| 1751 | -- | 1753 | Andrean Goede, Mathias Dunkel, Nina Mester, Cornelius Frömmel, Robert Preissner. SuperDrug: a conformational drug database |
| 1754 | -- | 1757 | Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John M. Arthur, Jonas S. Almeida. AGML Central: web based gel proteomic infrastructure |
| 1758 | -- | 1763 | Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita. Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa) |
| 1764 | -- | 1775 | Jeffrey S. Morris, Kevin R. Coombes, John Koomen, Keith A. Baggerly, Ryuji Kobayashi. Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum |
| 1776 | -- | 1781 | Darrell Conklin, Betty Haldeman, Zeren Gao. Gene finding for the helical cytokines |
| 1782 | -- | 178 | William H. Majoros, Mihaela Pertea, Sihaela Salzberg. Efficient implementation of a generalized pair hidden Markov model for comparative gene finding |
| 1789 | -- | 1796 | Maria Stepanova, Tatiana Tiazhelova, Mikle Skoblov, Ancha Baranova. A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas |
| 1797 | -- | 1806 | Dirk Husmeier, Frank Wright, Iain Milne. Detecting interspecific recombination with a pruned probabilistic divergence measure |
| 1807 | -- | 1814 | Shaun Mahony, David Hendrix, Aaron Golden, Terry J. Smith, Daniel S. Rokhsar. Transcription factor binding site identification using the self-organizing map |
| 1815 | -- | 1824 | Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, Jan Gorodkin. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40 |
| 1831 | -- | 1837 | Zheng Rong Yang. Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks |
| 1838 | -- | 1845 | Han-Lin Li, Chang-Jui Fu. A linear programming approach for identifying a consensus sequence on DNA sequences |
| 1846 | -- | 1852 | Niklaus Fankhauser, Pascal Mäser. Identification of GPI anchor attachment signals by a Kohonen self-organizing map |
| 1853 | -- | 1858 | Robel Y. Kahsay, Guang R. Gao, Li Liao. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes |
| 1859 | -- | 1875 | Thomas D. Wu, Colin K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequence |
| 1876 | -- | 1890 | Betty Lazareva-Ulitsky, Karen Diemer, Paul D. Thomas. On the quality of tree-based protein classification |
| 1891 | -- | 1900 | Karen Coeytaux, Anne Poupon. Prediction of unfolded segments in a protein sequence based on amino acid composition |
| 1901 | -- | 1907 | Fred P. Davis, Andrej Sali. PIBASE: a comprehensive database of structurally defined protein interfaces |
| 1908 | -- | 1916 | Alasdair T. R. Laurie, Richard M. Jackson. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites |
| 1917 | -- | 1926 | Håvard Nesvold, Anja Bråthen Kristoffersen, Arne Holst-Jensen, Knut G. Berdal. Design of a DNA chip for detection of unknown genetically modified organisms (GMOs) |
| 1927 | -- | 1934 | Dae Won Kim, Kwang Hyung Lee, Doheon Lee. Detecting clusters of different geometrical shapes in microarray gene expression data |
| 1935 | -- | 1942 | Cristian Mircean, Ilya Shmulevich, David Cogdell, Woonyoung Choi, Yu Jia, Ioan Tabus, Stanley R. Hamilton, Wei Zhang. Robust estimation of protein expression ratios with lysate microarray technology |
| 1943 | -- | 1949 | William T. Barry, Andrew B. Nobel, Fred A. Wright. Significance analysis of functional categories in gene expression studies: a structured permutation approach |
| 1950 | -- | 1957 | Jelle J. Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob K. Anninga, Hans C. van Houwelingen. Testing association of a pathway with survival using gene expression data |
| 1958 | -- | 1963 | Xiaojun Di, Hajime Matsuzaki, Teresa A. Webster, Earl Hubbell, Guoying Liu, Shoulian Dong, Dan Bartell, Jing Huang, Richard Chiles, Geoffrey Yang, Mei-mei Shen, David Kulp, Giulia C. Kennedy, Rui Mei, Keith W. Jones, Simon Cawley. Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays |
| 1964 | -- | 1970 | Staal A. Vinterbo, Eun-Young Kim, Lucila Ohno-Machado. Small, fuzzy and interpretable gene expression based classifiers |
| 1971 | -- | 1978 | Claudio Lottaz, Rainer Spang. Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data |
| 1979 | -- | 1986 | Wenjiang J. Fu, Raymond J. Carroll, Suojin Wang. Estimating misclassification error with small samples via bootstrap cross-validation |
| 1987 | -- | 1994 | Susmita Datta, Somnath Datta. Empirical Bayes screening of many p-values with applications to microarray studies |
| 1995 | -- | 2000 | Marie-Laure Martin-Magniette, Julie Aubert, Eric Cabannes, Jean-Jacques Daudin. Evaluation of the gene-specific dye bias in cDNA microarray experiments |
| 2001 | -- | 2007 | Shih-Chieh Su, C. C. Jay Kuo, Ting Chen. Inference of missing SNPs and information quantity measurements for haplotype blocks |
| 2008 | -- | 2016 | Marcin Imielinski, Calin Belta, Ádám M. Halász, Harvey Rubin. Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities |
| 2017 | -- | 2026 | Ross D. King, Simon M. Garrett, George Macleod Coghill. On the use of qualitative reasoning to simulate and identify metabolic pathway |
| 2027 | -- | 2035 | Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, Douglas A. Lauffenburger. Modeling of signal-response cascades using decision tree analysis |
| 2036 | -- | 2042 | Weijiang Li, Hiroyuki Kurata. A grid layout algorithm for automatic drawing of biochemical networks |
| 2043 | -- | 2048 | Kinya Okada, Shigehiko Kanaya, Kiyoshi Asai. Accurate extraction of functional associations between proteins based on common interaction partners and common domains |
| 2049 | -- | 2058 | Rob Jelier, Guido Jenster, Lambert C. J. Dorssers, C. Christiaan van der Eijk, Erik M. van Mulligen, Barend Mons, Jan A. Kors. Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes |
| 2059 | -- | 2066 | Oliver Hofmann, Dietmar Schomburg. Concept-based annotation of enzyme classes |
| 2067 | -- | 2075 | Gordon K. Smyth, Joëlle Michaud, Hamish S. Scott. Use of within-array replicate spots for assessing differential expression in microarray experiments |
| 2076 | -- | 2082 | Kevin R. Brown, Igor Jurisica. Online Predicted Human Interaction Database |
| 2083 | -- | 2084 | Jian Song, Yan Xu, Scott White, Kevin W. P. Miller, Murray Wolinsky. SNPsFinder - a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes |
| 2085 | -- | 2087 | Per Gärdén, Rikard Alm, Jari Häkkinen. PROTEIOS: an open source proteomics initiative |
| 2088 | -- | 2090 | Jason W. H. Wong, Gerard Cagney, Hugh M. Cartwright. SpecAlign - processing and alignment of mass spectra datasets |
| 2091 | -- | 2092 | Kuljeet S. Sandhu, Kshitish K. Acharya. ExPrimer: to design primers from exon-exon junctions |
| 2093 | -- | 2094 | Morris Michael, Christoph Dieterich, Martin Vingron. SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors |
| 2095 | -- | 2096 | Frédéric Chalmel, Aurélie Lardenois, Julie Dawn Thompson, Jean Muller, José-Alain Sahel, Thierry Léveillard, Olivier Poch. GOAnno: GO annotation based on multiple alignment |
| 2097 | -- | 2098 | Weixi Li, Cathryn J. Rehmeyer, Chuck Staben, Mark L. Farman. TruMatch - a BLAST post-processor that identifies bona fide sequence matches to genome assemblies |
| 2099 | -- | 2100 | Francisco Azuaje. Integrative data analysis for functional prediction: a multi-objective optimization approach |
| 2101 | -- | 2103 | Adi Doron-Faigenboim, Adi Stern, Itay Mayrose, Eran Bacharach, Tal Pupko. Selecton: a server for detecting evolutionary forces at a single amino-acid site |
| 2104 | -- | 2105 | Federico Abascal, Rafael Zardoya, David Posada. ProtTest: selection of best-fit models of protein evolution |
| 2106 | -- | 2107 | Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig, Thomas Lengauer. Mtreemix: a software package for learning and using mixture models of mutagenetic trees |
| 2108 | -- | 2109 | Joachim Friedrich, Thomas Dandekar, Matthias Wolf, Tobias Müller. ProfDist: a tool for the construction of large phylogenetic trees based on profile distances |
| 2110 | -- | 2111 | Andreas Möglich, Daniel Weinfurtner, Wolfram Gronwald, Till Maurer, Hans Robert Kalbitzer. PERMOL: restraint-based protein homology modeling using DYANA or CNS |
| 2112 | -- | 2113 | Joern Toedling, Sebastian Schmeier, Matthias Heinig, Benjamin Georgi, Stefan Roepcke. MACAT - microarray chromosome analysis tool |
| 2114 | -- | 2115 | Laurie J. Heyer, D. Z. Moskowitz, J. A. Abele, P. Karnik, D. Choi, A. Malcolm Campbell, E. E. Oldham, B. K. Akin. MAGIC Tool: integrated microarray data analysis |
| 2116 | -- | 2117 | Sek Won Kong, Kyu Baek Hwang, Richard D. Kim, Byoung-Tak Zhang, Steven A. Greenberg, Isaac S. Kohane, Peter J. Park. CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays |
| 2118 | -- | 2122 | Yuan Ji, Chunlei Wu, Ping Liu, Jing Wang, Kevin R. Coombes. Applications of beta-mixture models in bioinformatics |
| 2123 | -- | 2125 | Franz Rüschendorf, Peter J. Nürnberg. ALOHOMORA: a tool for linkage analysis using 10K SNP array data |
| 2126 | -- | 2127 | Hongyu Yang, Hongyu Wang, Alan R. Gingle. IntegratedMap: a Web interface for integrating genetic map data |
| 2128 | -- | 2129 | Kejun Liu, Spencer V. Muse. PowerMarker: an integrated analysis environment for genetic marker analysis |
| 2130 | -- | 2132 | David Posada, Taylor J. Maxwell, Alan R. Templeton. TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees |
| 2133 | -- | 2135 | Chih-Yu (Carol) Chang, Joshua LaBaer. DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequences |
| 2136 | -- | 2137 | Abhijit Chatterjee, Kapil Mayawala, Jeremy S. Edwards, Dionisios G. Vlachos. Time accelerated Monte Carlo simulations of biological networks using the binomial r-leap method |
| 2138 | -- | 2139 | Anna Divoli, Teresa K. Attwood. BioIE: extracting informative sentences from the biomedical literature |
| 2140 | -- | 2141 | Pedro A. Reche, Hong Zhang, John-Paul Glutting, Ellis L. Reinherz. EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology |
| 2142 | -- | 2143 | Pei Hao, Wei-Zhong He, Yin Huang, Liang-Xiao Ma, Ying Xu, Hong Xi, Chuan Wang, Bo-Shu Liu, Jin-Miao Wang, Yi-Xue Li, Yang Zhong. MPSS: an integrated database system for surveying a set of proteins |