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Contents: Volume 21, Number 16, August 15 2005   [Index by Author]       Other Issues: Previous Next  
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
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ORIGINAL PAPERS:

GENOME ANALYSIS:

Ryan T. Koehler and Nicolas Peyret
Thermodynamic properties of DNA sequences: characteristic values for the human genome
Bioinformatics Advance Access published on June 9, 2005
Bioinformatics 2005 21: 3333-3339; doi:10.1093/bioinformatics/bti530 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Sophia Yancopoulos, Oliver Attie, and Richard Friedberg
Efficient sorting of genomic permutations by translocation, inversion and block interchange
Bioinformatics Advance Access published on June 9, 2005
Bioinformatics 2005 21: 3340-3346; doi:10.1093/bioinformatics/bti535 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Daniel P. Aalberts, Eric G. Daub, and Jesse W. Dill
Quantifying optimal accuracy of local primary sequence bioinformatics methods
Bioinformatics Advance Access published on May 27, 2005
Bioinformatics 2005 21: 3347-3351; doi:10.1093/bioinformatics/bti521 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Sven Siebert and Rolf Backofen
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
Bioinformatics Advance Access published on June 21, 2005
Bioinformatics 2005 21: 3352-3359; doi:10.1093/bioinformatics/bti550 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jordi Espadaler, Oriol Romero-Isart, Richard M. Jackson, and Baldo Oliva
Prediction of protein–protein interactions using distant conservation of sequence patterns and structure relationships
Bioinformatics Advance Access published on June 16, 2005
Bioinformatics 2005 21: 3360-3368; doi:10.1093/bioinformatics/bti522 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zheng Rong Yang, Rebecca Thomson, Philip McNeil, and Robert M. Esnouf
RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins
Bioinformatics Advance Access published on June 9, 2005
Bioinformatics 2005 21: 3369-3376; doi:10.1093/bioinformatics/bti534 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Huiqing Liu, Jinyan Li, and Limsoon Wong
Use of extreme patient samples for outcome prediction from gene expression data
Bioinformatics Advance Access published on June 16, 2005
Bioinformatics 2005 21: 3377-3384; doi:10.1093/bioinformatics/bti544 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Wei Chu, Zoubin Ghahramani, Francesco Falciani, and David L. Wild
Biomarker discovery in microarray gene expression data with Gaussian processes
Bioinformatics Advance Access published on June 2, 2005
Bioinformatics 2005 21: 3385-3393; doi:10.1093/bioinformatics/bti526 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Thomas B. Kepler, Min He, John K. Tomfohr, Blythe H. Devlin, Marcella Sarzotti, and M. Louise Markert
Statistical analysis of antigen receptor spectratype data
Bioinformatics Advance Access published on June 14, 2005
Bioinformatics 2005 21: 3394-3400; doi:10.1093/bioinformatics/bti539 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Ron Y. Pinter, Oleg Rokhlenko, Esti Yeger-Lotem, and Michal Ziv-Ukelson
Alignment of metabolic pathways
Bioinformatics Advance Access published on June 28, 2005
Bioinformatics 2005 21: 3401-3408; doi:10.1093/bioinformatics/bti554 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jingchun Sun, Jinlin Xu, Zhen Liu, Qi Liu, Aimin Zhao, Tieliu Shi, and Yixue Li
Refined phylogenetic profiles method for predicting protein–protein interactions
Bioinformatics Advance Access published on June 9, 2005
Bioinformatics 2005 21: 3409-3415; doi:10.1093/bioinformatics/bti532 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Purvesh Khatri, Bogdan Done, Archana Rao, Arina Done, and Sorin Draghici
A semantic analysis of the annotations of the human genome
Bioinformatics Advance Access published on June 14, 2005
Bioinformatics 2005 21: 3416-3421; doi:10.1093/bioinformatics/bti538 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Tim J. Carver, Kim M. Rutherford, Matthew Berriman, Marie-Adele Rajandream, Barclay G. Barrell, and Julian Parkhill
ACT: the Artemis comparison tool
Bioinformatics Advance Access published on June 23, 2005
Bioinformatics 2005 21: 3422-3423; doi:10.1093/bioinformatics/bti553 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

B. DasGupta, K. M. Konwar, I. I. Mandoiu, and A. A. Shvartsman
DNA-BAR: distinguisher selection for DNA barcoding
Bioinformatics Advance Access published on June 16, 2005
Bioinformatics 2005 21: 3424-3426; doi:10.1093/bioinformatics/bti547 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Laurent Guéguen
Sarment: Python modules for HMM analysis and partitioning of sequences
Bioinformatics Advance Access published on June 9, 2005
Bioinformatics 2005 21: 3427-3428; doi:10.1093/bioinformatics/bti533 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Mike Smith, Victor Kunin, Leon Goldovsky, Anton J. Enright, and Christos A. Ouzounis
MagicMatch—cross-referencing sequence identifiers across databases
Bioinformatics Advance Access published on June 16, 2005
Bioinformatics 2005 21: 3429-3430; doi:10.1093/bioinformatics/bti548 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tim Oliver, Bertil Schmidt, Darran Nathan, Ralf Clemens, and Douglas Maskell
Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
Bioinformatics Advance Access published on May 26, 2005
Bioinformatics 2005 21: 3431-3432; doi:10.1093/bioinformatics/bti508 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Zsuzsanna Dosztányi, Veronika Csizmok, Peter Tompa, and István Simon
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
Bioinformatics Advance Access published on June 14, 2005
Bioinformatics 2005 21: 3433-3434; doi:10.1093/bioinformatics/bti541 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jaime Prilusky, Clifford E. Felder, Tzviya Zeev-Ben-Mordehai, Edwin H. Rydberg, Orna Man, Jacques S. Beckmann, Israel Silman, and Joel L. Sussman
FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded
Bioinformatics Advance Access published on June 14, 2005
Bioinformatics 2005 21: 3435-3438; doi:10.1093/bioinformatics/bti537 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma, and Wolfgang Huber
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
Bioinformatics 2005 21: 3439-3440; doi:10.1093/bioinformatics/bti525 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

M. Falque
IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains
Bioinformatics Advance Access published on June 16, 2005
Bioinformatics 2005 21: 3441-3442; doi:10.1093/bioinformatics/bti543 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

J.-L. Li, M.-X. Li, H.-Y. Deng, P. E. Duffy, and H.-W. Deng
PhD: a web database application for phenotype data management
Bioinformatics Advance Access published on June 28, 2005
Bioinformatics 2005 21: 3443-3444; doi:10.1093/bioinformatics/bti557 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Janis E. Wigginton and Gonçalo R. Abecasis
PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data
Bioinformatics Advance Access published on June 9, 2005
Bioinformatics 2005 21: 3445-3447; doi:10.1093/bioinformatics/bti529 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Steven Maere, Karel Heymans, and Martin Kuiper
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
Bioinformatics Advance Access published on June 21, 2005
Bioinformatics 2005 21: 3448-3449; doi:10.1093/bioinformatics/bti551 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Guido Dieterich, Uwe Kärst, Jürgen Wehland, and Lothar Jänsch
MineBlast: a literature presentation service supporting protein annotation by data mining of BLAST results
Bioinformatics Advance Access published on June 7, 2005
Bioinformatics 2005 21: 3450-3451; doi:10.1093/bioinformatics/bti528 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Weijian Xuan, Stanley J. Watson, and Fan Meng
GeneInfoMiner—a web server for exploring biomedical literature using batch sequence ID
Bioinformatics Advance Access published on June 30, 2005
Bioinformatics 2005 21: 3452-3453; doi:10.1093/bioinformatics/bti559 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Markus Krummenacker, Suzanne Paley, Lukas Mueller, Thomas Yan, and Peter D. Karp
Querying and computing with BioCyc databases
Bioinformatics Advance Access published on June 16, 2005
Bioinformatics 2005 21: 3454-3455; doi:10.1093/bioinformatics/bti546 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Piotr Kraj and Richard A. McIndoe
caBIONet—A .NET wrapper to access and process genomic data stored at the National Cancer Institute's Center for Bioinformatics databases
Bioinformatics Advance Access published on June 16, 2005
Bioinformatics 2005 21: 3456-3458; doi:10.1093/bioinformatics/bti545 [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.