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Previous Next 		Contents: Volume 23, Number 5, March 2007   [Index by Author] 
       DISCOVERY NOTE
                STRUCTURAL BIOINFORMATICS
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       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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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.

DISCOVERY NOTE:

STRUCTURAL BIOINFORMATICS:

Jerzy Orlowski, Michal Boniecki, and Janusz M. Bujnicki
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition
Bioinformatics Advance Access published on January 22, 2007
Bioinformatics 2007 23: 527-530; doi:10.1093/bioinformatics/btm007 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang, and Michael Q. Zhang
Computing exact P-values for DNA motifs
Bioinformatics Advance Access published on January 18, 2007
Bioinformatics 2007 23: 531-537; doi:10.1093/bioinformatics/btl662 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

David T. Jones
Improving the accuracy of transmembrane protein topology prediction using evolutionary information
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 538-544; doi:10.1093/bioinformatics/btl677 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Evan Keibler, Manimozhiyan Arumugam, and Michael R. Brent
The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs
Bioinformatics Advance Access published on January 18, 2007
Bioinformatics 2007 23: 545-554; doi:10.1093/bioinformatics/btl659 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

J. Bernauer, J. Azé, J. Janin, and A. Poupon
A new protein–protein docking scoring function based on interface residue properties
Bioinformatics Advance Access published on January 18, 2007
Bioinformatics 2007 23: 555-562; doi:10.1093/bioinformatics/btl654 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jianping Chen, Xi Zhang, and Ariel Fernández
Molecular basis for specificity in the druggable kinome: sequence-based analysis
Bioinformatics Advance Access published on January 25, 2007
Bioinformatics 2007 23: 563-572; doi:10.1093/bioinformatics/btl666 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Simon J. Cockell, Baldo Oliva, and Richard M. Jackson
Structure-based evaluation of in silico predictions of protein–protein interactions using Comparative Docking
Bioinformatics Advance Access published on January 18, 2007
Bioinformatics 2007 23: 573-581; doi:10.1093/bioinformatics/btl661 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

T. Sobha Rani, S. Durga Bhavani, and Raju S. Bapi
Analysis of E.coli promoter recognition problem in dinucleotide feature space
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 582-588; doi:10.1093/bioinformatics/btl670 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Jie Zhou and Hanchuan Peng
Automatic recognition and annotation of gene expression patterns of fly embryos
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 589-596; doi:10.1093/bioinformatics/btl680 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Ming-Hui Li, Lei Lin, Xiao-Long Wang, and Tao Liu
Protein–protein interaction site prediction based on conditional random fields
Bioinformatics Advance Access published on January 18, 2007
Bioinformatics 2007 23: 597-604; doi:10.1093/bioinformatics/btl660 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Matthias E. Futschik, Gautam Chaurasia, and Hanspeter Herzel
Comparison of human protein–protein interaction maps
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 605-611; doi:10.1093/bioinformatics/btl683 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Debojyoti Dutta and Ting Chen
Speeding up tandem mass spectrometry database search: metric embeddings and fast near neighbor search
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 612-618; doi:10.1093/bioinformatics/btl645 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

H. W. Ressom, R. S. Varghese, S. K. Drake, G. L. Hortin, M. Abdel-Hamid, C. A. Loffredo, and R. Goldman
Peak selection from MALDI-TOF mass spectra using ant colony optimization
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 619-626; doi:10.1093/bioinformatics/btl678 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Robert B. Scharpf, Jason C. Ting, Jonathan Pevsner, and Ingo Ruczinski
SNPchip: R classes and methods for SNP array data
Bioinformatics Advance Access published on January 4, 2007
Bioinformatics 2007 23: 627-628; doi:10.1093/bioinformatics/btl638 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, and Veli Mäkinen
Compressed suffix tree—a basis for genome-scale sequence analysis
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 629-630; doi:10.1093/bioinformatics/btl681 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Liping Du, Hongxia Zhou, and Hong Yan
OMWSA: detection of DNA repeats using moving window spectral analysis
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 631-633; doi:10.1093/bioinformatics/btm008 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Seungwoo Hwang, Zhenkun Gou, and Igor B. Kuznetsov
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 634-636; doi:10.1093/bioinformatics/btl672 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Ganesan Pugalenthi, P. N. Suganthan, R. Sowdhamini, and Saikat Chakrabarti
SMotif: a server for structural motifs in proteins
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 637-638; doi:10.1093/bioinformatics/btl679 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

Eugene Novikov and Emmanuel Barillot
Software package for automatic microarray image analysis (MAIA)
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 639-640; doi:10.1093/bioinformatics/btl644 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Brian S. Yandell, Tapan Mehta, Samprit Banerjee, Daniel Shriner, Ramprasad Venkataraman, Jee Young Moon, W. Whipple Neely, Hao Wu, Randy von Smith, and Nengjun Yi
R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 641-643; doi:10.1093/bioinformatics/btm011 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Juan R. González, Lluís Armengol, Xavier Solé, Elisabet Guinó, Josep M. Mercader, Xavier Estivill, and Víctor Moreno
SNPassoc: an R package to perform whole genome association studies
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 654-655; doi:10.1093/bioinformatics/btm025 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SYSTEMS BIOLOGY:

Henning Schmidt
SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB
Bioinformatics Advance Access published on January 18, 2007
Bioinformatics 2007 23: 646-647; doi:10.1093/bioinformatics/btl668 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Heinrich J. Huber, Markus Rehm, Martin Plchut, Heiko Düssmann, and Jochen H. M. Prehn
APOPTO-CELL—a simulation tool and interactive database for analyzing cellular susceptibility to apoptosis
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 648-650; doi:10.1093/bioinformatics/btl684 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Jan E. Gewehr, Martin Szugat, and Ralf Zimmer
BioWeka—extending the Weka framework for bioinformatics
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 651-653; doi:10.1093/bioinformatics/btl671 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

D. Guzman, D. Veit, V. Knerr, G. Kindle, B. Gathmann, A. M. Eades-Perner, and B. Grimbacher
The ESID Online Database network
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 654-655; doi:10.1093/bioinformatics/btl675 [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.