BMC Bioinformatics | Vol 8

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Volume 8 (2007) - May 2007

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sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database

Jyoti K Shah, Harold R Garner, Michael A White, David S Shames, John D Minna BMC Bioinformatics 2007, 8:178 (31 May 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base

Lucy Skrabanek, Marta Murcia, Michel Bouvier, Lakshmi Devi, Susan R George, Martin J Lohse, Graeme Milligan, Richard Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend, Jonathan A Javitch, Fabien Campagne, Marta Filizola BMC Bioinformatics 2007, 8:177 (30 May 2007)

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DNA-based watermarks using the DNA-Crypt algorithm

Dominik Heider, Angelika Barnekow BMC Bioinformatics 2007, 8:176 (29 May 2007)

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A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks

Asawari Samant, Babatunde A Ogunnaike, Dionisios G Vlachos BMC Bioinformatics 2007, 8:175 (24 May 2007)

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Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions

Davide Corà, Ferdinando Di Cunto, Michele Caselle, Paolo Provero BMC Bioinformatics 2007, 8:174 (24 May 2007)

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

Raja Jothi, Teresa M Przytycka, L Aravind BMC Bioinformatics 2007, 8:173 (23 May 2007)

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The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel BMC Bioinformatics 2007, 8:172 (23 May 2007)

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Comparing segmentations by applying randomization techniques

Niina Haiminen, Heikki Mannila, Evimaria Terzi BMC Bioinformatics 2007, 8:171 (23 May 2007)

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Estimating the annotation error rate of curated GO database sequence annotations

Craig E Jones, Alfred L Brown, Ute Baumann BMC Bioinformatics 2007, 8:170 (22 May 2007)

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A feature selection approach for identification of signature genes from SAGE data

Junior Barrera, Roberto M Cesar, Carlos Humes, David C Martins, Diogo FC Patrão, Paulo JS Silva, Helena Brentani BMC Bioinformatics 2007, 8:169 (22 May 2007)

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BioPP: a tool for web-publication of biological networks

Ganesh A Viswanathan, German Nudelman, Sonali Patil, Stuart C Sealfon BMC Bioinformatics 2007, 8:168 (22 May 2007)

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Hinge Atlas: relating protein sequence to sites of structural flexibility

Samuel C Flores, Long J Lu, Julie Yang, Nicholas Carriero, Mark B Gerstein BMC Bioinformatics 2007, 8:167 (22 May 2007)

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GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products

Holger Fröhlich, Nora Speer, Annemarie Poustka, Tim Beißbarth BMC Bioinformatics 2007, 8:166 (22 May 2007)

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Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue

Marc Strickert, Nese Sreenivasulu, Björn Usadel, Udo Seiffert BMC Bioinformatics 2007, 8:165 (22 May 2007)

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Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

Chun-Chi Liu, Chin-Chung Lin, Ker-Chau Li, Wen-Shyen E Chen, Jiun-Ching Chen, Ming-Te Yang, Pan-Chyr Yang, Pei-Chun Chang, Jeremy JW Chen BMC Bioinformatics 2007, 8:164 (22 May 2007)

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AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions

David SH Chew, Ming-Ying Leung, Kwok Choi BMC Bioinformatics 2007, 8:163 (21 May 2007)

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Robust detection and verification of linear relationships to generate metabolic networks using estimates of technical errors

Frank Kose, Jan Budczies, Matthias Holschneider, Oliver Fiehn BMC Bioinformatics 2007, 8:162 (21 May 2007)

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Large-scale clustering of CAGE tag expression data

Kazuro Shimokawa, Yuko Okamura-Oho, Takio Kurita, Martin C Frith, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki BMC Bioinformatics 2007, 8:161 (21 May 2007)

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TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets

Renato Vicentini, Marcelo Menossi BMC Bioinformatics 2007, 8:160 (21 May 2007)

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A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana

Mihaela Pertea, Stephen M Mount, Steven L Salzberg BMC Bioinformatics 2007, 8:159 (21 May 2007)

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TBMap: a taxonomic perspective on the phylogenetic database TreeBASE

Roderic DM Page BMC Bioinformatics 2007, 8:158 (18 May 2007)

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Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures

Xin Lu, David L Perkins BMC Bioinformatics 2007, 8:157 (18 May 2007)

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The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

BD Pascal, MJ Chalmers, SA Busby, CC Mader, MR Southern, NF Tsinoremas, PR Griffin BMC Bioinformatics 2007, 8:156 (16 May 2007)

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TAP score: torsion angle propensity normalization applied to local protein structure evaluation

Silvio CE Tosatto, Roberto Battistutta BMC Bioinformatics 2007, 8:155 (15 May 2007)

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Unexpected observations after mapping LongSAGE tags to the human genome

Céline Keime, Marie Sémon, Dominique Mouchiroud, Laurent Duret, Olivier Gandrillon BMC Bioinformatics 2007, 8:154 (15 May 2007)

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How accurate and statistically robust are catalytic site predictions based on closeness centrality?

Eric Chea, Dennis R Livesay BMC Bioinformatics 2007, 8:153 (11 May 2007)

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Reconstruction of human protein interolog network using evolutionary conserved network

Tao-Wei Huang, Chung-Yen Lin, Cheng-Yan Kao BMC Bioinformatics 2007, 8:152 (10 May 2007)

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Tracembler – software for in-silico chromosome walking in unassembled genomes

Qunfeng Dong, Matthew D Wilkerson, Volker Brendel BMC Bioinformatics 2007, 8:151 (9 May 2007)

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Detecting multivariate differentially expressed genes

Roland Nilsson, José M Peña, Johan Björkegren, Jesper Tegnér BMC Bioinformatics 2007, 8:150 (9 May 2007)

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Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli

Gunnar Schramm, Marc Zapatka, Roland Eils, Rainer König BMC Bioinformatics 2007, 8:149 (8 May 2007)

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primetv: a viewer for reconciled trees

Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad BMC Bioinformatics 2007, 8:148 (7 May 2007)

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Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins

Qiwen Dong, Xiaolong Wang, Lei Lin, Yi Guan BMC Bioinformatics 2007, 8:147 (5 May 2007)

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Analysis of probe level patterns in Affymetrix microarray data

Alexander C Cambon, Abdelnaby Khalyfa, Nigel GF Cooper, Caryn M Thompson BMC Bioinformatics 2007, 8:146 (4 May 2007)

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A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array

Tianwei Yu, Hui Ye, Wei Sun, Ker-Chau Li, Zugen Chen, Sharoni Jacobs, Dione K Bailey, David T Wong, Xiaofeng Zhou BMC Bioinformatics 2007, 8:145 (3 May 2007)

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Recursive Cluster Elimination (RCE) for classification and feature selection from gene expression data

Malik Yousef, Segun Jung, Louise C Showe, Michael K Showe BMC Bioinformatics 2007, 8:144 (2 May 2007)

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VSGdb: a database for trypanosome variant surface glycoproteins, a large and diverse family of coiled coil proteins

Lucio Marcello, Suraj Menon, Pauline Ward, Jonathan M Wilkes, Nicola G Jones, Mark Carrington, J David Barry BMC Bioinformatics 2007, 8:143 (2 May 2007)

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Pre-processing Agilent microarray data

Marianna Zahurak, Giovanni Parmigiani, Wayne Yu, Robert B Scharpf, David Berman, Edward Schaeffer, Shabana Shabbeer, Leslie Cope BMC Bioinformatics 2007, 8:142 (1 May 2007)

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