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Previous Next 		Contents: Volume 23, Number 21, 1 November 2007   [Index by Author] 
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
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ORIGINAL PAPERS:

GENOME ANALYSIS:

Ali Bashir, Yu-Tsueng Liu, Benjamin J. Raphael, Dennis Carson, and Vineet Bafna
Optimization of primer design for the detection of variable genomic lesions in cancer
Bioinformatics Advance Access published on August 30, 2007
Bioinformatics 2007 23: 2807-2815; doi:10.1093/bioinformatics/btm390 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Ersin Emre Oren, Candan Tamerler, Deniz Sahin, Marketa Hnilova, Urartu Ozgur Safak Seker, Mehmet Sarikaya, and Ram Samudrala
A novel knowledge-based approach to design inorganic-binding peptides
Bioinformatics Advance Access published on September 17, 2007
Bioinformatics 2007 23: 2816-2822; doi:10.1093/bioinformatics/btm436 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Bo Jiang, Michael Q. Zhang, and Xuegong Zhang
OSCAR: One-class SVM for accurate recognition of cis-elements
Bioinformatics Advance Access published on October 5, 2007
Bioinformatics 2007 23: 2823-2828; doi:10.1093/bioinformatics/btm473 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Michael J. Sweredoski, Kevin J. Donovan, Bao D. Nguyen, A.J. Shaka, and Pierre Baldi
Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling
Bioinformatics Advance Access published on September 25, 2007
Bioinformatics 2007 23: 2829-2835; doi:10.1093/bioinformatics/btm406 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Hung-Pin Peng and An-Suei Yang
Modeling protein loops with knowledge-based prediction of sequence-structure alignment
Bioinformatics Advance Access published on September 7, 2007
Bioinformatics 2007 23: 2836-2842; doi:10.1093/bioinformatics/btm456 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Ke Chen and Lukasz Kurgan
PFRES: protein fold classification by using evolutionary information and predicted secondary structure
Bioinformatics Advance Access published on October 17, 2007
Bioinformatics 2007 23: 2843-2850; doi:10.1093/bioinformatics/btm475 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Frank DiMaio, Dmitry A. Kondrashov, Eduard Bitto, Ameet Soni, Craig A. Bingman, George N. Phillips, Jr, and Jude W. Shavlik
Creating protein models from electron-density maps using particle-filtering methods
Bioinformatics Advance Access published on October 12, 2007
Bioinformatics 2007 23: 2851-2858; doi:10.1093/bioinformatics/btm480 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Sanghamitra Bandyopadhyay, Anirban Mukhopadhyay, and Ujjwal Maulik
An improved algorithm for clustering gene expression data
Bioinformatics Advance Access published on August 25, 2007
Bioinformatics 2007 23: 2859-2865; doi:10.1093/bioinformatics/btm418 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Blaise Hanczar, Jean-Daniel Zucker, Corneliu Henegar, and Lorenza Saitta
Feature construction from synergic pairs to improve microarray-based classification
Bioinformatics Advance Access published on October 9, 2007
Bioinformatics 2007 23: 2866-2872; doi:10.1093/bioinformatics/btm429 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Kathe E. Bjork and Karen Kafadar
Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips®
Bioinformatics Advance Access published on September 25, 2007
Bioinformatics 2007 23: 2873-2880; doi:10.1093/bioinformatics/btm450 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Mark D. Robinson and Gordon K. Smyth
Moderated statistical tests for assessing differences in tag abundance
Bioinformatics Advance Access published on September 19, 2007
Bioinformatics 2007 23: 2881-2887; doi:10.1093/bioinformatics/btm453 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Zhiwen Yu, Hau-San Wong, and Hongqiang Wang
Graph-based consensus clustering for class discovery from gene expression data
Bioinformatics Advance Access published on September 14, 2007
Bioinformatics 2007 23: 2888-2896; doi:10.1093/bioinformatics/btm463 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Willem Talloen, Djork-Arné Clevert, Sepp Hochreiter, Dhammika Amaratunga, Luc Bijnens, Stefan Kass, and Hinrich W.H. Göhlmann
I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data
Bioinformatics Advance Access published on October 5, 2007
Bioinformatics 2007 23: 2897-2902; doi:10.1093/bioinformatics/btm478 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jiexin Zhang, Yuan Ji, and Li Zhang
Extracting three-way gene interactions from microarray data
Bioinformatics Advance Access published on October 5, 2007
Bioinformatics 2007 23: 2903-2909; doi:10.1093/bioinformatics/btm482 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Sangeeta B. English and Atul J. Butte
Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes
Bioinformatics Advance Access published on October 5, 2007
Bioinformatics 2007 23: 2910-2917; doi:10.1093/bioinformatics/btm483 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENETICS AND POPULATION ANALYSIS:

Ali Torkamani and Nicholas J. Schork
Accurate prediction of deleterious protein kinase polymorphisms
Bioinformatics Advance Access published on September 12, 2007
Bioinformatics 2007 23: 2918-2925; doi:10.1093/bioinformatics/btm437 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

SYSTEMS BIOLOGY:

Ming Zheng, Peng Lu, Yanzhou Liu, Joseph Pease, Jonathan Usuka, Guochun Liao, and Gary Peltz
2D NMR metabonomic analysis: a novel method for automated peak alignment
Bioinformatics Advance Access published on September 10, 2007
Bioinformatics 2007 23: 2926-2933; doi:10.1093/bioinformatics/btm427 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Atsushi Hijikata, Hiroshi Kitamura, Yayoi Kimura, Ryo Yokoyama, Yuichi Aiba, Yanyuan Bao, Shigeharu Fujita, Koji Hase, Shohei Hori, Yasuyuki Ishii, Osami Kanagawa, Hiroshi Kawamoto, Kazuya Kawano, Haruhiko Koseki, Masato Kubo, Ai Kurita-Miki, Tomohiro Kurosaki, Kyoko Masuda, Mitsumasa Nakata, Keisuke Oboki, Hiroshi Ohno, Mariko Okamoto, Yoshimichi Okayama, Jiyang O-Wang, Hirohisa Saito, Takashi Saito, Machie Sakuma, Katsuaki Sato, Kaori Sato, Ken-ichiro Seino, Ruka Setoguchi, Yuki Tamura, Masato Tanaka, Masaru Taniguchi, Ichiro Taniuchi, Annabelle Teng, Takeshi Watanabe, Hiroshi Watarai, Sho Yamasaki, and Osamu Ohara
Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
Bioinformatics Advance Access published on September 24, 2007
Bioinformatics 2007 23: 2934-2941; doi:10.1093/bioinformatics/btm430 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTES:

GENOME ANALYSIS:

William R. Jeck, Josephine A. Reinhardt, David A. Baltrus, Matthew T. Hickenbotham, Vincent Magrini, Elaine R. Mardis, Jeffery L. Dangl, and Corbin D. Jones
Extending assembly of short DNA sequences to handle error
Bioinformatics Advance Access published on September 24, 2007
Bioinformatics 2007 23: 2942-2944; doi:10.1093/bioinformatics/btm451 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Taishin Kin and Yukiteru Ono
Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat
Bioinformatics Advance Access published on September 24, 2007
Bioinformatics 2007 23: 2945-2946; doi:10.1093/bioinformatics/btm455 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson, and D.G. Higgins
Clustal W and Clustal X version 2.0
Bioinformatics Advance Access published on September 10, 2007
Bioinformatics 2007 23: 2947-2948; doi:10.1093/bioinformatics/btm404 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Sergey A. Shiryev, Jason S. Papadopoulos, Alejandro A. Schäffer, and Richa Agarwala
Improved BLAST searches using longer words for protein seeding
Bioinformatics Advance Access published on October 6, 2007
Bioinformatics 2007 23: 2949-2951; doi:10.1093/bioinformatics/btm479 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

PHYLOGENETICS:

John Archer and David L. Robertson
CTree: comparison of clusters between phylogenetic trees made easy
Bioinformatics Advance Access published on August 23, 2007
Bioinformatics 2007 23: 2952-2953; doi:10.1093/bioinformatics/btm410 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Víctor Soria-Carrasco, Gerard Talavera, Javier Igea, and Jose Castresana
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees
Bioinformatics Advance Access published on September 22, 2007
Bioinformatics 2007 23: 2954-2956; doi:10.1093/bioinformatics/btm466 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, and Martin Middendorf
CREx: inferring genomic rearrangements based on common intervals
Bioinformatics Advance Access published on September 25, 2007
Bioinformatics 2007 23: 2957-2958; doi:10.1093/bioinformatics/btm468 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Namhee Kim, Jin Sup Shin, Shereef Elmetwaly, Hin Hark Gan, and Tamar Schlick
RAGPOOLS: RNA-As-Graph-Pools—a web server for assisting the design of structured RNA pools for in vitro selection
Bioinformatics Advance Access published on September 13, 2007
Bioinformatics 2007 23: 2959-2960; doi:10.1093/bioinformatics/btm439 [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.