Volume 7, issue 1, December 2006
544 articles in this issue
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A method for rapid similarity analysis of RNA secondary structures
Authors
- Na Liu
- Tianming Wang
- Content type: Methodology article
- Open Access
- Published: 08 November 2006
- Article: 493
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Automated recognition of malignancy mentions in biomedical literature
Authors (first, second and last of 9)
- Yang Jin
- Ryan T McDonald
- Peter S White
- Content type: Research article
- Open Access
- Published: 07 November 2006
- Article: 492
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Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction
Authors
- Zhengdeng Lei
- Yang Dai
- Content type: Methodology article
- Open Access
- Published: 07 November 2006
- Article: 491
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XML schemas for common bioinformatic data types and their application in workflow systems
Authors (first, second and last of 8)
- Philipp N Seibel
- Jan Krüger
- Robert Giegerich
- Content type: Software
- Open Access
- Published: 06 November 2006
- Article: 490
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A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Authors (first, second and last of 21)
- Tim F Rayner
- Philippe Rocca-Serra
- Alvis Brazma
- Content type: Commentary
- Open Access
- Published: 06 November 2006
- Article: 489
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Evaluation of clustering algorithms for protein-protein interaction networks
Authors
- Sylvain Brohée
- Jacques van Helden
- Content type: Research article
- Open Access
- Published: 06 November 2006
- Article: 488
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Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
Authors (first, second and last of 4)
- Rodrigo Malig
- Cristian Varela
- Francisco Melo
- Content type: Methodology article
- Open Access
- Published: 04 November 2006
- Article: 487
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GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima
Authors
- Kazuhito Shida
- Content type: Research article
- Open Access
- Published: 04 November 2006
- Article: 486
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Machine learning techniques in disease forecasting: a case study on rice blast prediction
Authors
- Rakesh Kaundal
- Amar S Kapoor
- Gajendra PS Raghava
- Content type: Methodology article
- Open Access
- Published: 03 November 2006
- Article: 485
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A statistical score for assessing the quality of multiple sequence alignments
Authors (first, second and last of 4)
- Virpi Ahola
- Tero Aittokallio
- Esa Uusipaikka
- Content type: Methodology article
- Open Access
- Published: 03 November 2006
- Article: 484
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Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems
Authors
- Maria Rodriguez-Fernandez
- Jose A Egea
- Julio R Banga
- Content type: Methodology article
- Open Access
- Published: 02 November 2006
- Article: 483
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Application of Petri net based analysis techniques to signal transduction pathways
Authors
- Andrea Sackmann
- Monika Heiner
- Ina Koch
- Content type: Research article
- Open Access
- Published: 02 November 2006
- Article: 482
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Mining expressed sequence tags identifies cancer markers of clinical interest
Authors
- Fabien Campagne
- Lucy Skrabanek
- Content type: Research article
- Open Access
- Published: 01 November 2006
- Article: 481
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RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes
Authors (first, second and last of 6)
- Jean-François Lucier
- Lucien Junior Bergeron
- Jean-Pierre Perreault
- Content type: Software
- Open Access
- Published: 31 October 2006
- Article: 480
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HybGFS: a hybrid method for genome-fingerprint scanning
Authors (first, second and last of 7)
- Kosaku Shinoda
- Nozomu Yachie
- Masaru Tomita
- Content type: Methodology article
- Open Access
- Published: 29 October 2006
- Article: 479
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Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae
Authors (first, second and last of 5)
- Illés J Farkas
- Chuang Wu
- Zoltán N Oltvai
- Content type: Research article
- Open Access
- Published: 28 October 2006
- Article: 478
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Browsing repeats in genomes: Pygram and an application to non-coding region analysis
Authors (first, second and last of 4)
- Patrick Durand
- Frédéric Mahé
- Jacques Nicolas
- Content type: Methodology article
- Open Access
- Published: 26 October 2006
- Article: 477
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Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Authors
- Micah Hamady
- M D Betterton
- Rob Knight
- Content type: Research article
- Open Access
- Published: 26 October 2006
- Article: 476
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Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: A proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE
Authors (first, second and last of 9)
- Kim Kultima
- Birger Scholz
- Ingrid Lönnstedt
- Content type: Research article
- Open Access
- Published: 26 October 2006
- Article: 475
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Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
Authors (first, second and last of 4)
- Oleksiy Kohany
- Andrew J Gentles
- Jerzy Jurka
- Content type: Software
- Open Access
- Published: 25 October 2006
- Article: 474
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CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Authors (first, second and last of 8)
- Coral del Val
- Vladimir Yurjevich Kuryshev
- Stefan Wiemann
- Content type: Software
- Open Access
- Published: 25 October 2006
- Article: 473
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CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes
Authors
- Ikuo Uchiyama
- Toshio Higuchi
- Ichizo Kobayashi
- Content type: Software
- Open Access
- Published: 24 October 2006
- Article: 472
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The accuracy of several multiple sequence alignment programs for proteins
Authors
- Paulo AS Nuin
- Zhouzhi Wang
- Elisabeth RM Tillier
- Content type: Research article
- Open Access
- Published: 24 October 2006
- Article: 471
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GeneTools – application for functional annotation and statistical hypothesis testing
Authors (first, second and last of 10)
- Vidar Beisvag
- Frode KR Jünge
- Astrid Lægreid
- Content type: Software
- Open Access
- Published: 24 October 2006
- Article: 470
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Evaluating different methods of microarray data normalization
Authors (first, second and last of 5)
- André Fujita
- João Ricardo Sato
- Mari Cleide Sogayar
- Content type: Methodology article
- Open Access
- Published: 23 October 2006
- Article: 469
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SNP-PHAGE – High throughput SNP discovery pipeline
Authors (first, second and last of 6)
- Lakshmi K Matukumalli
- John J Grefenstette
- Curtis P Van Tassell
- Content type: Software
- Open Access
- Published: 23 October 2006
- Article: 468
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Goulphar: rapid access and expertise for standard two-color microarray normalization methods
Authors (first, second and last of 4)
- Sophie Lemoine
- Florence Combes
- Stéphane Le Crom
- Content type: Software
- Open Access
- Published: 23 October 2006
- Article: 467
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ProFAT: a web-based tool for the functional annotation of protein sequences
Authors
- Charles Richard Bradshaw
- Vineeth Surendranath
- Bianca Habermann
- Content type: Software
- Open Access
- Published: 23 October 2006
- Article: 466
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Meta-All: a system for managing metabolic pathway information
Authors (first, second and last of 7)
- Stephan Weise
- Ivo Grosse
- Björn H Junker
- Content type: Software
- Open Access
- Published: 23 October 2006
- Article: 465
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A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database
Authors (first, second and last of 5)
- Simon Katz
- Rafael A Irizarry
- Mark W Porter
- Content type: Methodology article
- Open Access
- Published: 23 October 2006
- Article: 464
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SVRMHC prediction server for MHC-binding peptides
Authors (first, second and last of 6)
- Ji Wan
- Wen Liu
- Tongbin Li
- Content type: Software
- Open Access
- Published: 23 October 2006
- Article: 463
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Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis
Authors
- Aijazuddin Syed
- Chris Upton
- Content type: Software
- Open Access
- Published: 20 October 2006
- Article: 462
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inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons
Authors
- Chunguang Liang
- Thomas Dandekar
- Content type: Software
- Open Access
- Published: 20 October 2006
- Article: 461
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Representing and comparing protein structures as paths in three-dimensional space
Authors (first, second and last of 5)
- Degui Zhi
- S Sri Krishna
- Adam Godzik
- Content type: Research article
- Open Access
- Published: 20 October 2006
- Article: 460
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MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization
Authors (first, second and last of 8)
- Carol L Ecale Zhou
- Marisa W Lam
- Thomas R Slezak
- Content type: Database
- Open Access
- Published: 17 October 2006
- Article: 459
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NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm
Authors (first, second and last of 5)
- Yu Xue
- Hu Chen
- Xuebiao Yao
- Content type: Methodology article
- Open Access
- Published: 17 October 2006
- Article: 458
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Comparison of protein interaction networks reveals species conservation and divergence
Authors (first, second and last of 4)
- Zhi Liang
- Meng Xu
- Liwen Niu
- Content type: Research article
- Open Access
- Published: 17 October 2006
- Article: 457
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A framework for protein structure classification and identification of novel protein structures
Authors
- You Jung Kim
- Jignesh M Patel
- Content type: Methodology article
- Open Access
- Published: 16 October 2006
- Article: 456
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Building multiclass classifiers for remote homology detection and fold recognition
Authors
- Huzefa Rangwala
- George Karypis
- Content type: Research article
- Open Access
- Published: 16 October 2006
- Article: 455
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Whole genome association mapping by incompatibilities and local perfect phylogenies
Authors
- Thomas Mailund
- Søren Besenbacher
- Mikkel H Schierup
- Content type: Methodology article
- Open Access
- Published: 16 October 2006
- Article: 454
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REEF: searching REgionally Enriched Features in genomes
Authors
- Alessandro Coppe
- Gian Antonio Danieli
- Stefania Bortoluzzi
- Content type: Software
- Open Access
- Published: 16 October 2006
- Article: 453
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A fisheye viewer for microarray-based gene expression data
Authors (first, second and last of 4)
- Min Wu
- Cheng Thao
- Ethan V Munson
- Content type: Software
- Open Access
- Published: 13 October 2006
- Article: 452
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MIMOX: a web tool for phage display based epitope mapping
Authors (first, second and last of 4)
- Jian Huang
- Alex Gutteridge
- Minoru Kanehisa
- Content type: Software
- Open Access
- Published: 12 October 2006
- Article: 451
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Genepi: a blackboard framework for genome annotation
Authors (first, second and last of 4)
- Stéphane Descorps-Declère
- Danielle Ziébelin
- Alain Viari
- Content type: Software
- Open Access
- Published: 12 October 2006
- Article: 450
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Integrative missing value estimation for microarray data
Authors (first, second and last of 4)
- Jianjun Hu
- Haifeng Li
- Xianghong Jasmine Zhou
- Content type: Research article
- Open Access
- Published: 12 October 2006
- Article: 449
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Gene function classification using Bayesian models with hierarchy-based priors
Authors
- Babak Shahbaba
- Radford M Neal
- Content type: Research article
- Open Access
- Published: 12 October 2006
- Article: 448
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Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice
Authors (first, second and last of 8)
- Xiyin Wang
- Xiaoli Shi
- Jingchu Luo
- Content type: Methodology article
- Open Access
- Published: 12 October 2006
- Article: 447
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CpGcluster: a distance-based algorithm for CpG-island detection
Authors (first, second and last of 6)
- Michael Hackenberg
- Christopher Previti
- José L Oliver
- Content type: Research article
- Open Access
- Published: 12 October 2006
- Article: 446
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Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum
Authors
- Kalyan Gayen
- KV Venkatesh
- Content type: Research article
- Open Access
- Published: 12 October 2006
- Article: 445