| 2003 | Using hidden Markov models to analyze gene expression time course data. | Alexander Schliep, Alexander Schnhuth, Christine Steinhoff |
| 2003 | STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification. | Joanna M. Sasin, Michal A. Kurowski, Janusz M. Bujnicki |
| 2003 | A tool to assist the study of specific features at protein binding sites. | Victor Santander, Miguel Angel Portales, Francisco Melo |
| 2003 | Processing of natural language queries to a relational database. | Maria Samsonova, Andrei Pisarev, Maxim Blagov |
| 2003 | Pair hidden Markov models on tree structures. | Yasubumi Sakakibara |
| 2003 | The discovery net system for high throughput bioinformatics. | Anthony Rowe, Dimitrios Kalaitzopoulos, Michelle Osmond, Moustafa Ghanem, Yike Guo |
| 2003 | GeneLoc: exon-based integration of human genome maps. | Naomi Rosen, Vered Chalifa-Caspi, Orit Shmueli, Avital Adato, Michal Lapidot, Julie Stampnitzky, Marilyn Safran, Doron Lancet |
| 2003 | APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. | Orla O'Sullivan, Mark Zehnder, Desmond G. Higgins, Philipp Bucher, Aurlien Grosdidier, Cdric Notredame |
| 2003 | Talisman - rapid application development for the grid. | Thomas M. Oinn |
| 2003 | ISMB 2003 - Editorial. | Gene Myers |
| 2003 | An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. | Pier Luigi Martelli, Piero Fariselli, Rita Casadio |
| 2003 | Predicting protein function from protein/protein interaction data: a probabilistic approach. | Stanley Letovsky, Simon Kasif |
| 2003 | Detection and validation of single gene inversions. | Jean-Franois Lefebvre, Nadia El-Mabrouk, Elisabeth R. M. Tillier, David Sankoff |
| 2003 | Predicting phenotype from patterns of annotation. | Oliver D. King, Jeffrey C. Lee, Aime M. Dudley, Daniel M. Janse, George M. Church, Frederick P. Roth |
| 2003 | GENIA corpus - a semantically annotated corpus for bio-textmining. | Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii |
| 2003 | Complexity management in visualizing protein interaction networks. | Byong-Hyon Ju, Kyungsook Han |
| 2003 | Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. | jvind Johansson, Wynand Alkema, Wyeth W. Wasserman, Jens Lagergren |
| 2003 | Protein structure prediction via combinatorial assembly of sub-structural units. | Yuval Inbar, Hadar Benyamini, Ruth Nussinov, Haim J. Wolfson |
| 2003 | Using guide trees to construct multiple-sequence evolutionary HMMs. | Ian H. Holmes |
| 2003 | Deriving phylogenetic trees from the similarity analysis of metabolic pathways. | Maureen Heymans, Ambuj K. Singh |
| 2003 | Sensitive pattern discovery with 'fuzzy' alignments of distantly related proteins. | Andreas Heger, Liisa Holm |
| 2003 | Detecting protein sequence conservation via metric embeddings. | Eran Halperin, Jeremy Buhler, Richard M. Karp, Robert Krauthgamer, Ben Westover |
| 2003 | Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. | Richard E. Green, Benjamin P. Lewis, R. Tyler Hillman, Marco Blanchette, Liana F. Lareau, Aaron T. Garnett, Donald C. Rio, Steven E. Brenner |
| 2003 | Chain functions and scoring functions in genetic networks. | Irit Gat-Viks, Ron Shamir |
| 2003 | Annotation of bacterial genomes using improved phylogenomic profiles. | Franois Enault, Karsten Suhre, Chantal Abergel, Olivier Poirot, Jean-Michel Claverie |