Articles
Volume 8 (2007) - January 2007
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Research article
Computational RNA secondary structure design: empirical complexity and improved methods Rosalía Aguirre-Hernández, Holger H Hoos, Anne Condon BMC Bioinformatics 2007, 8:34 (31 January 2007) |
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Research article
Considerations in the identification of functional RNA structural elements in genomic alignments Tomas Babak, Benjamin J Blencowe, Timothy R Hughes BMC Bioinformatics 2007, 8:33 (30 January 2007) Search tools perform poorly at finding noncoding RNAs on a test set of known ncRNAs for which the sequences are randomly shuffled, although a combination of conservation and thermodynamic stability has promise for ncRNA detection.
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Research article
Context based mixture model for cell phase identification in automated fluorescence microscopy Meng Wang, Xiaobo Zhou, Randy W King, Stephen TC Wong BMC Bioinformatics 2007, 8:32 (30 January 2007) |
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Methodology article
Conceptual-level workflow modeling of scientific experiments using NMR as a case study Kacy K Verdi, Heidi JC Ellis, Michael R Gryk BMC Bioinformatics 2007, 8:31 (30 January 2007) |
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Methodology article
Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control Ana P Teixeira, Carlos Alves, Paula M Alves, Manuel JT Carrondo, Rui Oliveira BMC Bioinformatics 2007, 8:30 (29 January 2007) |
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Research article
Measuring similarities between gene expression profiles through new data transformations Kyungpil Kim, Shibo Zhang, Keni Jiang, Li Cai, In-Beum Lee, Lewis J Feldman, Haiyan Huang BMC Bioinformatics 2007, 8:29 (27 January 2007) |
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Research article
Detecting differential expression in microarray data: comparison of optimal procedures Elena Perelman, Alexander Ploner, Stefano Calza, Yudi Pawitan BMC Bioinformatics 2007, 8:28 (26 January 2007) |
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Research article
Scoring functions and enrichment: a case study on Hsp90 Chrysi Konstantinou-Kirtay, John BO Mitchell, James A Lumley BMC Bioinformatics 2007, 8:27 (26 January 2007) |
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Research article
Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data Andy G Lynch, David E Neal, John D Kelly, Glyn J Burtt, Natalie P Thorne BMC Bioinformatics 2007, 8:26 (25 January 2007) A missing channel of a two-channel microarray usually results in either low quality data included in analyses or exclusion of some good quality data, but a compromise approach outperforms either strategy.
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Methodology article
Bias in random forest variable importance measures: Illustrations, sources and a solution Carolin Strobl, Anne-Laure Boulesteix, Achim Zeileis, Torsten Hothorn BMC Bioinformatics 2007, 8:25 (25 January 2007) Random forest algorithms classify biological data, and can be biased when variables of different types are used such as sequence data and folding energy, but if the weighting of the importance of the variables is calculated differently this bias is corrected.
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Research article
Benchmarking natural-language parsers for biological applications using dependency graphs Andrew B Clegg, Adrian J Shepherd BMC Bioinformatics 2007, 8:24 (25 January 2007) |
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Research article
Motif kernel generated by genetic programming improves remote homology and fold detection Tony Håndstad, Arne JH Hestnes, Pål Sætrom BMC Bioinformatics 2007, 8:23 (25 January 2007) |
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Research article
Gene network interconnectedness and the generalized topological overlap measure Andy M Yip, Steve Horvath BMC Bioinformatics 2007, 8:22 (24 January 2007) |
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Software
GraphDNA: a Java program for graphical display of DNA composition analyses Jamie M Thomas, Daniel Horspool, Gordon Brown, Vasily Tcherepanov, Chris Upton BMC Bioinformatics 2007, 8:21 (23 January 2007) |
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Research article
Abdallah Sayyed-Ahmad, Kagan Tuncay, Peter J Ortoleva BMC Bioinformatics 2007, 8:20 (23 January 2007) Problems caused by errors in microarray data can be resolved using probabilistic modeling of transcriptional regulatory networks that includes estimates of transcription factor thermodynamics, mRNA degradation and transcription rate coefficients.
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Methodology article
Statistical significance of cis-regulatory modules Dustin E Schones, Andrew D Smith, Michael Q Zhang BMC Bioinformatics 2007, 8:19 (22 January 2007) |
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Software
PILER-CR: Fast and accurate identification of CRISPR repeats Robert C Edgar BMC Bioinformatics 2007, 8:18 (20 January 2007) |
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Commentary
Publishing perishing? Towards tomorrow's information architecture Michael R Seringhaus, Mark B Gerstein BMC Bioinformatics 2007, 8:17 (19 January 2007) |
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Methodology article
Multivariate Analysis and Visualization of Splicing Correlations in Single-Gene Transcriptomes Mark C Emerick, Giovanni Parmigiani, William S Agnew BMC Bioinformatics 2007, 8:16 (18 January 2007) |
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Software
Ayumu Saito, Masao Nagasaki, Masaaki Oyama, Hiroko Kozuka-Hata, Kentaro Semba, Sumio Sugano, Tadashi Yamamoto, Satoru Miyano BMC Bioinformatics 2007, 8:15 (18 January 2007) |
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Research article
Rob Jelier, Guido Jenster, Lambert CJ Dorssers, Bas J Wouters, Peter JM Hendriksen, Barend Mons, Ruud Delwel, Jan A Kors BMC Bioinformatics 2007, 8:14 (18 January 2007) |
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Research article
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips Maria A Stalteri, Andrew P Harrison BMC Bioinformatics 2007, 8:13 (15 January 2007) |
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Methodology article
Efficient classification of complete parameter regions based on semidefinite programming Lars Kuepfer, Uwe Sauer, Pablo A Parrilo BMC Bioinformatics 2007, 8:12 (15 January 2007) |
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Research article
Yukiko Yagi, Kotaro Terada, Takahisa Noma, Kazunori Ikebukuro, Koji Sode BMC Bioinformatics 2007, 8:11 (12 January 2007) |
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Methodology article
Bioinformatics analysis of the early inflammatory response in a rat thermal injury model Eric Yang, Timothy Maguire, Martin L Yarmush, Francois Berthiaume, Ioannis P Androulakis BMC Bioinformatics 2007, 8:10 (10 January 2007) |
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Software
IDconverter and IDClight: Conversion and annotation of gene and protein IDs Andreu Alibés, Patricio Yankilevich, Andrés Cañada, Ramón Díaz-Uriarte BMC Bioinformatics 2007, 8:9 (10 January 2007) |
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Methodology article
Least-squares methods for identifying biochemical regulatory networks from noisy measurements Jongrae Kim, Declan G Bates, Ian Postlethwaite, Pat Heslop-Harrison, Kwang-Hyun Cho BMC Bioinformatics 2007, 8:8 (10 January 2007) |
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Software
eQTL Viewer: visualizing how sequence variation affects genome-wide transcription Wei Zou, David L Aylor, Zhao-Bang Zeng BMC Bioinformatics 2007, 8:7 (9 January 2007) |
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Research article
Roger A Craig, Li Liao BMC Bioinformatics 2007, 8:6 (9 January 2007) |
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Research article
Nikhil R Pal, Kripamoy Aguan, Animesh Sharma, Shun-ichi Amari BMC Bioinformatics 2007, 8:5 (6 January 2007) |
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Methodology article
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines Irini A Doytchinova, Darren R Flower BMC Bioinformatics 2007, 8:4 (5 January 2007) |
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Methodology article
FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data Limin Fu, Enzo Medico BMC Bioinformatics 2007, 8:3 (4 January 2007) |
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Software
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences Manjunatha R Karpenahalli, Andrei N Lupas, Johannes Söding BMC Bioinformatics 2007, 8:2 (3 January 2007) |
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Research article
Comparing sequences without using alignments: application to HIV/SIV subtyping Gilles Didier, Laurent Debomy, Maude Pupin, Ming Zhang, Alexander Grossmann, Claudine Devauchelle, Ivan Laprevotte BMC Bioinformatics 2007, 8:1 (2 January 2007) |
