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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Maria Kowalczuk
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| | BMC Bioinformatics, Volume 6 |
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Volume 6 Suppl 4
Research articles
Milan, Italy. 17 19 March 2005
Volume 6 Suppl 3
Meeting abstracts A single PDF containing all abstracts in this Supplement is available here.
Edinburgh, UK. 1415 July 2005
Volume 6 Suppl 2
Proceedings
Little Rock, AR, USA. 79 October 2004
more supplements 
Methodology article
  
Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis
Nils E Magnusson, Alessandra K Cardozo, Mogens Kruh ffer, Decio L Eizirik, Torben F  rntoft, Jens L Jensen
BMC Bioinformatics 2005, 6:311 (29December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
Chenghai Xue, Fei Li, Tao He, Guo-Ping Liu, Yanda Li, Xuegong Zhang
BMC Bioinformatics 2005, 6:310 (29December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Comparison of normalization methods for CodeLink Bioarray data
Wei Wu, Nilesh Dave, George C Tseng, Thomas Richards, Eric P Xing, Naftali Kaminski
BMC Bioinformatics 2005, 6:309 (28December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Evolutionary programming as a platform for in silico metabolic engineering
Kiran Raosaheb Patil, Isabel Rocha, Jochen F rster, Jens Nielsen
BMC Bioinformatics 2005, 6:308 (23December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700 /Panther probe-to-gene annotations
Sebastian Noth, Arndt Benecke, systems epigenomics group
BMC Bioinformatics 2005, 6:307 (22December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
WebArray: an online platform for microarray data analysis
Xiaoqin Xia, Michael McClelland, Yipeng Wang
BMC Bioinformatics 2005, 6:306 (21December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
The Gene Set Builder: collation, curation, and distribution of sets of genes
Dimas Yusuf, Jonathan S Lim, Wyeth W Wasserman
BMC Bioinformatics 2005, 6:305 (21December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Internet-based profiler system as integrative framework to support translational research
Robert Kim, Francesca Demichelis, Jeffery Tang, Alberto Riva, Ronglai Shen, Doug F Gibbs, Vasudeva Mahavishno, Arul M Chinnaiyan, Mark A Rubin
BMC Bioinformatics 2005, 6:304 (19December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Analysis of concordance of different haplotype block partitioning algorithms
Amit R Indap, Gabor T Marth, Craig A Struble, Peter Tonellato, Michael Olivier
BMC Bioinformatics 2005, 6:303 (15December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Probabilistic annotation of protein sequences based on functional classifications
Emmanuel D Levy, Christos A Ouzounis, Walter R Gilks, Benjamin Audit
BMC Bioinformatics 2005, 6:302 (14December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
Federico Fogolari, Silvio CE Tosatto, Giorgio Colombo
BMC Bioinformatics 2005, 6:301 (14December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries
Ji-Ping Z Wang, Bruce G Lindsay, Liying Cui, P Kerr Wall, Josh Marion, Jiaxuan Zhang, Claude W dePamphilis
BMC Bioinformatics 2005, 6:300 (13December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
Katsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama, Masaru Tomita
BMC Bioinformatics 2005, 6:299 (13December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Kalign an accurate and fast multiple sequence alignment algorithm
Timo Lassmann, Erik LL Sonnhammer
BMC Bioinformatics 2005, 6:298 (12December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
InterferenceAnalyzer: Tools for the analysis and simulation of multi-locus genetic data
Lalitha Viswanath, Elizabeth A Housworth
BMC Bioinformatics 2005, 6:297 (12December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Oligomeric protein structure networks: insights into protein-protein interactions
KV Brinda, Saraswathi Vishveshwara
BMC Bioinformatics 2005, 6:296 (10December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords
Takashi Yoneya
BMC Bioinformatics 2005, 6:295 (10December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Harshlight: a "corrective make-up" program for microarray chips
Mayte Su rez-Fari as, Maurizio Pellegrino, Knut M Wittkowski, Marcelo O Magnasco
BMC Bioinformatics 2005, 6:294 (10December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments
Eugene Novikov, Emmanuel Barillot
BMC Bioinformatics 2005, 6:293 (9December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SNP-VISTA: An interactive SNP visualization tool
Nameeta Shah, Michael V Teplitsky, Simon Minovitsky, Len A Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna L Dubchak
BMC Bioinformatics 2005, 6:292 (8December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
An SVM-based system for predicting protein subnuclear localizations
Zhengdeng Lei, Yang Dai
BMC Bioinformatics 2005, 6:291 (7December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Efficient analysis and extraction of MS/MS result data from Mascot result files
Florian Grosse-Coosmann, Andreas M Boehm, Albert Sickmann
BMC Bioinformatics 2005, 6:290 (7December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
GenClust: A genetic algorithm for clustering gene expression data
Vito Di Ges , Raffaele Giancarlo, Giosu Lo Bosco, Alessandra Raimondi, Davide Scaturro
BMC Bioinformatics 2005, 6:289 (7December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Genetic interaction motif finding by expectation maximization a novel statistical model for inferring gene modules from synthetic lethality
Yan Qi, Ping Ye, Joel S Bader
BMC Bioinformatics 2005, 6:288 (6December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
ArrayQuest: a web resource for the analysis of DNA microarray data
Gary L Argraves, Saurin Jani, Jeremy L Barth, W Scott Argraves
BMC Bioinformatics 2005, 6:287 (1December2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Identification of significant periodic genes in microarray gene expression data
Jie Chen
BMC Bioinformatics 2005, 6:286 (30November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process
Witold E Wolski, Maciej Lalowski, Peter Martus, Ralf Herwig, Patrick Giavalisco, Johan Gobom, Albert Sickmann, Hans Lehrach, Knut Reinert
BMC Bioinformatics 2005, 6:285 (30November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality
Kimberly M Mayer, Sean R McCorkle, John Shanklin
BMC Bioinformatics 2005, 6:284 (30November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
DSD An integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities
Christopher P Toseland, Helen M McSparron, Darren R Flower
BMC Bioinformatics 2005, 6:283 (30November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The distance-profile representation and its application to detection of distantly related protein families
Chin-Jen Ku, Golan Yona
BMC Bioinformatics 2005, 6:282 (29November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
An algorithm for the determination and quantification of components of nucleic acid mixtures based on single sequencing reactions
Alexander Pozhitkov, Kathryn Stemshorn, Diethard Tautz
BMC Bioinformatics 2005, 6:281 (29November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
Computational identification of strain-, species- and genus-specific proteins
Raja Mazumder, Darren A Natale, Sudhir Murthy, Rathi Thiagarajan, Cathy H Wu
BMC Bioinformatics 2005, 6:279 (23November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Multiple sequence alignment accuracy and evolutionary distance estimation
Michael S Rosenberg
BMC Bioinformatics 2005, 6:278 (23November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Discover protein sequence signatures from protein-protein interaction data
Jianwen Fang, Ryan J Haasl, Yinghua Dong, Gerald H Lushington
BMC Bioinformatics 2005, 6:277 (23November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Principal component analysis for predicting transcription-factor binding motifs from array-derived data
Yunlong Liu, Matthew P Vincenti, Hiroki Yokota
BMC Bioinformatics 2005, 6:276 (18November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis
Emmitt R Jolly, Chen-Shan Chin, Ira Herskowitz, Hao Li
BMC Bioinformatics 2005, 6:275 (18November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A stepwise framework for the normalization of array CGH data
Mehrnoush Khojasteh, Wan L Lam, Rabab K Ward, Calum MacAulay
BMC Bioinformatics 2005, 6:274 (18November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Ancestral sequence alignment under optimal conditions
Alexander K Hudek, Daniel G Brown
BMC Bioinformatics 2005, 6:273 (17November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Automated methods of predicting the function of biological sequences using GO and BLAST
Craig E Jones, Ute Baumann, Alfred L Brown
BMC Bioinformatics 2005, 6:272 (15November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
The yeast kinome displays scale free topology with functional hub clusters
Robin EC Lee, Lynn A Megeney
BMC Bioinformatics 2005, 6:271 (9November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast
Ping Ye, Brian D Peyser, Forrest A Spencer, Joel S Bader
BMC Bioinformatics 2005, 6:270 (9November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
ErmineJ: Tool for functional analysis of gene expression data sets
Homin K Lee, William Braynen, Kiran Keshav, Paul Pavlidis
BMC Bioinformatics 2005, 6:269 (9November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Database
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data
Mahendra Navarange, Laurence Game, Derek Fowler, Vihar Wadekar, Helen Banks, Nicola Cooley, Fatimah Rahman, Justin Hinshelwood, Peter Broderick, Helen C Causton
BMC Bioinformatics 2005, 6:268 (9November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Identification of clustered microRNAs using an ab initio prediction method
Alain Sewer, Nicod me Paul, Pablo Landgraf, Alexei Aravin, Sbastien Pfeffer, Michael J Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan
BMC Bioinformatics 2005, 6:267 (7November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Alternative splicing and protein function
AD Neverov, II Artamonova, RN Nurtdinov, D Frishman, MS Gelfand, AA Mironov
BMC Bioinformatics 2005, 6:266 (7November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
Patrick Warnat, Roland Eils, Benedikt Brors
BMC Bioinformatics 2005, 6:265 (4November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
David Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, A Joseph Wood, Karim Nashar, Douglas B Kell, Andy Brass
BMC Bioinformatics 2005, 6:264 (3November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Selecting additional tag SNPs for tolerating missing data in genotyping
Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao
BMC Bioinformatics 2005, 6:263 (1November2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Using hexamers to predict cis-regulatory motifs in Drosophila
Bob Y Chan, Dennis Kibler
BMC Bioinformatics 2005, 6:262 (27October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
A method of precise mRNA/DNA homology-based gene structure prediction
Alexander Churbanov, Mark Pauley, Daniel Quest, Hesham Ali
BMC Bioinformatics 2005, 6:261 (21October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
SpectralNET an application for spectral graph analysis and visualization
Joshua J Forman, Paul A Clemons, Stuart L Schreiber, Stephen J Haggarty
BMC Bioinformatics 2005, 6:260 (19October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function
Markey C McNutt, Ron Tongbai, Wenwu Cui, Irene Collins, Wendy J Freebern, Idalia Montano, Cynthia M Haggerty, GVR Chandramouli, Kevin Gardner
BMC Bioinformatics 2005, 6:259 (18October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification
Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen
BMC Bioinformatics 2005, 6:258 (18October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Statistical distributions of optimal global alignment scores of random protein sequences
Hongxia Pang, Jiaowei Tang, Su-Shing Chen, Shiheng Tao
BMC Bioinformatics 2005, 6:257 (15October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Evaluating eukaryotic secreted protein prediction
Eric W Klee, Lynda BM Ellis
BMC Bioinformatics 2005, 6:256 (14October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases
Fran ois Ferron, Ccile Bussetta, Hlne Dutartre, Bruno Canard
BMC Bioinformatics 2005, 6:255 (14October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Prediction of  -barrel membrane proteins by searching for restricted domains
Oliver Mirus, Enrico Schleiff
BMC Bioinformatics 2005, 6:254 (14October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins
Tomas Ohlson, Arne Elofsson
BMC Bioinformatics 2005, 6:253 (14October2005)
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