Bioinformatics

AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context
pp. 837-840(4)
Author: Kochetov, Alex V.

Profile-based detection of microRNA precursors in animal genomes
pp. 841-845(5)
Authors: Legendre, Matthieu; Lambert, André; Gautheret, Daniel

ColorHOR—novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome
pp. 846-852(7)
Authors: Paar, Vladimir; Pavin, Nenad; Rosandi, Marija; Gluni, Matko; Basar, Ivan; Pezer, Robert; ini, Sonja Durajlija

BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
pp. 853-859(7)
Authors: Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Folker; Schuster, Stephan C.

Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data
pp. 860-868(9)
Authors: Jarvis, Roger M.; Goodacre, Royston

Theoretical and practical advances in genome halving
pp. 869-879(11)
Authors: Yin, Peng; Hartemink, Alexander J.

Operon prediction without a training set
pp. 880-888(9)
Authors: Westover, B. P.; Buhler, J. D.; Sonnenburg, J. L.; Gordon, J. I.

A parallel graph decomposition algorithm for DNA sequencing with nanopores
pp. 889-896(8)
Authors: Bokhari, Shahid H.; Sauer, Jon R.

Accurate identification of alternatively spliced exons using support vector machine
pp. 897-901(5)
Authors: Dror, Gideon; Sorek, Rotem; Shamir, Ron

The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
pp. 902-911(10)
Authors: Yu, Yi-Kuo; Altschul, Stephen F.

Fast and accurate database homology search using upper bounds of local alignment scores
pp. 912-921(10)
Authors: Itoh, Masumi; Goto, Susumu; Akutsu, Tatsuya; Kanehisa, Minoru

Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites
pp. 922-931(10)
Authors: Sabatti, Chiara; Rohlin, Lars; Lange, Kenneth; Liao, James C.

Rapid motif-based prediction of circular permutations in multi-domain proteins
pp. 932-937(6)
Authors: Weiner, January; Thomas, Geraint; Bornberg-Bauer, Erich

Relation between weight matrix and substitution matrix: motif search by similarity
pp. 938-943(6)
Author: Zheng, Wei-Mou

Predicting protein localization in budding Yeast
pp. 944-950(7)
Authors: Chou, Kuo-Chen; Cai, Yu-Dong

Protein homology detection by HMM–HMM comparison
pp. 951-960(10)
Authors: Söding, Johannes

A simple statistical method for discriminating outer membrane proteins with better accuracy
pp. 961-968(8)
Authors: Gromiha, M. Michael; Suwa, Makiko

DPRml: distributed phylogeny reconstruction by maximum likelihood
pp. 969-974(6)
Authors: Keane, T. M.; Naughton, T. J.; Travers, S. A. A.; McInerney, J. O.; McCormack, G. P.

An alternative model of amino acid replacement
pp. 975-980(6)
Authors: Crooks, Gavin E.; Brenner, Steven E.

A new approach to prediction of short-range conformational propensities in proteins
pp. 981-987(7)
Authors: Gront, Dominik; Kolinski, Andrzej

PDBML: the representation of archival macromolecular structure data in XML
pp. 988-992(5)
Authors: Westbrook, John; Ito, Nobutoshi; Nakamura, Haruki; Henrick, Kim; Berman, Helen M.

Statistical analysis of domains in interacting protein pairs
pp. 993-1001(9)
Authors: Nye, Tom M. W.; Berzuini, Carlo; Gilks, Walter R.; Babu, M. Madan; Teichmann, Sarah A.

Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach
pp. 1002-1009(8)
Author: Sandelin, Erik

Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins
pp. 1010-1019(10)
Authors: Yuan, Xin; Bystroff, Christopher

Predicting fold novelty based on ProtoNet hierarchical classification
pp. 1020-1027(8)
Authors: Kifer, Ilona; Sasson, Ori; Linial, Michal

Solving and analyzing side-chain positioning problems using linear and integer programming
pp. 1028-1039(12)
Authors: Kingsford, Carleton L.; Chazelle, Bernard; Singh, Mona

Local correlation of expression profiles with gene annotations—proof of concept for a general conciliatory method
pp. 1037-1045(9)
Authors: Pinto, F. R.; Cowart, L. Ashley; Hannun, Yusuf A.; Rohrer, B.; Almeida, J. S.

Superior feature-set ranking for small samples using bolstered error estimation
pp. 1046-1054(9)
Authors: Sima, Chao; Braga-Neto, Ulisses; Dougherty, Edward R.

A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples
pp. 1055-1061(7)
Authors: Ji, Yuan; Tsui, Kam-Wah; Kim, KyungMann

Extracting relations between promoter sequences and their strengths from microarray data
pp. 1062-1068(7)
Authors: Kiryu, Hisanori; Oshima, Taku; Asai, Kiyoshi

Clustering of gene expression data using a local shape-based similarity measure
pp. 1069-1077(9)
Authors: Balasubramaniyan, Rajarajeswari; Hüllermeier, Eyke; Weskamp, Nils; Kämper, Jörg

Normalization of two-channel microarray experiments: a semiparametric approach
pp. 1078-1083(6)
Authors: Eckel, J. E.; Gennings, C.; Therneau, T. M.; Burgoon, L. D.; Boverhof, D. R.; Zacharewski, T. R.

Identifying differentially expressed genes from microarray experiments via statistic synthesis
pp. 1084-1093(10)
Authors: Yang, Yee Hwa; Xiao, Yuanyuan

GoArrays: highly dynamic and efficient microarray probe design
pp. 1094-1103(10)
Authors: Rimour, Sébastien; Hill, David; Militon, Cécile; Peyret, Pierre

Classification using partial least squares with penalized logistic regression
pp. 1104-1111(8)
Authors: Fort, Gersende; Lambert-Lacroix, Sophie

Validation of alternative methods of data normalization in gene co-expression studies
pp. 1112-1120(9)
Authors: Reverter, Antonio; Barris, Wes; McWilliam, Sean; Byrne, Keren A.; Wang, Yong H.; Tan, Siok H.; Hudson, Nick; Dalrymple, Brian P.

Probabilities of spurious connections in gene networks: application to expression time series
pp. 1121-1128(8)
Author: Bickel, David R.

Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression
pp. 1129-1137(9)
Authors: Ben-Shaul, Yoram; Bergman, Hagai; Soreq, Hermona

Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays
pp. 1138-1145(8)
Authors: Bilke, Sven; Chen, Qing-Rong; Khan, Javed

Quantile smoothing of array CGH data
pp. 1146-1153(8)
Authors: Eilers, Paul H. C.; de Menezes, Renée X.

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
pp. 1154-1163(10)
Authors: Kimura, Shuhei; Ide, Kaori; Kashihara, Aiko; Kano, Makoto; Hatakeyama, Mariko; Masui, Ryoji; Nakagawa, Noriko; Yokoyama, Shigeyuki; Kuramitsu, Seiki; Konagaya, Akihiko

Comparison of computational methods for the identification of cell cycle-regulated genes
pp. 1164-1171(8)
Authors: de Lichtenberg, Ulrik; Jensen, Lars Juhl; Jensen, Thomas S.; Bork, Peer; Brunak, Søren

Finding regulatory modules through large-scale gene-expression data analysis
pp. 1172-1179(8)
Authors: Kloster, M.; Tang, C.; Wingreen, N.S.

Evolutionary optimization with data collocation for reverse engineering of biological networks
pp. 1180-1188(9)
Authors: Tsai, Kuan-Yao; Wang, Feng-Sheng

Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
pp. 1189-1193(5)
Authors: Rahman, S. A.; Advani, P.; Schunk, R.; Schrader, R.; Schomburg, Dietmar

Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling
pp. 1194-1202(9)
Authors: Liu, Gang; Swihart, Mark T.; Neelamegham, Sriram

An improved algorithm for stoichiometric network analysis: theory and applications
pp. 1203-1210(8)
Authors: Urbanczik, R.; Wagner, C.

Intervention in context-sensitive probabilistic Boolean networks
pp. 1211-1218(8)
Authors: Pal, Ranadip; Datta, Aniruddha; Bittner, Michael L.; Dougherty, Edward R.

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
pp. 1219-1226(8)
Authors: Koch, Ina; Junker, Björn H.; Heiner, Monika

Automatic extraction of gene/protein biological functions from biomedical text
pp. 1227-1236(10)
Authors: Koike, Asako; Niwa, Yoshiki; Takagi, Toshihisa

In silico gene function prediction using ontology-based pattern identification
pp. 1237-1245(9)
Authors: Zhou, Yingyao; Young, Jason A.; Santrosyan, Andrey; Chen, Kaisheng; Yan, S. Frank; Winzeler, Elizabeth A.

ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems
pp. 1246-1256(11)
Authors: Chabalier, Julie; Capponi, Cécile; Quentin, Yves; Fichant, Gwennaele

CRAVE: a database, middleware and visualization system for phenotype ontologies
pp. 1257-1262(6)
Authors: Gkoutos, Georgios V.; Green, Eain C.J.; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M.

Primaclade—a flexible tool to find conserved PCR primers across multiple species
pp. 1263-1264(2)
Authors: Gadberry, Michael D.; Malcomber, Simon T.; Doust, Andrew N.; Kellogg, Elizabeth A.

MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly
pp. 1265-1266(2)
Authors: Xu, Jian; Gordon, Jeffrey I.

SABmark—a benchmark for sequence alignment that covers the entire known fold space
pp. 1267-1268(2)
Authors: Van Walle, Ivo; Lasters, Ignace; Wyns, Lode

NetAcet: prediction of N-terminal acetylation sites
pp. 1269-1270(2)
Authors: Kiemer, Lars; Bendtsen, Jannick Dyrløv; Blom, Nikolaj

Multiple sequence alignment with user-defined constraints at GOBICS
pp. 1271-1273(3)
Authors: Morgenstern, Burkhard; Werner, Nadine; Prohaska, Sonja J.; Steinkamp, Rasmus; Schneider, Isabelle; Subramanian, Amarendran R.; Stadler, Peter F.; Weyer-Menkhoff, Jan

SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference
pp. 1274-1275(2)
Authors: Paraskevis, D.; Deforche, K.; Lemey, P.; Magiorkinis, G.; Hatzakis, A.; Vandamme, A.-M.

TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates
pp. 1276-1277(2)
Authors: Tusnády, Gábor E.; Dosztányi, Zsuzsanna; Simon, István

A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns
pp. 1278-1279(2)
Authors: Gerth, Victor E.; Vize, Peter D.

PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order
pp. 1280-1281(2)
Authors: Caraux, Gilles; Pinloche, Sylvie

CyDAS: a cytogenetic data analysis system
pp. 1282-1283(2)
Authors: Hiller, Bernhard; Bradtke, Jutta; Balz, Harald; Rieder, Harald

Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes
pp. 1284-1287(4)
Authors: Dhar, Pawan K.; Meng, Tan Chee; Somani, Sandeep; Ye, Li; Sakharkar, Kishore; Krishnan, Arun; Ridwan, Azmi B.M.; Wah, Sebastian Ho Kok; Chitre, Mandar; Hao, Zhu

hp-DPI: Helicobacter pylori Database of Protein Interactomes—embracing experimental and inferred interactions
pp. 1288-1290(3)
Authors: Lin, Chung-Yen; Chen, Chia-Ling; Cho, Chi-Shiang; Wang, Li-Ming; Chang, Chia-Ming; Chen, Pao-Yang; Lo, Chen-Zen; Hsiung, Chao A.

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool
pp. 1291-1293(3)
Authors: Reichelt, Joachim; Dieterich, Guido; Kvesic, Marsel; Schomburg, Dietmar; Heinz, Dirk W.