Volume 6, issue 1, December 2005
310 articles in this issue
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Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
Authors (first, second and last of 6)
- Chenghai Xue
- Fei Li
- Xuegong Zhang
- Content type: Methodology article
- Open Access
- Published: 29 December 2005
- Article: 310
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Comparison of normalization methods for CodeLink Bioarray data
Authors (first, second and last of 6)
- Wei Wu
- Nilesh Dave
- Naftali Kaminski
- Content type: Research article
- Open Access
- Published: 28 December 2005
- Article: 309
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Evolutionary programming as a platform for in silico metabolic engineering
Authors (first, second and last of 4)
- Kiran Raosaheb Patil
- Isabel Rocha
- Jens Nielsen
- Content type: Research article
- Open Access
- Published: 23 December 2005
- Article: 308
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Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700â„¢/Pantherâ„¢ probe-to-gene annotations
Authors
- Sebastian Noth
- Arndt Benecke
- systems epigenomics group
- Content type: Research article
- Open Access
- Published: 22 December 2005
- Article: 307
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WebArray: an online platform for microarray data analysis
Authors
- Xiaoqin Xia
- Michael McClelland
- Yipeng Wang
- Content type: Software
- Open Access
- Published: 21 December 2005
- Article: 306
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The Gene Set Builder: collation, curation, and distribution of sets of genes
Authors
- Dimas Yusuf
- Jonathan S Lim
- Wyeth W Wasserman
- Content type: Database
- Open Access
- Published: 21 December 2005
- Article: 305
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Internet-based profiler system as integrative framework to support translational research
Authors (first, second and last of 9)
- Robert Kim
- Francesca Demichelis
- Mark A Rubin
- Content type: Research article
- Open Access
- Published: 19 December 2005
- Article: 304
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Analysis of concordance of different haplotype block partitioning algorithms
Authors (first, second and last of 5)
- Amit R Indap
- Gabor T Marth
- Michael Olivier
- Content type: Research article
- Open Access
- Published: 15 December 2005
- Article: 303
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Probabilistic annotation of protein sequences based on functional classifications
Authors (first, second and last of 4)
- Emmanuel D Levy
- Christos A Ouzounis
- Benjamin Audit
- Content type: Research article
- Open Access
- Published: 14 December 2005
- Article: 302
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A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
Authors
- Federico Fogolari
- Silvio CE Tosatto
- Giorgio Colombo
- Content type: Research article
- Open Access
- Published: 14 December 2005
- Article: 301
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Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries
Authors (first, second and last of 7)
- Ji-Ping Z Wang
- Bruce G Lindsay
- Claude W dePamphilis
- Content type: Methodology article
- Open Access
- Published: 13 December 2005
- Article: 300
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A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
Authors (first, second and last of 5)
- Katsuyuki Yugi
- Yoichi Nakayama
- Masaru Tomita
- Content type: Research article
- Open Access
- Published: 13 December 2005
- Article: 299
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Kalign – an accurate and fast multiple sequence alignment algorithm
Authors
- Timo Lassmann
- Erik LL Sonnhammer
- Content type: Software
- Open Access
- Published: 12 December 2005
- Article: 298
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InterferenceAnalyzer: Tools for the analysis and simulation of multi-locus genetic data
Authors
- Lalitha Viswanath
- Elizabeth A Housworth
- Content type: Software
- Open Access
- Published: 12 December 2005
- Article: 297
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Oligomeric protein structure networks: insights into protein-protein interactions
Authors
- KV Brinda
- Saraswathi Vishveshwara
- Content type: Research article
- Open Access
- Published: 10 December 2005
- Article: 296
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PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords
Authors
- Takashi Yoneya
- Content type: Software
- Open Access
- Published: 10 December 2005
- Article: 295
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Harshlight: a "corrective make-up" program for microarray chips
Authors (first, second and last of 4)
- Mayte Suárez-Fariñas
- Maurizio Pellegrino
- Marcelo O Magnasco
- Content type: Software
- Open Access
- Published: 10 December 2005
- Article: 294
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An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments
Authors
- Eugene Novikov
- Emmanuel Barillot
- Content type: Methodology article
- Open Access
- Published: 09 December 2005
- Article: 293
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SNP-VISTA: An interactive SNP visualization tool
Authors (first, second and last of 7)
- Nameeta Shah
- Michael V Teplitsky
- Inna L Dubchak
- Content type: Software
- Open Access
- Published: 08 December 2005
- Article: 292
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An SVM-based system for predicting protein subnuclear localizations
Authors
- Zhengdeng Lei
- Yang Dai
- Content type: Methodology article
- Open Access
- Published: 07 December 2005
- Article: 291
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Efficient analysis and extraction of MS/MS result data from Mascotâ„¢ result files
Authors
- Florian Grosse-Coosmann
- Andreas M Boehm
- Albert Sickmann
- Content type: Software
- Open Access
- Published: 07 December 2005
- Article: 290
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GenClust: A genetic algorithm for clustering gene expression data
Authors (first, second and last of 5)
- Vito Di Gesú
- Raffaele Giancarlo
- Davide Scaturro
- Content type: Software
- Open Access
- Published: 07 December 2005
- Article: 289
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Genetic interaction motif finding by expectation maximization – a novel statistical model for inferring gene modules from synthetic lethality
Authors
- Yan Qi
- Ping Ye
- Joel S Bader
- Content type: Methodology article
- Open Access
- Published: 06 December 2005
- Article: 288
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ArrayQuest: a web resource for the analysis of DNA microarray data
Authors (first, second and last of 4)
- Gary L Argraves
- Saurin Jani
- W Scott Argraves
- Content type: Software
- Open Access
- Published: 01 December 2005
- Article: 287
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Identification of significant periodic genes in microarray gene expression data
Authors
- Jie Chen
- Content type: Research article
- Open Access
- Published: 30 November 2005
- Article: 286
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Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process
Authors (first, second and last of 9)
- Witold E Wolski
- Maciej Lalowski
- Knut Reinert
- Content type: Methodology article
- Open Access
- Published: 30 November 2005
- Article: 285
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Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality
Authors
- Kimberly M Mayer
- Sean R McCorkle
- John Shanklin
- Content type: Software
- Open Access
- Published: 30 November 2005
- Article: 284
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DSD – An integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities
Authors
- Christopher P Toseland
- Helen M McSparron
- Darren R Flower
- Content type: Database
- Open Access
- Published: 30 November 2005
- Article: 283
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The distance-profile representation and its application to detection of distantly related protein families
Authors
- Chin-Jen Ku
- Golan Yona
- Content type: Research article
- Open Access
- Published: 29 November 2005
- Article: 282
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An algorithm for the determination and quantification of components of nucleic acid mixtures based on single sequencing reactions
Authors
- Alexander Pozhitkov
- Kathryn Stemshorn
- Diethard Tautz
- Content type: Methodology article
- Open Access
- Published: 29 November 2005
- Article: 281
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Computational identification of strain-, species- and genus-specific proteins
Authors (first, second and last of 5)
- Raja Mazumder
- Darren A Natale
- Cathy H Wu
- Content type: Database
- Open Access
- Published: 23 November 2005
- Article: 279
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Multiple sequence alignment accuracy and evolutionary distance estimation
Authors
- Michael S Rosenberg
- Content type: Research article
- Open Access
- Published: 23 November 2005
- Article: 278
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Discover protein sequence signatures from protein-protein interaction data
Authors (first, second and last of 4)
- Jianwen Fang
- Ryan J Haasl
- Gerald H Lushington
- Content type: Research article
- Open Access
- Published: 23 November 2005
- Article: 277
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Principal component analysis for predicting transcription-factor binding motifs from array-derived data
Authors
- Yunlong Liu
- Matthew P Vincenti
- Hiroki Yokota
- Content type: Methodology article
- Open Access
- Published: 18 November 2005
- Article: 276
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Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis
Authors (first, second and last of 4)
- Emmitt R Jolly
- Chen-Shan Chin
- Hao Li
- Content type: Methodology article
- Open Access
- Published: 18 November 2005
- Article: 275
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A stepwise framework for the normalization of array CGH data
Authors (first, second and last of 4)
- Mehrnoush Khojasteh
- Wan L Lam
- Calum MacAulay
- Content type: Methodology article
- Open Access
- Published: 18 November 2005
- Article: 274
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Ancestral sequence alignment under optimal conditions
Authors
- Alexander K Hudek
- Daniel G Brown
- Content type: Research article
- Open Access
- Published: 17 November 2005
- Article: 273
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Automated methods of predicting the function of biological sequences using GO and BLAST
Authors
- Craig E Jones
- Ute Baumann
- Alfred L Brown
- Content type: Methodology article
- Open Access
- Published: 15 November 2005
- Article: 272
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The yeast kinome displays scale free topology with functional hub clusters
Authors
- Robin EC Lee
- Lynn A Megeney
- Content type: Research article
- Open Access
- Published: 09 November 2005
- Article: 271
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Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast
Authors (first, second and last of 4)
- Ping Ye
- Brian D Peyser
- Joel S Bader
- Content type: Research article
- Open Access
- Published: 09 November 2005
- Article: 270
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ErmineJ: Tool for functional analysis of gene expression data sets
Authors (first, second and last of 4)
- Homin K Lee
- William Braynen
- Paul Pavlidis
- Content type: Software
- Open Access
- Published: 09 November 2005
- Article: 269
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MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data
Authors (first, second and last of 10)
- Mahendra Navarange
- Laurence Game
- Helen C Causton
- Content type: Database
- Open Access
- Published: 09 November 2005
- Article: 268
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Identification of clustered microRNAs using an ab initio prediction method
Authors (first, second and last of 9)
- Alain Sewer
- Nicodème Paul
- Mihaela Zavolan
- Content type: Research article
- Open Access
- Published: 07 November 2005
- Article: 267
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Alternative splicing and protein function
Authors (first, second and last of 6)
- AD Neverov
- II Artamonova
- AA Mironov
- Content type: Research article
- Open Access
- Published: 07 November 2005
- Article: 266
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Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
Authors
- Patrick Warnat
- Roland Eils
- Benedikt Brors
- Content type: Methodology article
- Open Access
- Published: 04 November 2005
- Article: 265
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maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
Authors (first, second and last of 10)
- David Hancock
- Michael Wilson
- Andy Brass
- Content type: Software
- Open Access
- Published: 03 November 2005
- Article: 264
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Selecting additional tag SNPs for tolerating missing data in genotyping
Authors (first, second and last of 4)
- Yao-Ting Huang
- Kui Zhang
- Kun-Mao Chao
- Content type: Methodology article
- Open Access
- Published: 01 November 2005
- Article: 263
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Using hexamers to predict cis-regulatory motifs in Drosophila
Authors
- Bob Y Chan
- Dennis Kibler
- Content type: Methodology article
- Open Access
- Published: 27 October 2005
- Article: 262
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A method of precise mRNA/DNA homology-based gene structure prediction
Authors (first, second and last of 4)
- Alexander Churbanov
- Mark Pauley
- Hesham Ali
- Content type: Methodology article
- Open Access
- Published: 21 October 2005
- Article: 261