Volume 6, issue 1, December 2005
182 articles in this issue
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Effect of dataset selection on the topological interpretation of protein interaction networks
Authors
- Luke Hakes
- David L Robertson
- Stephen G Oliver
- Content type: Research article
- Open Access
- Published: 20 September 2005
- Article: 131
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Characterization of the global profile of genes expressed in cervical epithelium by Serial Analysis of Gene Expression (SAGE)
Authors (first, second and last of 8)
- Carlos Pérez-Plasencia
- Gregory Riggins
- Mauricio Salcedo
- Content type: Research article
- Open Access
- Published: 19 September 2005
- Article: 130
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Diversity in domain architectures of Ser/Thr kinases and their homologues in prokaryotes
Authors
- A Krupa
- N Srinivasan
- Content type: Research article
- Open Access
- Published: 19 September 2005
- Article: 129
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Genome annotation of Anopheles gambiae using mass spectrometry-derived data
Authors (first, second and last of 7)
- Dário E Kalume
- Suraj Peri
- Akhilesh Pandey
- Content type: Research article
- Open Access
- Published: 19 September 2005
- Article: 128
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Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi
Authors (first, second and last of 4)
- Marilyn Parsons
- Elizabeth A Worthey
- Jeremy C Mottram
- Content type: Research article
- Open Access
- Published: 15 September 2005
- Article: 127
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Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray
Authors (first, second and last of 8)
- Kristian R von Schalburg
- Matthew L Rise
- Ben F Koop
- Content type: Methodology article
- Open Access
- Published: 15 September 2005
- Article: 126
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Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene
Authors (first, second and last of 5)
- Ping Liang
- Jayakumar R Nair
- Bruce J Dolnick
- Content type: Research article
- Open Access
- Published: 14 September 2005
- Article: 125
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Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts
Authors (first, second and last of 6)
- Willem Albert Rensink
- Yuandan Lee
- C Robin Buell
- Content type: Research article
- Open Access
- Published: 14 September 2005
- Article: 124
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XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Authors (first, second and last of 5)
- Alexander Sczyrba
- Michael Beckstette
- Curtis R Altmann
- Content type: Database
- Open Access
- Published: 14 September 2005
- Article: 123
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Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
Authors (first, second and last of 11)
- Stefano Campanaro
- Alessandro Vezzi
- Douglas H Bartlett
- Content type: Research article
- Open Access
- Published: 14 September 2005
- Article: 122
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Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction
Authors (first, second and last of 7)
- Christian Rückert
- Daniel J Koch
- Jörn Kalinowski
- Content type: Research article
- Open Access
- Published: 13 September 2005
- Article: 121
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Duplication and positive selection among hominin-specific PRAME genes
Authors
- Zoë Birtle
- Leo Goodstadt
- Chris Ponting
- Content type: Research article
- Open Access
- Published: 13 September 2005
- Article: 120
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Computational evidence for hundreds of non-conserved plant microRNAs
Authors
- Morten Lindow
- Anders Krogh
- Content type: Research article
- Open Access
- Published: 13 September 2005
- Article: 119
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Rapid single nucleotide polymorphism mapping in C. elegans
Authors (first, second and last of 6)
- M Wayne Davis
- Marc Hammarlund
- Erik M Jorgensen
- Content type: Methodology article
- Open Access
- Published: 12 September 2005
- Article: 118
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Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes
Authors (first, second and last of 7)
- Nathalie de Parseval
- Gora Diop
- Thierry Heidmann
- Content type: Research article
- Open Access
- Published: 09 September 2005
- Article: 117
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Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution
Authors (first, second and last of 4)
- Soumyadeep Nandi
- Nipun Mehra
- Alok Bhattacharya
- Content type: Research article
- Open Access
- Published: 09 September 2005
- Article: 116
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Microarray analysis of Pseudomonas aeruginosa reveals induction of pyocin genes in response to hydrogen peroxide
Authors (first, second and last of 4)
- Wook Chang
- David A Small
- William E Bentley
- Content type: Research article
- Open Access
- Published: 08 September 2005
- Article: 115
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Identification and characterization of the fibrinogen-like domain of fibrinogen-related proteins in the mosquito, Anopheles gambiae, and the fruitfly, Drosophila melanogaster, genomes
Authors
- Xinguo Wang
- Qin Zhao
- Bruce M Christensen
- Content type: Research article
- Open Access
- Published: 08 September 2005
- Article: 114
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Improved tagging strategy for protein identification in mammalian cells
Authors
- Agnieszka Bialkowska
- Xian-Yang Zhang
- Jakob Reiser
- Content type: Methodology article
- Open Access
- Published: 04 September 2005
- Article: 113
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GH97 is a new family of glycoside hydrolases, which is related to the α-galactosidase superfamily
Authors
- Daniil G Naumoff
- Content type: Research article
- Open Access
- Published: 30 August 2005
- Article: 112
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Hypoxia-activated genes from early placenta are elevated in Preeclampsia, but not in Intra-Uterine Growth Retardation
Authors (first, second and last of 16)
- Daniel Vaiman
- Françoise Mondon
- Françoise Ferré
- Content type: Research article
- Open Access
- Published: 29 August 2005
- Article: 111
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Reverse transcriptional profiling: non-correspondence of transcript level variation and proximal promoter polymorphism
Authors
- Rebecca Petersen Brown
- Martin E Feder
- Content type: Research article
- Open Access
- Published: 17 August 2005
- Article: 110
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Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data
Authors (first, second and last of 7)
- Juan Jose Lozano
- Marta Soler
- Angel R Ortiz
- Content type: Research article
- Open Access
- Published: 17 August 2005
- Article: 109
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Comparative analysis of expression of histone H2a genes in mouse
Authors (first, second and last of 5)
- Hiromi Nishida
- Takahiro Suzuki
- Yoshihide Hayashizaki
- Content type: Research article
- Open Access
- Published: 13 August 2005
- Article: 108
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Transcribed Tc1-like transposons in salmonid fish
Authors (first, second and last of 4)
- Aleksei Krasnov
- Heikki Koskinen
- Hannu Mölsä
- Content type: Research article
- Open Access
- Published: 12 August 2005
- Article: 107
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Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors
Authors
- Raghu Prasad Rao Metpally
- Ramanathan Sowdhamini
- Content type: Research article
- Open Access
- Published: 10 August 2005
- Article: 106
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The complete mitochondrial genome of the stomatopod crustacean Squilla mantis
Authors
- Charles E Cook
- Content type: Research article
- Open Access
- Published: 09 August 2005
- Article: 105
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A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription
Authors
- Tomas Babak
- Benjamin J Blencowe
- Timothy R Hughes
- Content type: Research article
- Open Access
- Published: 05 August 2005
- Article: 104
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Conjugative plasmid pAW63 brings new insights into the genesis of the Bacillus anthracis virulence plasmid pXO2 and of the Bacillus thuringiensis plasmid pBT9727
Authors
- Géraldine A Van der Auwera
- Lars Andrup
- Jacques Mahillon
- Content type: Research article
- Open Access
- Published: 26 July 2005
- Article: 103
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Computational tradeoffs in multiplex PCR assay design for SNP genotyping
Authors (first, second and last of 4)
- John Rachlin
- Chunming Ding
- Simon Kasif
- Content type: Research article
- Open Access
- Published: 25 July 2005
- Article: 102
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Application of four dyes in gene expression analyses by microarrays
Authors (first, second and last of 4)
- Yvonne CM Staal
- Marcel HM van Herwijnen
- Joost HM van Delft
- Content type: Methodology article
- Open Access
- Published: 25 July 2005
- Article: 101
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Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes
Authors (first, second and last of 5)
- Isabelle Callebaut
- Karine Prat
- Stanislas Tomavo
- Content type: Research article
- Open Access
- Published: 23 July 2005
- Article: 100
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Comparing independent microarray studies: the case of human embryonic stem cells
Authors (first, second and last of 5)
- Mayte Suárez-Fariñas
- Scott Noggle
- Marcelo O Magnasco
- Content type: Methodology article
- Open Access
- Published: 22 July 2005
- Article: 99
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Muscle regeneration in dystrophin-deficient mdx mice studied by gene expression profiling
Authors (first, second and last of 6)
- R Turk
- E Sterrenburg
- PAC 't Hoen
- Content type: Research article
- Open Access
- Published: 13 July 2005
- Article: 98
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Positional and functional mapping of a neuroblastoma differentiation gene on chromosome 11
Authors (first, second and last of 13)
- Katleen De Preter
- Jo Vandesompele
- Frank Speleman
- Content type: Research article
- Open Access
- Published: 06 July 2005
- Article: 97
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Bacillus thuringiensis Cry1Ca-resistant Spodoptera exigua lacks expression of one of four Aminopeptidase N genes
Authors (first, second and last of 5)
- Salvador Herrero
- Tsanko Gechev
- Ruud A de Maagd
- Content type: Research article
- Open Access
- Published: 24 June 2005
- Article: 96
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A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus
Authors (first, second and last of 8)
- Yvan Charbonnier
- Brian Gettler
- Jacques Schrenzel
- Content type: Research article
- Open Access
- Published: 17 June 2005
- Article: 95
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Signature proteins that are distinctive of alpha proteobacteria
Authors
- Pinay Kainth
- Radhey S Gupta
- Content type: Research article
- Open Access
- Published: 16 June 2005
- Article: 94
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Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome
Authors (first, second and last of 5)
- Moshe Havilio
- Erez Y Levanon
- Eli Eisenberg
- Content type: Research article
- Open Access
- Published: 16 June 2005
- Article: 93
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Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium : Evidence for gene duplications and extensive gene clustering
Authors
- Harshavardhan Doddapaneni
- Ranajit Chakraborty
- Jagjit S Yadav
- Content type: Research article
- Open Access
- Published: 14 June 2005
- Article: 92
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Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips
Authors (first, second and last of 7)
- Fred van Ruissen
- Jan M Ruijter
- Frank Baas
- Content type: Methodology article
- Open Access
- Published: 14 June 2005
- Article: 91
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Inferring yeast cell cycle regulators and interactions using transcription factor activities
Authors (first, second and last of 5)
- Young-Lyeol Yang
- Jason Suen
- James C Liao
- Content type: Research article
- Open Access
- Published: 10 June 2005
- Article: 90
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A BAC-based physical map of the Nile tilapia genome
Authors (first, second and last of 9)
- Takayuki Katagiri
- Celeste Kidd
- Thomas D Kocher
- Content type: Research article
- Open Access
- Published: 09 June 2005
- Article: 89
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Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method
Authors
- Craig Burgler
- Paul M Macdonald
- Content type: Software
- Open Access
- Published: 08 June 2005
- Article: 88
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Microsatellite mapping of QTL affecting growth, feed consumption, egg production, tonic immobility and body temperature of Japanese quail
Authors (first, second and last of 9)
- Francis Minvielle
- Boniface B Kayang
- Shin'ichi Ito
- Content type: Research article
- Open Access
- Published: 08 June 2005
- Article: 87
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The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences
Authors (first, second and last of 5)
- Iris Brune
- Karina Brinkrolf
- Andreas Tauch
- Content type: Research article
- Open Access
- Published: 07 June 2005
- Article: 86
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Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii
Authors
- Jing-Ke Weng
- Milos Tanurdzic
- Clint Chapple
- Content type: Research article
- Open Access
- Published: 06 June 2005
- Article: 85
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Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data
Authors (first, second and last of 4)
- Anne-Sophie Carpentier
- Bruno Torrésani
- Alain Hénaut
- Content type: Research article
- Open Access
- Published: 06 June 2005
- Article: 84
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(TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length
Authors
- Vineet K Sharma
- Samir K Brahmachari
- Srinivasan Ramachandran
- Content type: Research article
- Open Access
- Published: 03 June 2005
- Article: 83