| 837 | -- | 840 | Alexey V. Kochetov. AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context |
| 841 | -- | 845 | Matthieu Legendre, André Lambert, Daniel Gautheret. Profile-based detection of microRNA precursors in animal genomes |
| 846 | -- | 852 | Vladimir Paar, Nenad Pavin, Marija Rosandic, Matko Gluncic, Ivan Basar, Robert Pezer, Sonja Durajlija Zinic. ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome |
| 853 | -- | 859 | Daniela Bartels, Sebastian Kespohl, Stefan P. Albaum, Tanja Drüke, Alexander Goesmann, Julia Herold, Olaf Kaiser, Alfred Pühler, Friedhelm Pfeiffer, Günter Raddatz, Jens Stoye, Folker Meyer, Stephan C. Schuster. BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison |
| 860 | -- | 868 | Roger M. Jarvis, Royston Goodacre. Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data |
| 869 | -- | 879 | Peng Yin, Alexander J. Hartemink. Theoretical and practical advances in genome halving |
| 880 | -- | 888 | Benjamin P. Westover, Jeremy D. Buhler, Justin L. Sonnenburg, Jeffrey I. Gordon. Operon prediction without a training set |
| 889 | -- | 896 | Shahid H. Bokhari, Jon R. Sauer. A parallel graph decomposition algorithm for DNA sequencing with nanopores |
| 897 | -- | 901 | Gideon Dror, Rotem Sorek, Ron Shamir. Accurate identification of alternatively spliced exons using support vector machine |
| 902 | -- | 911 | Yi-Kuo Yu, Stephen F. Altschul. The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions |
| 912 | -- | 921 | Masumi Itoh, Susumu Goto, Tatsuya Akutsu, Minoru Kanehisa. Fast and accurate database homology search using upper bounds of local alignment scores |
| 922 | -- | 931 | Chiara Sabatti, Lars Rohlin, Kenneth Lange, James C. Liao. Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites |
| 932 | -- | 937 | January Weiner, Geraint Thomas, Erich Bornberg-Bauer. Rapid motif-based prediction of circular permutations in multi-domain proteins |
| 938 | -- | 943 | Wei-Mou Zheng. Relation between weight matrix and substitution matrix: motif search by similarity |
| 944 | -- | 950 | Kuo-Chen Chou, Yu-Dong Cai. Predicting protein localization in budding Yeast |
| 951 | -- | 960 | Johannes Söding. Protein homology detection by HMM?CHMM comparison |
| 961 | -- | 968 | M. Michael Gromiha, Makiko Suwa. A simple statistical method for discriminating outer membrane proteins with better accuracy |
| 969 | -- | 974 | Thomas M. Keane, Thomas J. Naughton, Simon A. A. Travers, James O. McInerney, G. P. McCormack. DPRml: distributed phylogeny reconstruction by maximum likelihood |
| 975 | -- | 980 | Gavin E. Crooks, Steven E. Brenner. An alternative model of amino acid replacement |
| 981 | -- | 987 | Dominik Gront, Andrzej Kolinski. A new approach to prediction of short-range conformational propensities in proteins |
| 988 | -- | 992 | John D. Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman. PDBML: the representation of archival macromolecular structure data in XML |
| 993 | -- | 1001 | Tom M. W. Nye, Carlo Berzuini, Walter R. Gilks, M. Madan Babu, Sarah A. Teichmann. Statistical analysis of domains in interacting protein pairs |
| 1002 | -- | 1009 | Erik Sandelin. Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach |
| 1010 | -- | 1019 | Xin Yuan, Christopher Bystroff. Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins |
| 1020 | -- | 1027 | Ilona Kifer, Ori Sasson, Michal Linial. Predicting fold novelty based on ProtoNet hierarchical classification |
| 1028 | -- | 1039 | Carleton L. Kingsford, Bernard Chazelle, Mona Singh. Solving and analyzing side-chain positioning problems using linear and integer programming |
| 1037 | -- | 1045 | Francisco R. Pinto, L. Ashley Cowart, Yusuf A. Hannun, B. Rohrer, Jonas S. Almeida. Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory method |
| 1046 | -- | 1054 | Chao Sima, Ulisses Braga-Neto, Edward R. Dougherty. Superior feature-set ranking for small samples using bolstered error estimation |
| 1055 | -- | 1061 | Yuan Ji, Kam-Wah Tsui, KyungMann Kim. A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples |
| 1062 | -- | 1068 | Hisanori Kiryu, Taku Oshima, Kiyoshi Asai. Extracting relations between promoter sequences and their strengths from microarray data |
| 1069 | -- | 1077 | Rajarajeswari Balasubramaniyan, Eyke Hüllermeier, Nils Weskamp, Jörg Kämper. Clustering of gene expression data using a local shape-based similarity measure |
| 1078 | -- | 1083 | J. E. Eckel, C. Gennings, Terry M. Therneau, L. D. Burgoon, D. R. Boverhof, T. R. Zacharewski. Normalization of two-channel microarray experiments: a semiparametric approach |
| 1084 | -- | 1093 | Yee Hwa Yang, Yuanyuan Xiao, Mark R. Segal. Identifying differentially expressed genes from microarray experiments via statistic synthesis |
| 1094 | -- | 1103 | Sébastien Rimour, David R. C. Hill, Cécile Militon, Pierre Peyret. GoArrays: highly dynamic and efficient microarray probe design |
| 1104 | -- | 1111 | Gersende Fort, Sophie Lambert-Lacroix. Classification using partial least squares with penalized logistic regression |
| 1112 | -- | 1120 | Antonio Reverter, Wes Barris, Sean McWilliam, Keren A. Byrne, Yong H. Wang, Siok-Hwee Tan, Nick Hudson, Brian P. Dalrymple. Validation of alternative methods of data normalization in gene co-expression studies |
| 1121 | -- | 1128 | David R. Bickel. Probabilities of spurious connections in gene networks: application to expression time series |
| 1129 | -- | 1137 | Yoram Ben-Shaul, Hagai Bergman, Hermona Soreq. Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression |
| 1138 | -- | 1145 | Sven Bilke, Qing-Rong Chen, Craig C. Whiteford, Javed I. Khan. Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays |
| 1146 | -- | 1153 | Paul H. C. Eilers, Renée X. de Menezes. Quantile smoothing of array CGH data |
| 1154 | -- | 1163 | Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, Noriko Nakagawa, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya. Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm |
| 1164 | -- | 1171 | Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork, Søren Brunak. Comparison of computational methods for the identification of cell cycle-regulated genes |
| 1172 | -- | 1179 | M. Kloster, C. Tang, N. S. Wingreen. Finding regulatory modules through large-scale gene-expression data analysis |
| 1180 | -- | 1188 | Kuan-Yao Tsai, Feng-Sheng Wang. Evolutionary optimization with data collocation for reverse engineering of biological networks |
| 1189 | -- | 1193 | Syed Asad Rahman, P. Advani, R. Schunk, Rainer Schrader, Dietmar Schomburg. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC) |
| 1194 | -- | 1202 | Gang Liu, Mark T. Swihart, Sriram Neelamegham. Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling |
| 1203 | -- | 1210 | Robert Urbanczik, C. Wagner. An improved algorithm for stoichiometric network analysis: theory and applications |
| 1211 | -- | 1218 | Ranadip Pal, Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty. Intervention in context-sensitive probabilistic Boolean networks |
| 1219 | -- | 1226 | Ina Koch, Björn H. Junker, Monika Heiner. Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber |
| 1227 | -- | 1236 | Asako Koike, Yoshiki Niwa, Toshihisa Takagi. Automatic extraction of gene/protein biological functions from biomedical text |
| 1237 | -- | 1245 | Yingyao Zhou, Jason A. Young, Andrey Santrosyan, Kaisheng Chen, S. Frank Yan, Elizabeth A. Winzeler. In silico gene function prediction using ontology-based pattern identification |
| 1246 | -- | 1256 | Julie Chabalier, Cécile Capponi, Yves Quentin, Gwennaele Fichant. ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems |
| 1257 | -- | 1262 | Georgios V. Gkoutos, Eain C. J. Green, Simon Greenaway, Andrew Blake, Ann-Marie Mallon, John M. Hancock. CRAVE: a database, middleware and visualization system for phenotype ontologies |
| 1263 | -- | 1264 | Michael D. Gadberry, Simon T. Malcomber, Andrew N. Doust, Elizabeth A. Kellogg. Primaclade - a flexible tool to find conserved PCR primers across multiple species |
| 1265 | -- | 1266 | Jian Xu, Jeffrey I. Gordon. MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly |
| 1267 | -- | 1268 | Ivo Van Walle, Ignace Lasters, Lode Wyns. SABmark- a benchmark for sequence alignment that covers the entire known fold space |
| 1269 | -- | 1270 | Lars Kiemer, Jannick Dyrløv Bendtsen, Nikolaj Blom. NetAcet: prediction of N-terminal acetylation sites |
| 1271 | -- | 1273 | Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler, Jan Weyer-Menkhoff. Multiple sequence alignment with user-defined constraints at GOBICS |
| 1274 | -- | 1275 | Dimitris Paraskevis, Koen Deforche, Philippe Lemey, G. Magiorkinis, A. Hatzakis, Anne-Mieke Vandamme. SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference |
| 1276 | -- | 1277 | Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon. TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates |
| 1278 | -- | 1279 | Victor E. Gerth, Peter D. Vize. A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns |
| 1280 | -- | 1281 | Gilles Caraux, Sylvie Pinloche. PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order |
| 1282 | -- | 1283 | Bernhard Hiller, Jutta Bradtke, Harald Balz, Harald Rieder. CyDAS: a cytogenetic data analysis system |
| 1284 | -- | 1287 | Pawan Dhar, Tan Chee Meng, Sandeep Somani, Li Ye, Kishore R. Sakharkar, Arun Krishnan, Azmi B. M. Ridwan, Sebastian Ho Kok Wah, Mandar Chitre, Hao Zhu. Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes |
| 1288 | -- | 1290 | Chung-Yen Lin, Chia-Ling Chen, Chi-Shiang Cho, Li-Ming Wang, Chia-Ming Chang, Pao-Yang Chen, Chen-Zen Lo, Chao A. Hsiung. hp-DPI: Helicobacter pylori Database of Protein Interactomes-embracing experimental and inferred interactions |
| 1291 | -- | 1293 | Joachim Reichelt, Guido Dieterich, Marsel Kvesic, Dietmar Schomburg, Dirk W. Heinz. BRAGI: linking and visualization of database information in a 3D viewer and modeling tool |