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| Graph kernels for disease outcome prediction from protein-protein interaction networks | p. 4 |
| Chalkboard : ontology-based pathway modeling and qualitative inference of disease mechanisms | p. 16 |
| Mining gene-disease relationships from biomedical literature weighting protein-protein interactions and connectivity measures | p. 28 |
| Predicting structure and dynamics of loosely-ordered protein complexes : influenza hemagglutinin fusion peptide | p. 40 |
| Protein interactions and disease phenotypes in the ABC Transporter Superfamily | p. 51 |
| LTHREADER : prediction of ligand-receptor interactions using localized threading | p. 64 |
| Discovery of protein interaction networks shared by diseases | p. 76 |
| An iterative algorithm for metabolic network-based drug target identification | p. 88 |
| Transcriptional interactions during smallpox infection and identification of early infection biomarkers | p. 100 |
| Leveraging latent information in NMR spectra for robust predictive models | p. 115 |
| Bioinformatics data profiling tools : a prelude to metabolic profiling | p. 127 |
| Comparative QSAR analysis of bacterial, fungal, plant and human metabolites | p. 133 |
| BioSpider : a Web server for automating metabolome annotations | p. 145 |
| New bioinformatics resources for metabolomics | p. 157 |
| Setup X - a public study design database for metabolomic projects | p. 169 |
| Comparative metabolomics of breast cancer | p. 181 |
| Metabolic flux profiling of reaction modules in liver drug transformation | p. 193 |
| Extracting semantic predications from medline citations for pharmacogenomics | p. 209 |
| Annotating genes using textual patterns | p. 221 |
| A fault model for ontology mapping, alignment, and linking systems | p. 233 |
| Integrating natural language processing with flybase curation | p. 245 |
| A stacked graphical model for associating sub-images with sub-captions | p. 257 |
| GeneRIF quality assurance as summary revision | p. 269 |
| Evaluating the automatic mapping of human gene and protein mentions to unique identifiers | p. 281 |
| Multiple approaches to fine-grained indexing of the biomedical literature | p. 292 |
| Mining patents using molecular similarity search | p. 304 |
| Discovering implicit associations between genes and hereditary diseases | p. 316 |
| A cognitive evaluation of four online search engines for answering definitional questions posed by physicians | p. 328 |
| Biomediator data integration and inference for functional annotation of anonymous sequences | p. 343 |
| Absent sequences : nullomers and primes | p. 355 |
| An anatomical ontology for amphibians | p. 367 |
| Recommending pathway genes using a compendium of clustering solutions | p. 379 |
| Semi-automated XML markup of biosystematic legacy literature with the goldengate editor | p. 391 |
| Advancement in protein inference from shotgun proteomics using peptide detectability | p. 409 |
| Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification | p. 421 |
| Assessing and combining reliability of protein interaction sources | p. 433 |
| Probabilistic modeling of systematic errors in two-hybrid experiments | p. 445 |
| Prospective exploration of biochemical tissue composition via imaging mass spectrometry guided by principal component analysis | p. 458 |
| Discovering motifs with transcription factor domain knowledge | p. 472 |
| Ab initio prediction of transcription factor binding sites | p. 484 |
| Comparative pathway annotation with protein-DNA interaction and operon information via graph tree decomposition | p. 496 |
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