bahar:
  Mining frequent patterns in protein structures: a study of protease families. 77-85
  
• Sarah Cohen Boulakia, Séverine Lair, Nicolas Stransky, Stéphane Graziani, François Radvanyi, Emmanuel Barillot, Christine Froidevaux:
  Selecting biomedical data sources according to user preferences. 86-93
  
• Lachlan James M. Coin, Richard Durbin:
  Improved techniques for the identification of pseudogenes. 94-100
  
• Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano:
  Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. 101-108
  
• Christoph Dieterich, Sven Rahmann, Martin Vingron:
  Functional inference from non-random distributions of conserved predicted transcription factor binding sites. 109-115
  
• Hernán Dopazo, Javier Santoyo, Joaquín Dopazo:
  Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. 116-121
  
• Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, Dan Halperin:
  Assigning transmembrane segments to helices in intermediate-resolution structures. 122-129
  
• Richard A. George, Ruth V. Spriggs, Janet M. Thornton, Bissan Al-Lazikani, Mark B. Swindells:
  SCOPEC: a database of protein catalytic domains. 130-136
  
• Gideon Greenspan, Dan Geiger:
  High density linkage disequilibrium mapping using models of haplotype block variation. 137-144
  
• Cigdem Gunduz, Bülent Yener, S. Humayun Gultekin:
  The cell graphs of cancer. 145-151
  
• Naohiko Heida, Yoshikazu Hasegawa, Yoshiki Mochizuki, Katsura Hirosawa, Akihiko Konagaya, Tetsuro Toyoda:
  TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks. 152-160
  
• Vladimir Jojic, Nebojsa Jojic, Christopher Meek, Dan Geiger, Adam C. Siepel, David Haussler, David Heckerman:
  Efficient approximations for learning phylogenetic HMM models from data. 161-168
  
• Cliff Joslyn, Susan M. Mniszewski, Andy W. Fulmer, Gary Heaton:
  The Gene Ontology Categorizer. 169-177
  
• Peter Kharchenko, Dennis Vitkup, George M. Church:
  Filling gaps in a metabolic network using expression information. 178-185
  
• Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert:
  Optimal robust non-unique probe selection using Integer Linear Programming. 186-193
  
• Dennis Kostka, Rainer Spang:
  Finding disease specific alterations in the co-expression of genes. 194-199
  
• Mehmet Koyutürk, Ananth Grama, Wojciech Szpankowski:
  An efficient algorithm for detecting frequent subgraphs in biological networks. 200-207
  
• Hongzhe Li, Jiang Gui:
  Partial Cox regression analysis for high-dimensional microarray gene expression data. 208-215
  
• Gerton Lunter, Jotun Hein:
  A nucleotide substitution model with nearest-neighbour interactions. 216-223
  
• Robert M. MacCallum:
  Striped sheets and protein contact prediction. 224-231
  
• Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina S. Leslie:
  Predicting genetic regulatory response using classification. 232-240
  
• Sven Mika, Burkhard Rost:
  Protein names precisely peeled off free text. 241-247
  
• Iftach Nachman, Aviv Regev, Nir Friedman:
  Inferring quantitative models of regulatory networks from expression data. 248-256
  
• Stephen A. Racunas, N. H. Shah, I. Albert, Nina V. Fedoroff:
  HyBrow: a prototype system for computer-aided hypothesis evaluation. 257-264
  
• Benjamin J. Raphael, Pavel A. Pevzner:
  Reconstructing tumor amplisomes. 265-273
  
• David J. Reiss, Benno Schwikowski:
  Predicting protein-peptide interactions via a network-based motif sampler. 274-282
  
• Alexander Schliep, Christine Steinhoff, Alexander Schönhuth:
  Robust inference of groups in gene expression time-courses using mixtures of HMMs. 283-289
  
• Padmini Srinivasan, Bisharah Libbus:
  Mining MEDLINE for implicit links between dietary substances and diseases. 290-296
  
• Kellathur N. Srinivasan, Guanglan Zhang, Asif M. Khan, J. Thomas August, Vladimir Brusic:
  Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens. 297-302
  
• Robert D. Stevens, Hannah J. Tipney, Chris Wroe, Thomas M. Oinn, Martin Senger, Phillip W. Lord, Carole A. Goble, Andy Brass, M. Tassabehji:
  Exploring Williams-Beuren syndrome using ^myGrid. 303-310
  
• Radek Szklarczyk, Jaap Heringa:
  Tracking repeats using significance and transitivity. 311-317
  
• Phil Trinh, Aoife McLysaght, David Sankoff:
  Genomic features in the breakpoint regions between syntenic blocks. 318-325
  
• Koji Tsuda, William Stafford Noble:
  Learning kernels from biological networks by maximizing entropy. 326-333
  
• Zasha Weinberg, Walter L. Ruzzo:
  Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. 334-341
  
• Daniela Wieser, Ernst Kretschmann, Rolf Apweiler:
  Filtering erroneous protein annotation. 342-347
  
• M. D. Woodhams, Michael D. Hendy:
  Reconstructing phylogeny by Quadratically Approximated Maximum Likelihood. 348-354
  
• Weijia Xu, Willard J. Briggs, Joanna Padolina, Ruth E. Timme, Wenguo Liu, C. Randal Linder, Daniel P. Miranker:
  Using MoBIoS' scalable genome join to find conserved primer pair candidates between two genomes. 355-362
  
• Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa:
  Protein network inference from multiple genomic data: a supervised approach. 363-370
  
• Changhui Yan, Drena Dobbs, Vasant Honavar:
  A two-stage classifier for identification of protein-protein interface residues. 371-378
  
• Mehdi Yousfi Monod, Véronique Giudicelli, Denys Chaume, Marie-Paule Lefranc:
  IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. 379-385
  
• Mohammed Javeed Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff:
  Predicting protein folding pathways. 386-393
  

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