Volume 7, issue 1, December 2006
544 articles in this issue
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A probabilistic classifier for olfactory receptor pseudogenes
Authors
- Idan Menashe
- Ronny Aloni
- Doron Lancet
- Content type: Methodology article
- Open Access
- Published: 29 August 2006
- Article: 393
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GeneLibrarian: an effective gene-information summarization and visualization system
Authors (first, second and last of 4)
- Jung-Hsien Chiang
- Jyh-Wei Shin
- Chong-Liang Chin
- Content type: Software
- Open Access
- Published: 29 August 2006
- Article: 392
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Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression
Authors
- Sébastien Lemieux
- Content type: Research article
- Open Access
- Published: 25 August 2006
- Article: 391
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PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
Authors (first, second and last of 8)
- Kuo Ping Chiu
- Chee-Hong Wong
- Yijun Ruan
- Content type: Software
- Open Access
- Published: 25 August 2006
- Article: 390
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Fast index based algorithms and software for matching position specific scoring matrices
Authors (first, second and last of 4)
- Michael Beckstette
- Robert Homann
- Stefan Kurtz
- Content type: Methodology article
- Open Access
- Published: 24 August 2006
- Article: 389
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Selecting normalization genes for small diagnostic microarrays
Authors
- Jochen Jaeger
- Rainer Spang
- Content type: Methodology article
- Open Access
- Published: 22 August 2006
- Article: 388
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On the statistical assessment of classifiers using DNA microarray data
Authors (first, second and last of 10)
- N Ancona
- R Maglietta
- F Perri
- Content type: Research article
- Open Access
- Published: 19 August 2006
- Article: 387
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Hierarchical modularity of nested bow-ties in metabolic networks
Authors (first, second and last of 5)
- Jing Zhao
- Hong Yu
- Yi-Xue Li
- Content type: Research article
- Open Access
- Published: 18 August 2006
- Article: 386
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Incorporating background frequency improves entropy-based residue conservation measures
Authors
- Kai Wang
- Ram Samudrala
- Content type: Methodology article
- Open Access
- Published: 17 August 2006
- Article: 385
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Analysis of promoter regions of co-expressed genes identified by microarray analysis
Authors
- Srinivas Veerla
- Mattias Höglund
- Content type: Methodology article
- Open Access
- Published: 17 August 2006
- Article: 384
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Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping
Authors (first, second and last of 18)
- B Jayashree
- Praveen T Reddy
- David A Hoisington
- Content type: Software
- Open Access
- Published: 17 August 2006
- Article: 383
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MultiSeq: unifying sequence and structure data for evolutionary analysis
Authors (first, second and last of 4)
- Elijah Roberts
- John Eargle
- Zaida Luthey-Schulten
- Content type: Software
- Open Access
- Published: 16 August 2006
- Article: 382
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Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae
Authors (first, second and last of 5)
- Shawn Cokus
- Sherri Rose
- Matteo Pellegrini
- Content type: Research article
- Open Access
- Published: 16 August 2006
- Article: 381
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Validation and functional annotation of expression-based clusters based on gene ontology
Authors
- Ralf Steuer
- Peter Humburg
- Joachim Selbig
- Content type: Research article
- Open Access
- Published: 15 August 2006
- Article: 380
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V-MitoSNP: visualization of human mitochondrial SNPs
Authors (first, second and last of 7)
- Li-Yeh Chuang
- Cheng-Hong Yang
- Hsueh-Wei Chang
- Content type: Database
- Open Access
- Published: 15 August 2006
- Article: 379
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Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays
Authors (first, second and last of 10)
- Xujing Wang
- Shuang Jia
- Martin J Hessner
- Content type: Research article
- Open Access
- Published: 14 August 2006
- Article: 378
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A novel data mining method to identify assay-specific signatures in functional genomic studies
Authors (first, second and last of 6)
- Derrick K Rollins
- Dongmei Zhai
- Ramon Gonzalez
- Content type: Methodology article
- Open Access
- Published: 14 August 2006
- Article: 377
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Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
Authors (first, second and last of 4)
- Daniel A Pollard
- Alan M Moses
- Michael B Eisen
- Content type: Research article
- Open Access
- Published: 14 August 2006
- Article: 376
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PeanutMap: an online genome database for comparative molecular maps of peanut
Authors
- Arun M Jesubatham
- Mark D Burow
- Content type: Database
- Open Access
- Published: 11 August 2006
- Article: 375
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Genome comparison using Gene Ontology (GO) with statistical testing
Authors (first, second and last of 4)
- Zhaotao Cai
- Xizeng Mao
- Liping Wei
- Content type: Methodology article
- Open Access
- Published: 11 August 2006
- Article: 374
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Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line
Authors (first, second and last of 8)
- Jeyakumar Natarajan
- Daniel Berrar
- Eric G Bremer
- Content type: Research article
- Open Access
- Published: 10 August 2006
- Article: 373
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Gene and protein nomenclature in public databases
Authors
- Katrin Fundel
- Ralf Zimmer
- Content type: Research article
- Open Access
- Published: 09 August 2006
- Article: 372
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UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context
Authors
- Catherine Lozupone
- Micah Hamady
- Rob Knight
- Content type: Software
- Open Access
- Published: 07 August 2006
- Article: 371
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Automatic document classification of biological literature
Authors
- David Chen
- Hans-Michael Müller
- Paul W Sternberg
- Content type: Methodology article
- Open Access
- Published: 07 August 2006
- Article: 370
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Robust computational reconstitution – a new method for the comparative analysis of gene expression in tissues and isolated cell fractions
Authors (first, second and last of 6)
- Martin Hoffmann
- Dirk Pohlers
- Raimund W Kinne
- Content type: Methodology article
- Open Access
- Published: 04 August 2006
- Article: 369
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G-InforBIO: integrated system for microbial genomics
Authors (first, second and last of 4)
- Naoto Tanaka
- Takashi Abe
- Hideaki Sugawara
- Content type: Software
- Open Access
- Published: 04 August 2006
- Article: 368
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Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus
Authors
- Michal Dabrowski
- Stein Aerts
- Bozena Kaminska
- Content type: Research article
- Open Access
- Published: 02 August 2006
- Article: 367
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bioNMF: a versatile tool for non-negative matrix factorization in biology
Authors (first, second and last of 6)
- Alberto Pascual-Montano
- Pedro Carmona-Saez
- Roberto D Pascual-Marqui
- Content type: Software
- Open Access
- Published: 28 July 2006
- Article: 366
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PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
Authors (first, second and last of 12)
- Sylvain Pitre
- Frank Dehne
- Ashkan Golshani
- Content type: Research article
- Open Access
- Published: 27 July 2006
- Article: 365
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Improving the quality of protein structure models by selecting from alignment alternatives
Authors (first, second and last of 5)
- Ingolf Sommer
- Stefano Toppo
- Silvio CE Tosatto
- Content type: Methodology article
- Open Access
- Published: 27 July 2006
- Article: 364
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A literature-based similarity metric for biological processes
Authors (first, second and last of 5)
- Monica Chagoyen
- Pedro Carmona-Saez
- Alberto Pascual-Montano
- Content type: Methodology article
- Open Access
- Published: 26 July 2006
- Article: 363
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A fast SCOP fold classification system using content-based E-Predict algorithm
Authors
- Pin-Hao Chi
- Chi-Ren Shyu
- Dong Xu
- Content type: Software
- Open Access
- Published: 26 July 2006
- Article: 362
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Cluster analysis for DNA methylation profiles having a detection threshold
Authors (first, second and last of 4)
- Paul Marjoram
- Jing Chang
- Kimberly D Siegmund
- Content type: Methodology article
- Open Access
- Published: 26 July 2006
- Article: 361
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A direct comparison of protein interaction confidence assignment schemes
Authors (first, second and last of 5)
- Silpa Suthram
- Tomer Shlomi
- Trey Ideker
- Content type: Research article
- Open Access
- Published: 26 July 2006
- Article: 360
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Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
Authors
- Ian B Jeffery
- Desmond G Higgins
- AedÃn C Culhane
- Content type: Research article
- Open Access
- Published: 26 July 2006
- Article: 359
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Identification of biomarkers from mass spectrometry data using a "common" peak approach
Authors
- Tadayoshi Fushiki
- Hironori Fujisawa
- Shinto Eguchi
- Content type: Methodology article
- Open Access
- Published: 26 July 2006
- Article: 358
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Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps
Authors (first, second and last of 4)
- Tomas Ohlson
- Varun Aggarwal
- Robert M MacCallum
- Content type: Methodology article
- Open Access
- Published: 25 July 2006
- Article: 357
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New directions in biomedical text annotation: definitions, guidelines and corpus construction
Authors
- W John Wilbur
- Andrey Rzhetsky
- Hagit Shatkay
- Content type: Methodology article
- Open Access
- Published: 25 July 2006
- Article: 356
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Functional clustering of yeast proteins from the protein-protein interaction network
Authors
- Taner Z Sen
- Andrzej Kloczkowski
- Robert L Jernigan
- Content type: Research article
- Open Access
- Published: 24 July 2006
- Article: 355
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A combined approach to data mining of textual and structured data to identify cancer-related targets
Authors (first, second and last of 4)
- Pavel Pospisil
- Lakshmanan K Iyer
- Amin I Kassis
- Content type: Methodology article
- Open Access
- Published: 20 July 2006
- Article: 354
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A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates
Authors
- Anne-Mette K Hein
- Sylvia Richardson
- Content type: Research article
- Open Access
- Published: 20 July 2006
- Article: 353
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Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator
Authors
- Pier-Luigi Lollini
- Santo Motta
- Francesco Pappalardo
- Content type: Methodology article
- Open Access
- Published: 20 July 2006
- Article: 352
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MANET: tracing evolution of protein architecture in metabolic networks
Authors
- Hee Shin Kim
- Jay E Mittenthal
- Gustavo Caetano-Anollés
- Content type: Database
- Open Access
- Published: 19 July 2006
- Article: 351
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Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences
Authors (first, second and last of 4)
- Alexander F Auch
- Stefan R Henz
- Markus Göker
- Content type: Research article
- Open Access
- Published: 19 July 2006
- Article: 350
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Simulation of microarray data with realistic characteristics
Authors (first, second and last of 6)
- Matti Nykter
- Tommi Aho
- Olli Yli-Harja
- Content type: Methodology article
- Open Access
- Published: 18 July 2006
- Article: 349
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Integrated functional visualization of eukaryotic genomes
Authors
- Rohit Ghai
- Hannes Lindemann
- Trinad Chakraborty
- Content type: Software
- Open Access
- Published: 18 July 2006
- Article: 348
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BBP: Brucella genome annotation with literature mining and curation
Authors
- Zuoshuang Xiang
- Wenjie Zheng
- Yongqun He
- Content type: Research article
- Open Access
- Published: 16 July 2006
- Article: 347
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Structure alignment based on coding of local geometric measures
Authors
- Peter L Chang
- Andrew W Rinne
- T Gregory Dewey
- Content type: Methodology article
- Open Access
- Published: 14 July 2006
- Article: 346
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Individualized markers optimize class prediction of microarray data
Authors
- Pavlos Pavlidis
- Panayiota Poirazi
- Content type: Research article
- Open Access
- Published: 14 July 2006
- Article: 345