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Previous Next 		Contents: Volume 23, Number 20, 15 October 2007   [Index by Author] 
       REVIEW
                SYSTEMS BIOLOGY
       DISCOVERY NOTE
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                SYSTEMS BIOLOGY
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REVIEW:

SYSTEMS BIOLOGY:

Matthew Suderman and Michael Hallett
Tools for visually exploring biological networks
Bioinformatics Advance Access published on August 25, 2007
Bioinformatics 2007 23: 2651-2659; doi:10.1093/bioinformatics/btm401 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Lakshminarayan M. Iyer, Vivek Anantharaman, and L. Aravind
The DOMON domains are involved in heme and sugar recognition
Bioinformatics Advance Access published on September 18, 2007
Bioinformatics 2007 23: 2660-2664; doi:10.1093/bioinformatics/btm411 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Chris Reed, Viacheslav Fofanov, Catherine Putonti, Sergei Chumakov, Tom Slezak, and Yuriy Fofanov
Effect of the mutation rate and background size on the quality of pathogen identification
Bioinformatics Advance Access published on September 19, 2007
Bioinformatics 2007 23: 2665-2671; doi:10.1093/bioinformatics/btm420 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Issaac Rajan, Sarang Aravamuthan, and Sharmila S. Mande
Identification of compositionally distinct regions in genomes using the centroid method
Bioinformatics Advance Access published on August 27, 2007
Bioinformatics 2007 23: 2672-2677; doi:10.1093/bioinformatics/btm405 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Csaba Hetényi, Uko Maran, Alfonso T. García-Sosa, and Mati Karelson
Structure-based calculation of drug efficiency indices
Bioinformatics Advance Access published on September 5, 2007
Bioinformatics 2007 23: 2678-2685; doi:10.1093/bioinformatics/btm431 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

GENE EXPRESSION:

Thomas Tang, Nicolas François, Annie Glatigny, Nicolas Agier, Marie-Hélène Mucchielli, Lawrence Aggerbeck, and Hervé Delacroix
Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment
Bioinformatics Advance Access published on August 12, 2007
Bioinformatics 2007 23: 2686-2691; doi:10.1093/bioinformatics/btm399 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Matthew A. Hibbs, David C. Hess, Chad L. Myers, Curtis Huttenhower, Kai Li, and Olga G. Troyanskaya
Exploring the functional landscape of gene expression: directed search of large microarray compendia
Bioinformatics Advance Access published on August 27, 2007
Bioinformatics 2007 23: 2692-2699; doi:10.1093/bioinformatics/btm403 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Matthew E. Ritchie, Jeremy Silver, Alicia Oshlack, Melissa Holmes, Dileepa Diyagama, Andrew Holloway, and Gordon K. Smyth
A comparison of background correction methods for two-colour microarrays
Bioinformatics Advance Access published on August 25, 2007
Bioinformatics 2007 23: 2700-2707; doi:10.1093/bioinformatics/btm412 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Michele Leone, Sumedha, and Martin Weigt
Clustering by soft-constraint affinity propagation: applications to gene-expression data
Bioinformatics Advance Access published on September 25, 2007
Bioinformatics 2007 23: 2708-2715; doi:10.1093/bioinformatics/btm414 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Duygu Ucar, Isaac Neuhaus, Petra Ross-MacDonald, Charles Tilford, Srinivasan Parthasarathy, Nathan Siemers, and Rui-Ru Ji
Construction of a reference gene association network from multiple profiling data: application to data analysis
Bioinformatics Advance Access published on September 10, 2007
Bioinformatics 2007 23: 2716-2724; doi:10.1093/bioinformatics/btm423 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Giacomo Gamberoni, Evelina Lamma, Gianluca Lodo, Jlenia Marchesini, Nicoletta Mascellani, Simona Rossi, Sergio Storari, Luca Tagliavini, and Stefano Volinia
Fun&Co: identification of key functional differences in transcriptomes
Bioinformatics Advance Access published on September 23, 2007
Bioinformatics 2007 23: 2725-2732; doi:10.1093/bioinformatics/btm425 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Carla S. Möller-Levet, Catharine M. West, and Crispin J. Miller
Exploiting sample variability to enhance multivariate analysis of microarray data
Bioinformatics Advance Access published on September 7, 2007
Bioinformatics 2007 23: 2733-2740; doi:10.1093/bioinformatics/btm441 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Yik Y. Teo, Michael Inouye, Kerrin S. Small, Rhian Gwilliam, Panagiotis Deloukas, Dominic P. Kwiatkowski, and Taane G. Clark
A genotype calling algorithm for the Illumina BeadArray platform
Bioinformatics Advance Access published on September 10, 2007
Bioinformatics 2007 23: 2741-2746; doi:10.1093/bioinformatics/btm443 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

C. Kreutz, M.M. Bartolome Rodriguez, T. Maiwald, M. Seidl, H.E. Blum, L. Mohr, and J. Timmer
An error model for protein quantification
Bioinformatics Advance Access published on September 3, 2007
Bioinformatics 2007 23: 2747-2753; doi:10.1093/bioinformatics/btm397 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Raman Lall and Julie Mitchell
Metal reduction kinetics in Shewanella
Bioinformatics Advance Access published on August 25, 2007
Bioinformatics 2007 23: 2754-2759; doi:10.1093/bioinformatics/btm400 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Yizhi Cai, Brian Hartnett, Claes Gustafsson, and Jean Peccoud
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
Bioinformatics Advance Access published on September 5, 2007
Bioinformatics 2007 23: 2760-2767; doi:10.1093/bioinformatics/btm446 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

DATA AND TEXT MINING:

Yoshimasa Tsuruoka, John McNaught, Jun'i;chi Tsujii, and Sophia Ananiadou
Learning string similarity measures for gene/protein name dictionary look-up using logistic regression
Bioinformatics Advance Access published on August 12, 2007
Bioinformatics 2007 23: 2768-2774; doi:10.1093/bioinformatics/btm393 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Ali Cakmak and Gultekin Ozsoyoglu
Mining biological networks for unknown pathways
Bioinformatics Advance Access published on August 30, 2007
Bioinformatics 2007 23: 2775-2783; doi:10.1093/bioinformatics/btm409 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Norman Warthmann, Joffrey Fitz, and Detlef Weigel
MSQT for choosing SNP assays from multiple DNA alignments
Bioinformatics Advance Access published on September 4, 2007
Bioinformatics 2007 23: 2784-2787; doi:10.1093/bioinformatics/btm428 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Zhanfeng Wang, Yuan-chin I. Chang, Zhiliang Ying, Liang Zhu, and Yaning Yang
A parsimonious threshold-independent protein feature selection method through the area under receiver operating characteristic curve
Bioinformatics Advance Access published on September 18, 2007
Bioinformatics 2007 23: 2788-2794; doi:10.1093/bioinformatics/btm442 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

SEQUENCE ANALYSIS:

Madhavi Ganapathiraju, Christopher Jon Jursa, Hassan A. Karimi, and Judith Klein-Seetharaman
TMpro web server and web service: transmembrane helix prediction through amino acid property analysis
Bioinformatics Advance Access published on August 27, 2007
Bioinformatics 2007 23: 2795-2796; doi:10.1093/bioinformatics/btm398 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Ekachai Jenwitheesuk and Ram Samudrala
Identification of potential HIV-1 targets of minocycline
Bioinformatics Advance Access published on September 5, 2007
Bioinformatics 2007 23: 2797-2799; doi:10.1093/bioinformatics/btm424 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Sean Sedwards and Tommaso Mazza
Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes
Bioinformatics Advance Access published on September 13, 2007
Bioinformatics 2007 23: 2800-2802; doi:10.1093/bioinformatics/btm416 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Seth I. Berger, Ravi Iyengar, and Avi Ma’ayan
AVIS: AJAX viewer of interactive signaling networks
Bioinformatics Advance Access published on September 12, 2007
Bioinformatics 2007 23: 2803-2805; doi:10.1093/bioinformatics/btm444 [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.