Volume 4, issue 1, December 2003
66 articles in this issue
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Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency
Authors
- Anna G Nazina
- Dmitri A Papatsenko
- Content type: Research article
- Open Access
- Published: 22 December 2003
- Article: 65
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The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold
Authors
- Francesca D Ciccarelli
- Elisa Izaurralde
- Peer Bork
- Content type: Research article
- Open Access
- Published: 19 December 2003
- Article: 64
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AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
Authors (first, second and last of 4)
- Elarbi Badidi
- Cristina De Sousa
- Gertraud Burger
- Content type: Research article
- Open Access
- Published: 16 December 2003
- Article: 63
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Statistical significance for hierarchical clustering in genetic association and microarray expression studies
Authors
- Mark A Levenstien
- Yaning Yang
- Jürg Ott
- Content type: Methodology article
- Open Access
- Published: 11 December 2003
- Article: 62
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PubMatrix: a tool for multiplex literature mining
Authors (first, second and last of 7)
- Kevin G Becker
- Douglas A Hosack
- Jim Engel
- Content type: Software
- Open Access
- Published: 10 December 2003
- Article: 61
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Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
Authors (first, second and last of 5)
- Junbai Wang
- Trond Hellem Bø
- Eivind Hovig
- Content type: Methodology article
- Open Access
- Published: 02 December 2003
- Article: 60
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Cross-platform comparison and visualisation of gene expression data using co-inertia analysis
Authors
- AedÃn C Culhane
- Guy Perrière
- Desmond G Higgins
- Content type: Research article
- Open Access
- Published: 21 November 2003
- Article: 59
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Online tool for the discrimination of equi-distributions
Authors
- Thorsten Pöschel
- Cornelius Frömmel
- Christoph Gille
- Content type: Methodology article
- Open Access
- Published: 21 November 2003
- Article: 58
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Conservation of regulatory elements between two species of Drosophila
Authors
- Eldon Emberly
- Nikolaus Rajewsky
- Eric D Siggia
- Content type: Research article
- Open Access
- Published: 20 November 2003
- Article: 57
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PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis
Authors (first, second and last of 8)
- Deyun Pan
- Ning Sun
- Hongyu Zhao
- Content type: Software
- Open Access
- Published: 07 November 2003
- Article: 56
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Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses
Authors
- Stefan Washietl
- Frank Eisenhaber
- Content type: Research article
- Open Access
- Published: 07 November 2003
- Article: 55
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Entropy-based gene ranking without selection bias for the predictive classification of microarray data
Authors (first, second and last of 4)
- Cesare Furlanello
- Maria Serafini
- Giuseppe Jurman
- Content type: Research article
- Open Access
- Published: 06 November 2003
- Article: 54
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GeneViTo: Visualizing gene-product functional and structural features in genomic datasets
Authors (first, second and last of 4)
- Georgios S Vernikos
- Christos G Gkogkas
- Stavros J Hamodrakas
- Content type: Software
- Open Access
- Published: 31 October 2003
- Article: 53
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LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles
Authors
- Michael J Wise
- Content type: Research article
- Open Access
- Published: 29 October 2003
- Article: 52
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A knowledge discovery object model API for Java
Authors
- Scott D Zuyderduyn
- Steven JM Jones
- Content type: Software
- Open Access
- Published: 28 October 2003
- Article: 51
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Eval: A software package for analysis of genome annotations
Authors
- Evan Keibler
- Michael R Brent
- Content type: Software
- Open Access
- Published: 17 October 2003
- Article: 50
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The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins
Authors
- Alex Bateman
- Valerie Kickhoefer
- Content type: Research article
- Open Access
- Published: 16 October 2003
- Article: 49
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Trustworthiness and metrics in visualizing similarity of gene expression
Authors (first, second and last of 6)
- Samuel Kaski
- Janne Nikkilä
- Eero Castrén
- Content type: Research article
- Open Access
- Published: 13 October 2003
- Article: 48
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OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
Authors (first, second and last of 5)
- GPS Raghava
- Stephen MJ Searle
- Geoffrey J Barton
- Content type: Methodology article
- Open Access
- Published: 10 October 2003
- Article: 47
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Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization
Authors
- Marcin Grynberg
- Lukasz Jaroszewski
- Adam Godzik
- Content type: Research article
- Open Access
- Published: 10 October 2003
- Article: 46
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Visualisation and graph-theoretic analysis of a large-scale protein structural interactome
Authors (first, second and last of 5)
- Dan Bolser
- Panos Dafas
- Michael Schroeder
- Content type: Research article
- Open Access
- Published: 08 October 2003
- Article: 45
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RSEARCH: Finding homologs of single structured RNA sequences
Authors
- Robert J Klein
- Sean R Eddy
- Content type: Methodology article
- Open Access
- Published: 22 September 2003
- Article: 44
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Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Authors
- Yee Leng Yap
- Xue Wu Zhang
- Antoine Danchin
- Content type: Research article
- Open Access
- Published: 20 September 2003
- Article: 43
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Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals
Authors
- Soren Prag
- Josephine C Adams
- Content type: Research article
- Open Access
- Published: 17 September 2003
- Article: 42
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The COG database: an updated version includes eukaryotes
Authors (first, second and last of 17)
- Roman L Tatusov
- Natalie D Fedorova
- Darren A Natale
- Content type: Research article
- Open Access
- Published: 11 September 2003
- Article: 41
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Probabilistic estimation of microarray data reliability and underlying gene expression
Authors
- Sven Bilke
- Thomas Breslin
- Mikael Sigvardsson
- Content type: Methodology article
- Open Access
- Published: 10 September 2003
- Article: 40
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cDNA2Genome: A tool for mapping and annotating cDNAs
Authors
- Coral del Val
- Karl-Heinz Glatting
- Sandor Suhai
- Content type: Software
- Open Access
- Published: 10 September 2003
- Article: 39
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Genome-wide prediction, display and refinement of binding sites with information theory-based models
Authors (first, second and last of 4)
- Sashidhar Gadiraju
- Carrie A Vyhlidal
- Peter K Rogan
- Content type: Software
- Open Access
- Published: 08 September 2003
- Article: 38
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Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.
Authors (first, second and last of 8)
- Hanga C Galfalvy
- Loubna Erraji-Benchekroun
- Victoria Arango
- Content type: Research article
- Open Access
- Published: 08 September 2003
- Article: 37
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Cluster stability scores for microarray data in cancer studies
Authors
- Mark Smolkin
- Debashis Ghosh
- Content type: Methodology article
- Open Access
- Published: 06 September 2003
- Article: 36
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OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies
Authors
- Steven B Cannon
- Nevin D Young
- Content type: Software
- Open Access
- Published: 02 September 2003
- Article: 35
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ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations
Authors (first, second and last of 6)
- Boris E Shakhnovich
- John M Harvey
- Eugene Shakhnovich
- Content type: Database
- Open Access
- Published: 02 September 2003
- Article: 34
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Evaluation of normalization methods for microarray data
Authors (first, second and last of 6)
- Taesung Park
- Sung-Gon Yi
- Richard Simon
- Content type: Research article
- Open Access
- Published: 02 September 2003
- Article: 33
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The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)
Authors
- Patrick J Killion
- Gavin Sherlock
- Vishwanath R Iyer
- Content type: Database
- Open Access
- Published: 20 August 2003
- Article: 32
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Comparison of mode estimation methods and application in molecular clock analysis
Authors
- S Blair Hedges
- Prachi Shah
- Content type: Methodology article
- Open Access
- Published: 31 July 2003
- Article: 31
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Evolutionary algorithms for the selection of single nucleotide polymorphisms
Authors
- Robert M Hubley
- Eckart Zitzler
- Jared C Roach
- Content type: Methodology article
- Open Access
- Published: 23 July 2003
- Article: 30
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MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences
Authors
- James J Campanella
- Ledion Bitincka
- John Smalley
- Content type: Methodology article
- Open Access
- Published: 10 July 2003
- Article: 29
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Optimizationof neural network architecture using genetic programming improvesdetection and modeling of gene-gene interactions in studies of humandiseases
Authors (first, second and last of 5)
- Marylyn D Ritchie
- Bill C White
- Jason H Moore
- Content type: Methodology article
- Open Access
- Published: 07 July 2003
- Article: 28
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Reproducibility of gene expression across generations of Affymetrix microarrays
Authors (first, second and last of 7)
- Ashish Nimgaonkar
- Despina Sanoudou
- Isaac S Kohane
- Content type: Methodology article
- Open Access
- Published: 25 June 2003
- Article: 27
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Statistical implications of pooling RNA samples for microarray experiments
Authors (first, second and last of 6)
- Xuejun Peng
- Constance L Wood
- Arnold J Stromberg
- Content type: Methodology article
- Open Access
- Published: 24 June 2003
- Article: 26
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AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
Authors (first, second and last of 7)
- Ramana V Davuluri
- Hao Sun
- Erich Grotewold
- Content type: Methodology article
- Open Access
- Published: 23 June 2003
- Article: 25
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A data review and re-assessment of ovarian cancer serum proteomic profiling
Authors
- James M Sorace
- Min Zhan
- Content type: Research article
- Open Access
- Published: 09 June 2003
- Article: 24
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Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project
Authors (first, second and last of 4)
- Gautam Aggarwal
- EA Worthey
- Peter J Myler
- Content type: Research article
- Open Access
- Published: 07 June 2003
- Article: 23
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Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA
Authors
- Jeff W Bizzaro
- Kenneth A Marx
- Content type: Methodology article
- Open Access
- Published: 05 June 2003
- Article: 22
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EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance
Authors
- Thomas Schou Larsen
- Anders Krogh
- Content type: Research article
- Open Access
- Published: 03 June 2003
- Article: 21
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Information extraction from full text scientific articles: Where are the keywords?
Authors (first, second and last of 4)
- Parantu K Shah
- Carolina Perez-Iratxeta
- Miguel A Andrade
- Content type: Methodology article
- Open Access
- Published: 29 May 2003
- Article: 20
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Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences
Authors
- HJ Purohit
- DV Raje
- A Kapley
- Content type: Research article
- Open Access
- Published: 22 May 2003
- Article: 19
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Genome wide identification of regulatory motifs in Bacillus subtilis
Authors
- Michael M Mwangi
- Eric D Siggia
- Content type: Research article
- Open Access
- Published: 16 May 2003
- Article: 18
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A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.
Authors (first, second and last of 4)
- David J Studholme
- Neil D Rawlings
- Alex Bateman
- Content type: Research article
- Open Access
- Published: 09 May 2003
- Article: 17