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Page 237 of 249

Phylogenetic detection of conserved gene clusters in microbial genomes

Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functiona...

Authors: Yu Zheng, Brian P Anton, Richard J Roberts and Simon Kasif

Citation: BMC Bioinformatics 2005 6:243

Content type: Research article Published on: 3 October 2005
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Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks

The sequencing of the human genome has enabled us to access a comprehensive list of genes (both experimental and predicted) for further analysis. While a majority of the approximately 30000 known and predicted...

Authors: Qicheng Ma, Gung-Wei Chirn, Richard Cai, Joseph D Szustakowski and NR Nirmala

Citation: BMC Bioinformatics 2005 6:242

Content type: Methodology article Published on: 3 October 2005
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A comparison of RNA folding measures

In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investig...

Authors: Eva Freyhult, Paul P Gardner and Vincent Moulton

Citation: BMC Bioinformatics 2005 6:241

Content type: Research article Published on: 3 October 2005
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Sequence variation in ligand binding sites in proteins

The recent explosion in the availability of complete genome sequences has led to the cataloging of tens of thousands of new proteins and putative proteins. Many of these proteins can be structurally or functio...

Authors: Thomas J Magliery and Lynne Regan

Citation: BMC Bioinformatics 2005 6:240

Content type: Research article Published on: 30 September 2005
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Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data

A recent publication described a supervised classification method for microarray data: Between Group Analysis (BGA). This method which is based on performing multivariate ordination of groups proved to be very...

Authors: Florent Baty, Michel P Bihl, Guy Perrière, Aedín C Culhane and Martin H Brutsche

Citation: BMC Bioinformatics 2005 6:239

Content type: Methodology article Published on: 28 September 2005
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Mathematical design of prokaryotic clone-based microarrays

Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome seq...

Authors: Bart Pieterse, Elisabeth J Quirijns, Frank HJ Schuren and Mariët J van der Werf

Citation: BMC Bioinformatics 2005 6:238

Content type: Methodology article Published on: 28 September 2005
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Measuring similarities between transcription factor binding sites

Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of tra...

Authors: Szymon M Kielbasa, Didier Gonze and Hanspeter Herzel

Citation: BMC Bioinformatics 2005 6:237

Content type: Software Published on: 28 September 2005
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SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificia...

Authors: Andy Pang, Andrew D Smith, Paulo AS Nuin and Elisabeth RM Tillier

Citation: BMC Bioinformatics 2005 6:236

Content type: Software Published on: 27 September 2005
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An analysis of extensible modelling for functional genomics data

Several data formats have been developed for large scale biological experiments, using a variety of methodologies. Most data formats contain a mechanism for allowing extensions to encode unanticipated data types....

Authors: Andrew R Jones and Norman W Paton

Citation: BMC Bioinformatics 2005 6:235

Content type: Methodology article Published on: 27 September 2005
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Quality determination and the repair of poor quality spots in array experiments

A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots a...

Authors: Brian DM Tom, Walter R Gilks, Elizabeth T Brooke-Powell and James W Ajioka

Citation: BMC Bioinformatics 2005 6:234

Content type: Methodology article Published on: 26 September 2005
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A Method of Gene Expression Data Partitioning for the Construction of Context-Sensitive PBNs

Authors: Le Yu and Stephen Marshall

Citation: BMC Bioinformatics 2005 6(Suppl 3):P29

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Jalview: Visualization and Analysis of Molecular Sequences, Alignments, and Structures

Authors: Andrew Waterhouse, Jim Procter, David A Martin and Geoffrey J Barton

Citation: BMC Bioinformatics 2005 6(Suppl 3):P28

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Exploring Parasite Gene Space

Authors: James Wasmuth, Ralf Schmid, Alasdair Anthony, John Parkinson and Mark Blaxter

Citation: BMC Bioinformatics 2005 6(Suppl 3):P27

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Stochastic Petri Nets in Systems Biology

Authors: Ole Schulz-Trieglaff

Citation: BMC Bioinformatics 2005 6(Suppl 3):P25

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Distinguishing between enzyme sequences & non-enzymes without using alignments

Authors: Ajanthah Sangaralingam and Andrew J Doig

Citation: BMC Bioinformatics 2005 6(Suppl 3):P24

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Genomics and Pathway Biology – a new post-genomics M.Sc. programme from Edinburgh University

Authors: Douglas Roy and Peter Ghazal

Citation: BMC Bioinformatics 2005 6(Suppl 3):P23

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Bioinformatics in phylogeography: analitical methods and applications

Authors: Oscar Moya Mesa, Hermans Goar Contreras Díaz, Pedro Oromí Masoliver and Carlos Juan Clar

Citation: BMC Bioinformatics 2005 6(Suppl 3):P22

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Modelling Lipid Metabolism to Improve Healthy Ageing

Authors: Mark Mc Auley, Janette Jones, Darren Wilkinson and Tom Kirkwood

Citation: BMC Bioinformatics 2005 6(Suppl 3):P21

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Theoretical and quantitative aspects of iron acquisition by a bovine isolate of Pasteurella multocida A:3

Authors: Sandy J Macdonald, Colin W Bayne, Malcolm Quirie, Frederick A Lainson, Junli Liu and John C Hodgson

Citation: BMC Bioinformatics 2005 6(Suppl 3):P20

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Automated Terminological and Structural Analysis of Human-Mouse Anatomical Ontology Mappings

Authors: Sarah Luger, Stuart Aitken and Bonnie Webber

Citation: BMC Bioinformatics 2005 6(Suppl 3):P19

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Evolution@home: Global computing quantifies evolution due to Muller's ratchet

Authors: Laurence Loewe

Citation: BMC Bioinformatics 2005 6(Suppl 3):P18

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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An analysis of allele sharing in a region of linkage with bipolar affective disorder

Authors: Andrew Lee

Citation: BMC Bioinformatics 2005 6(Suppl 3):P17

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Gene Expression-Based Cross Species Tissue Mapping

Authors: Ajit Kumar Gopee

Citation: BMC Bioinformatics 2005 6(Suppl 3):P16

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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System level visualization of eQTLs and pQTLs

Authors: Joanna Jakubowska, Ela Hunt, Matthew Chalmers, David Leader, Martin McBride and Anna F Dominiczak

Citation: BMC Bioinformatics 2005 6(Suppl 3):P15

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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The Important Role of Calcium in Regulation of Adhesion Disassembly and Cell Migration: Mathematical Modelling

Authors: Najl Valeyev, Andrei Skorinkin, Kristy Downing, Iain Campbell and Nikolai Kotov

Citation: BMC Bioinformatics 2005 6(Suppl 3):S15

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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CaliBayes: Integration of GRID based simulation and data resources for Bayesian calibration of biological models

Authors: Richard Boys, Daniel Henderson, Tom Kirkwood, Darren Wilkinson and W Eryk Wolski

Citation: BMC Bioinformatics 2005 6(Suppl 3):P14

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Prioritisation of Disease Gene Candidates: A Systems Biology Approach

Authors: Frances S Turner

Citation: BMC Bioinformatics 2005 6(Suppl 3):S14

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Nonlinear Data Mining of Microarray Data Using Michaelis Menten Functions

Authors: Dov J Stekel, Tim W Overton, Jon L Hobman, Charles W Penn, Jeff A Cole and Chrystala Constantinidou

Citation: BMC Bioinformatics 2005 6(Suppl 3):S13

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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GPX – An Integrative Environment for the Storage and Retrieval of Raw and Processed Microarray Data

Authors: Graeme Grimes

Citation: BMC Bioinformatics 2005 6(Suppl 3):P13

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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PROVAT – a versatile tool for Voronoi tessellation analysis of protein structures and complexes

Authors: Swanand P Gore, David F Burke and Tom L Blundell

Citation: BMC Bioinformatics 2005 6(Suppl 3):P12

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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N-terminal sequence-based prediction of subcellular location

Authors: Evangelia I Petsalakis, Pantelis G Bagos, Zoi I Litou and Stavros J Hamodrakas

Citation: BMC Bioinformatics 2005 6(Suppl 3):S11

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Integration of open source software tools for the in silico design of metabolic pathways using flux balance analysis – an application to the production of recombinant human proteins

Authors: Ana Sofia Figueiredo

Citation: BMC Bioinformatics 2005 6(Suppl 3):P11

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Text-mining, milk proteins and nutraceutical potential – the MilkER project

Authors: Stephen Edwards, Bonnie Webber, Carl Holt and Lindsay Sawyer

Citation: BMC Bioinformatics 2005 6(Suppl 3):P10

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Nestor3D: multiple alignment of protein structures based on ligand or prosthetic group position

Authors: Jean-Christophe Nebel

Citation: BMC Bioinformatics 2005 6(Suppl 3):S10

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Computational Analysis of Insulin in the Ageing Fruit Fly

Authors: John Cumbers and J Douglas Armstrong

Citation: BMC Bioinformatics 2005 6(Suppl 3):P9

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Extraction of Genetic Networks (GN) Using Static Bayesian Belief Networks From Genome-Wide Temporal Microarray Data

Authors: Judit Kumuthini

Citation: BMC Bioinformatics 2005 6(Suppl 3):S8

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data

Authors: Paul Craig, Jessie Kennedy and Andrew Cumming

Citation: BMC Bioinformatics 2005 6(Suppl 3):P8

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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ZF-Human Disease Database: A Database for Zebrafish Models of Human Genetic Diseases

Authors: Pedro Coutinho

Citation: BMC Bioinformatics 2005 6(Suppl 3):P7

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Computational inference of regulator activity in a single input motif from gene expression data

Authors: Raya Khanin, Veronica Vinciotti, Vassilis Mersinias, Colin Smith and Ernst Wit

Citation: BMC Bioinformatics 2005 6(Suppl 3):S7

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Living longer by dieting: analysis of transcriptional response after caloric restriction

Authors: Nicola D Kerrison, Colin Selman, Steven J Lingard, Janet M Thornton, Linda Partridge and Dominic J Withers

Citation: BMC Bioinformatics 2005 6(Suppl 3):S6

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Using Comparative Genomics & RNA Structure to Find RNA Editing Sites

Authors: Daniel Clutterbuck

Citation: BMC Bioinformatics 2005 6(Suppl 3):P6

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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NanoSNP: A computational platform for high throughput Quantum Dot encoded microsphere SNP genotyping

Authors: Colin Clarke, Michael Malecha and Selly Saini

Citation: BMC Bioinformatics 2005 6(Suppl 3):P5

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Investigation of mRNA Splicing in Saccharomyces cerevisiae using Microarrays

Authors: J David Barrass and Jean D Beggs

Citation: BMC Bioinformatics 2005 6(Suppl 3):S5

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Inferring gene regulatory networks from classified microarray data: Initial results

Authors: Stuart Aitken, Thanyaluk Jirapech-Umpai and Ronan Daly

Citation: BMC Bioinformatics 2005 6(Suppl 3):S4

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Codon pair bias in prokaryotic and eukaryotic genomes

Authors: Ross Buchan and Ian Stansfield

Citation: BMC Bioinformatics 2005 6(Suppl 3):P4

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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The evolutionary origin of protein complexes

Authors: Jose Pereira-Leal

Citation: BMC Bioinformatics 2005 6(Suppl 3):S3

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Use Of Neural Networks To Predict And Analyse Membrane Proteins In The Proteome

Authors: Subrata K Bose, Hassan Kazemian, Kenneth White and Antony Browne

Citation: BMC Bioinformatics 2005 6(Suppl 3):P3

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Sequence Analysis In Promoter Regions

Authors: Jeremy Austin

Citation: BMC Bioinformatics 2005 6(Suppl 3):P2

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Transcription regulation: a genomic network

Authors: Nicholas Luscombe

Citation: BMC Bioinformatics 2005 6(Suppl 3):S1

Content type: Oral presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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Speeding Disease Gene Discovery with SUSPECTS

Authors: Euan Adie

Citation: BMC Bioinformatics 2005 6(Suppl 3):P1

Content type: Poster presentation Published on: 21 September 2005

This article is part of a Supplement: Volume 6 Supplement 3
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