| 2005 | Supervised enzyme network inference from the integration of genomic data and chemical information. | Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa |
| 2005 | Experimental design for three-color and four-color gene expression microarrays. | Yong Woo, Winfried Krueger, Anupinder Kaur, Gary A. Churchill |
| 2005 | How old is your fold? | Henry F. Winstanley, Sanne Abeln, Charlotte M. Deane |
| 2005 | Adaptive String Similarity Metrics for Biomedical Reference Resolution. | Ben Wellner, Jos M. Castao, James Pustejovsky |
| 2005 | Weakly Supervised Learning Methods for Improving the Quality of Gene Name Normalization Data. | Ben Wellner |
| 2005 | A Machine Learning Approach to Acronym Generation. | Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii |
| 2005 | Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. | Kannan Tharakaraman, Leonardo Mario-Ramrez, Sergey Sheetlin, David Landsman, John L. Spouge |
| 2005 | Automated interpretation of MS/MS spectra of oligosaccharides. | Haixu Tang, Yehia Mechref, Milos V. Novotny |
| 2005 | Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. | Sanjay Joshua Swamidass, Jonathan H. Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, Pierre Baldi |
| 2005 | Robust classification modeling on microarray data using misclassification penalized posterior. | Mat Soukup, HyungJun Cho, Jae K. Lee |
| 2005 | Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. | Yun S. Song, Yufeng Wu, Dan Gusfield |
| 2005 | MedTag: A Collection of Biomedical Annotations. | Lawrence H. Smith, Lorraine K. Tanabe, Thomas C. Rindflesch, W. John Wilbur |
| 2005 | Mining ChIP-chip data for transcription factor and cofactor binding sites. | Andrew D. Smith, Pavel Sumazin, Debopriya Das, Michael Q. Zhang |
| 2005 | Search for folding nuclei in native protein structures. | Alena Shmygelska |
| 2005 | A motif-based framework for recognizing sequence families. | Roded Sharan, Eugene W. Myers |
| 2005 | Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains. | Tali Sadka, Michal Linial |
| 2005 | RASE: recognition of alternatively spliced exons in | Gunnar Rtsch, Sren Sonnenburg, Bernhard Schlkopf |
| 2005 | Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions. | Arun K. Ramani, Razvan C. Bunescu, Raymond J. Mooney, Edward M. Marcotte |
| 2005 | Untitled record | Alkes L. Price, Neil Christopher Jones, Pavel A. Pevzner |
| 2005 | Statistics of local multiple alignments. | Amol Prakash, Martin Tompa |
| 2005 | Predicting the | William Stafford Noble, Scott Kuehn, Robert E. Thurman, Man Yu, John A. Stamatoyannopoulos |
| 2005 | Untitled record | Guy Nimrod, Fabian Glaser, David Steinberg, Nir Ben-Tal, Tal Pupko |
| 2005 | Beyond the clause: extraction of phosphorylation information from medline abstracts. | Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker |
| 2005 | Computing the P-value of the information content from an alignment of multiple sequences. | Niranjan Nagarajan, Neil Jones, Uri Keich |
| 2005 | Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. | Elena Nabieva, Kam Jim, Amit Agarwal, Bernard Chazelle, Mona Singh |