| 2004 | Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens. | Kellathur N. Srinivasan, Guanglan Zhang, Asif M. Khan, J. Thomas August, Vladimir Brusic |
| 2004 | Mining MEDLINE for implicit links between dietary substances and diseases. | Padmini Srinivasan, Bisharah Libbus |
| 2004 | Robust inference of groups in gene expression time-courses using mixtures of HMMs. | Alexander Schliep, Christine Steinhoff, Alexander Schnhuth |
| 2004 | Predicting protein-peptide interactions via a network-based motif sampler. | David J. Reiss, Benno Schwikowski |
| 2004 | Reconstructing tumor amplisomes. | Benjamin J. Raphael, Pavel A. Pevzner |
| 2004 | HyBrow: a prototype system for computer-aided hypothesis evaluation. | Stephen A. Racunas, N. H. Shah, Istvn Albert, Nina V. Fedoroff |
| 2004 | Inferring quantitative models of regulatory networks from expression data. | Iftach Nachman, Aviv Regev, Nir Friedman |
| 2004 | IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. | Mehdi Yousfi Monod, Vronique Giudicelli, Denys Chaume, Marie-Paule Lefranc |
| 2004 | Protein names precisely peeled off free text. | Sven Mika, Burkhard Rost |
| 2004 | Predicting genetic regulatory response using classification. | Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina S. Leslie |
| 2004 | Striped sheets and protein contact prediction. | Robert M. MacCallum |
| 2004 | A nucleotide substitution model with nearest-neighbour interactions. | Gerton Lunter, Jotun Hein |
| 2004 | Partial Cox regression analysis for high-dimensional microarray gene expression data. | Hongzhe Li, Jiang Gui |
| 2004 | An efficient algorithm for detecting frequent subgraphs in biological networks. | Mehmet Koyutrk, Ananth Grama, Wojciech Szpankowski |
| 2004 | Finding disease specific alterations in the co-expression of genes. | Dennis Kostka, Rainer Spang |
| 2004 | Optimal robust non-unique probe selection using Integer Linear Programming. | Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert |
| 2004 | Filling gaps in a metabolic network using expression information. | Peter V. Kharchenko, Dennis Vitkup, George M. Church |
| 2004 | The Gene Ontology Categorizer. | Cliff A. Joslyn, Susan M. Mniszewski, Andy W. Fulmer, Gary Heaton |
| 2004 | Efficient approximations for learning phylogenetic HMM models from data. | Vladimir Jojic, Nebojsa Jojic, Christopher Meek, Dan Geiger, Adam C. Siepel, David Haussler, David Heckerman |
| 2004 | Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. | Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano |
| 2004 | TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks. | Naohiko Heida, Yoshikazu Hasegawa, Yoshiki Mochizuki, Katsura Hirosawa, Akihiko Konagaya, Tetsuro Toyoda |
| 2004 | The cell graphs of cancer. | Cigdem Gunduz, Blent Yener, S. Humayun Gultekin |
| 2004 | High density linkage disequilibrium mapping using models of haplotype block variation. | Gideon Greenspan, Dan Geiger |
| 2004 | SCOPEC: a database of protein catalytic domains. | Richard A. George, Ruth V. Spriggs, Janet M. Thornton, Bissan Al-Lazikani, Mark B. Swindells |
| 2004 | Assigning transmembrane segments to helices in intermediate-resolution structures. | Angela Enosh, Sarel Jacob Fleishman, Nir Ben-Tal, Dan Halperin |