Bioinformatics

DISCOVERY NOTES:

Yong Zhang, Zhihua Zhang, Lunjiang Ling, Baochen Shi, and Runsheng Chen

Conservation analysis of small RNA genes in Escherichia coli
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 599-603; doi:10.1093/bioinformatics/btg457 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Svetalana Novichkova, Alexander Nikitin, and Ilya Mazo

Extracting human protein interactions from MEDLINE using a full-sentence parser
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 604-611; doi:10.1093/bioinformatics/btg452 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ren Zhang and Chun-Ting Zhang

A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 612-622; doi:10.1093/bioinformatics/btg453 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Paul H. C. Eilers and Jelle J. Goeman

Enhancing scatterplots with smoothed densities
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 623-628; doi:10.1093/bioinformatics/btg454 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. Lavigne, W.D. Sun, and G. Volckaert

PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 629-635; doi:10.1093/bioinformatics/btg456 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, and Inna Dubchak

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 636-643; doi:10.1093/bioinformatics/btg459 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alexey V. Antonov, Igor V. Tetko, Michael T. Mader, Jan Budczies, and Hans W. Mewes

Optimization models for cancer classification: extracting gene interaction information from microarray expression data
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 644-652; doi:10.1093/bioinformatics/btg462 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alessandro Vullo and Paolo Frasconi

Disulfide connectivity prediction using recursive neural networks and evolutionary information
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 653-659; doi:10.1093/bioinformatics/btg463 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Blythe P. Durbin and David M. Rocke

Variance-stabilizing transformations for two-color microarrays
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 660-667; doi:10.1093/bioinformatics/btg464 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jonathan D. Wren

404 not found: the stability and persistence of URLs published in MEDLINE
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 668-672; doi:10.1093/bioinformatics/btg465 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Feng Gao and Chun-Ting Zhang

Comparison of various algorithms for recognizing short coding sequences of human genes
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 673-681; doi:10.1093/bioinformatics/btg467 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David R. Bickel

Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 682-688; doi:10.1093/bioinformatics/btg468 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Michael A. Gilchrist, Laura A. Salter, and Andreas Wagner

A statistical framework for combining and interpreting proteomic datasets
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 689-700; doi:10.1093/bioinformatics/btg469 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Akito Taneda

Adplot: detection and visualization of repetitive patterns in complete genomes
Bioinformatics Advance Access published on January 22, 2004
Bioinformatics 2004 20: 701-708; doi:10.1093/bioinformatics/btg470 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

P. R. Romero and P. D. Karp

Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 709-717; doi:10.1093/bioinformatics/btg471 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

H. Fujisawa, S. Eguchi, M. Ushijima, S. Miyata, Y. Miki, T. Muto, and M. Matsuura

Genotyping of single nucleotide polymorphism using model-based clustering
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 718-726; doi:10.1093/bioinformatics/btg475 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Hao Sun and Ramana V. Davuluri

Java-based application framework for visualization of gene regulatory region annotations
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 727-734; doi:10.1093/bioinformatics/btg476 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Zheng Rong Yang and Kuo-Chen Chou

Bio-support vector machines for computational proteomics
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 735-741; doi:10.1093/bioinformatics/btg477 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Lap Kun Yeung, Lap Keung Szeto, Alan Wee-Chung Liew, and Hong Yan

Dominant spectral component analysis for transcriptional regulations using microarray time-series data
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 742-749; doi:10.1093/bioinformatics/btg479 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tu Minh Phuong, Doheon Lee, and Kwang Hyung Lee

Regression trees for regulatory element identification
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 750-757; doi:10.1093/bioinformatics/btg480 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yinon Shafrir and H. Robert Guy

STAM: simple Transmembrane Alignment Method
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 758-769; doi:10.1093/bioinformatics/btg482 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

I. Sommer, J. Rahnenführer, F.S. Domingues, U. de Lichtenberg, and T. Lengauer

Predicting protein structure classes from function predictions
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 770-776; doi:10.1093/bioinformatics/btg483 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Keith A. Baggerly, Jeffrey S. Morris, and Kevin R. Coombes

Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 777-785; doi:10.1093/bioinformatics/btg484 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Jakob C. Mueller and Christophe Andreoli

Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 786-787; doi:10.1093/bioinformatics/btg481 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gill Bejerano

Algorithms for variable length Markov chain modeling
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 788-789; doi:10.1093/bioinformatics/btg489 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

L. Frangeul, P. Glaser, C. Rusniok, C. Buchrieser, E. Duchaud, P. Dehoux, and F. Kunst

CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 790-797; doi:10.1093/bioinformatics/btg490 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Joseba Bikandi, Rosario San Millán, Aitor Rementeria, and Javier Garaizar

In silico analysis of complete bacterial genomes: PCR, AFLP–PCR and endonuclease restriction
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 798-799; doi:10.1093/bioinformatics/btg491 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andre R. O. Cavalcanti and Laura F. Landweber

Gene Unscrambler for detangling scrambled genes in ciliates
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 800-802; doi:10.1093/bioinformatics/bth003 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Martti T. Tammi, Erik Arner, Ellen Kindlund, and Björn Andersson

ReDiT: Repeat Discrepancy Tagger—a shotgun assembly finishing aid
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 803-804; doi:10.1093/bioinformatics/bth004 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Gernot Stocker, Dietmar Rieder, and Zlatko Trajanoski

ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 805-807; doi:10.1093/bioinformatics/bth014 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

C. Wiederkehr, R. Basavaraj, C. Sarrauste de Menthière, R. Koch, U. Schlecht, L. Hermida, B. Masdoua, R. Ishii, V. Cassen, M. Yamamoto, C. Lane, M. Cherry, N. Lamb, and M. Primig

Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 808-811; doi:10.1093/bioinformatics/bth030 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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