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Previous Next 		Contents: Volume 22, Number 18, 15 September 2006   [Index by Author] 
       EDITORIALS
       DISCOVERY NOTE
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
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EDITORIALS:

Wentian Li
The-more-the-better and the-less-the-better
Bioinformatics 2006 22: 2187-2188; doi:10.1093/bioinformatics/btl189 [Extract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Quan-yuan He, Xiang-hua Liu, Qiang Li, David J. Studholme, Xuan-wen Li, and Song-ping Liang
G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 2189-2191; doi:10.1093/bioinformatics/btl123 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Jonathan W. Arthur, Angeles Sanchez-Perez, and David I. Cook
Scoring of predicted GRK2 phosphorylation sites in Nedd4-2
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2192-2195; doi:10.1093/bioinformatics/btl381 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Georgios S. Vernikos and Julian Parkhill
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
Bioinformatics Advance Access published on July 12, 2006
Bioinformatics 2006 22: 2196-2203; doi:10.1093/bioinformatics/btl369 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

SEQUENCE ANALYSIS:

Fang Fang, Shicai Fan, Xuegong Zhang, and Michael Q. Zhang
Predicting methylation status of CpG islands in the human brain
Bioinformatics Advance Access published on July 12, 2006
Bioinformatics 2006 22: 2204-2209; doi:10.1093/bioinformatics/btl377 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Lang Li, Alfred S. L. Cheng, Victor X. Jin, Henry H. Paik, Meiyun Fan, Xiaoman Li, Wei Zhang, Jason Robarge, Curtis Balch, Ramana V. Davuluri, Sun Kim, Tim H.-M. Huang, and Kenneth P. Nephew
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-{alpha}
Bioinformatics Advance Access published on June 29, 2006
Bioinformatics 2006 22: 2210-2216; doi:10.1093/bioinformatics/btl329 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Henry C. M. Leung and Francis Y. L. Chin
Finding motifs from all sequences with and without binding sites
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2217-2223; doi:10.1093/bioinformatics/btl371 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Thomas Lingner and Peter Meinicke
Remote homology detection based on oligomer distances
Bioinformatics Advance Access published on July 12, 2006
Bioinformatics 2006 22: 2224-2231; doi:10.1093/bioinformatics/btl376 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ketil Malde, Korbinian Schneeberger, Eivind Coward, and Inge Jonassen
RBR: library-less repeat detection for ESTs
Bioinformatics Advance Access published on July 12, 2006
Bioinformatics 2006 22: 2232-2236; doi:10.1093/bioinformatics/btl368 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Jordi Espadaler, Enrique Querol, Francesc X. Aviles, and Baldo Oliva
Identification of function-associated loop motifs and application to protein function prediction
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2237-2243; doi:10.1093/bioinformatics/btl382 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Yifan Huang, Haiyan Xu, Violeta Calian, and Jason C. Hsu
To permute or not to permute
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2244-2248; doi:10.1093/bioinformatics/btl383 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Dougu Nam, Sang-Bae Kim, Seon-Kyu Kim, Sungjin Yang, Seon-Young Kim, and In-Sun Chu
ADGO: analysis of differentially expressed gene sets using composite GO annotation
Bioinformatics Advance Access published on July 12, 2006
Bioinformatics 2006 22: 2249-2253; doi:10.1093/bioinformatics/btl378 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Ariadni Papana and Hemant Ishwaran
CART variance stabilization and regularization for high-throughput genomic data
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2254-2261; doi:10.1093/bioinformatics/btl384 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Naijun Sha, Mahlet G. Tadesse, and Marina Vannucci
Bayesian variable selection for the analysis of microarray data with censored outcomes
Bioinformatics Advance Access published on July 15, 2006
Bioinformatics 2006 22: 2262-2268; doi:10.1093/bioinformatics/btl362 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Andrew E. Teschendorff, Ali Naderi, Nuno L. Barbosa-Morais, and Carlos Caldas
PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
Bioinformatics Advance Access published on May 8, 2006
Bioinformatics 2006 22: 2269-2275; doi:10.1093/bioinformatics/btl174 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Yu-Hsiang Chang, Yu-Chao Wang, and Bor-Sen Chen
Identification of transcription factor cooperativity via stochastic system model
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2276-2282; doi:10.1093/bioinformatics/btl380 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jingchun Chen and Bo Yuan
Detecting functional modules in the yeast protein–protein interaction network
Bioinformatics Advance Access published on July 12, 2006
Bioinformatics 2006 22: 2283-2290; doi:10.1093/bioinformatics/btl370 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Pall F. Jonsson and Paul A. Bates
Global topological features of cancer proteins in the human interactome
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2291-2297; doi:10.1093/bioinformatics/btl390 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATA AND TEXT MINING:

James Lewis, Stephan Ossowski, Justin Hicks, Mounir Errami, and Harold R. Garner
Text similarity: an alternative way to search MEDLINE
Bioinformatics Advance Access published on August 22, 2006
Bioinformatics 2006 22: 2298-2304; doi:10.1093/bioinformatics/btl388 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Eun-Kyung Lee, Sung-Gon Yi, and Taesung Park
arrayQCplot: software for checking the quality of microarray data
Bioinformatics Advance Access published on July 24, 2006
Bioinformatics 2006 22: 2305-2307; doi:10.1093/bioinformatics/btl367 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Haiming Wang, Yanqi Su, Aaron J. Mackey, Eileen T. Kraemer, and Jessica C. Kissinger
SynView: a GBrowse-compatible approach to visualizing comparative genome data
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2308-2309; doi:10.1093/bioinformatics/btl389 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Rajesh Chowdhary, Sin Lam Tan, R. Ayesha Ali, Brent Boerlage, Limsoon Wong, and Vladimir B Bajic
Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures
Bioinformatics Advance Access published on April 13, 2006
Bioinformatics 2006 22: 2310-2312; doi:10.1093/bioinformatics/btl125 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

PHYLOGENETICS:

Patricia Buendia and Giri Narasimhan
Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2313-2314; doi:10.1093/bioinformatics/btl387 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Claudio Lottaz, Xinan Yang, Stefanie Scheid, and Rainer Spang
OrderedList—a bioconductor package for detecting similarity in ordered gene lists
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2315-2316; doi:10.1093/bioinformatics/btl385 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Jesper N. Madsen, Jotun Hein, and Leif Schauser
GeneRecon—a coalescent based tool for fine-scale association mapping
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 2317-2318; doi:10.1093/bioinformatics/btl153 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.