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Editor-in-Chief Melissa Norton, MD Biology Editor Penelope Webb, PhD In-house Editor Tim Sands PhD
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| | BMC Bioinformatics, Volume 6 | |
Volume 6 Suppl 4
Research articles
Milan, Italy. 17 19 March 2005
Volume 6 Suppl 3
Meeting abstracts
Edinburgh, UK. 14 15 July 2005
Volume 6 Suppl 2
Proceedings
Little Rock, AR, USA. 7 9 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 (29 December 2005) [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 (29 December 2005) [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 (28 December 2005) [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 (23 December 2005) [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 (22 December 2005) [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 (21 December 2005) [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 (21 December 2005) [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 (19 December 2005) [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 (15 December 2005) [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 (14 December 2005) [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 (14 December 2005) [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 (13 December 2005) [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 (13 December 2005) [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 (12 December 2005) [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 (12 December 2005) [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 (10 December 2005) [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 (10 December 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] 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 (10 December 2005) [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 (9 December 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] 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 (8 December 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     An SVM-based system for predicting protein subnuclear localizations Zhengdeng Lei, Yang Dai BMC Bioinformatics 2005, 6:291 (7 December 2005) [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 (7 December 2005) [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 (7 December 2005) [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 (6 December 2005) [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 (1 December 2005) [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 (30 November 2005) [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 (30 November 2005) [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 (30 November 2005) [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 (30 November 2005) [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 (29 November 2005) [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 (29 November 2005) [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 (23 November 2005) [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 (23 November 2005) [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 (23 November 2005) [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 (18 November 2005) [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 (18 November 2005) [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 (18 November 2005) [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 (17 November 2005) [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 (15 November 2005) [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 (9 November 2005) [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 (9 November 2005) [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 (9 November 2005) [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 (9 November 2005) [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, S bastien Pfeffer, Michael J Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan BMC Bioinformatics 2005, 6:267 (7 November 2005) [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 (7 November 2005) [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 (4 November 2005) [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 (3 November 2005) [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 (1 November 2005) [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 (27 October 2005) [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 (21 October 2005) [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 (19 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] 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 (18 October 2005) [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 (18 October 2005) [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 (15 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Evaluating eukaryotic secreted protein prediction Eric W Klee, Lynda BM Ellis BMC Bioinformatics 2005, 6:256 (14 October 2005) [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, C cile Bussetta, H l ne Dutartre, Bruno Canard BMC Bioinformatics 2005, 6:255 (14 October 2005) [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 (14 October 2005) [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 (14 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     CoaSim: A flexible environment for simulating genetic data under coalescent models Thomas Mailund, Mikkel H Schierup, Christian NS Pedersen, Peter JM Mechlenborg, Jesper N Madsen, Leif Schauser BMC Bioinformatics 2005, 6:252 (14 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment] Research article
    Differentiation of regions with atypical oligonucleotide composition in bacterial genomes Oleg N Reva, Burkhard T mmler BMC Bioinformatics 2005, 6:251 (14 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    MASQOT: a method for cDNA microarray spot quality control Max Bylesj , Daniel Eriksson, Andreas Sj din, Michael Sj str m, Stefan Jansson, Henrik Antti, Johan Trygg BMC Bioinformatics 2005, 6:250 (13 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Database
     SPdb a signal peptide database Khar Heng Choo, Tin Wee Tan, Shoba Ranganathan BMC Bioinformatics 2005, 6:249 (13 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Better prediction of protein contact number using a support vector regression analysis of amino acid sequence Zheng Yuan BMC Bioinformatics 2005, 6:248 (13 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis Fran ois Enault, Karsten Suhre, Jean-Michel Claverie BMC Bioinformatics 2005, 6:247 (12 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory St phanie Monnier, David G Cox, Tim Albion, Federico Canzian BMC Bioinformatics 2005, 6:246 (12 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Extension of Lander-Waterman theory for sequencing filtered DNA libraries Michael C Wendl, W Brad Barbazuk BMC Bioinformatics 2005, 6:245 (10 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole BMC Bioinformatics 2005, 6:244 (5 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Phylogenetic detection of conserved gene clusters in microbial genomes Yu Zheng, Brian P Anton, Richard J Roberts, Simon Kasif BMC Bioinformatics 2005, 6:243 (3 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks Qicheng Ma, Gung-Wei Chirn, Richard Cai, Joseph D Szustakowski, NR Nirmala BMC Bioinformatics 2005, 6:242 (3 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Research article
    A comparison of RNA folding measures Eva Freyhult, Paul P Gardner, Vincent Moulton BMC Bioinformatics 2005, 6:241 (3 October 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Sequence variation in ligand binding sites in proteins Thomas J Magliery, Lynne Regan BMC Bioinformatics 2005, 6:240 (30 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data Florent Baty, Michel P Bihl, Guy Perri re, Aed n C Culhane, Martin H Brutsche BMC Bioinformatics 2005, 6:239 (28 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Mathematical design of prokaryotic clone-based microarrays Bart Pieterse, Elisabeth J Quirijns, Frank HJ Schuren, Mari t J van der Werf BMC Bioinformatics 2005, 6:238 (28 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
     Measuring similarities between transcription factor binding sites Szymon M Kielbasa, Didier Gonze, Hanspeter Herzel BMC Bioinformatics 2005, 6:237 (28 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution Andy Pang, Andrew D Smith, Paulo AS Nuin, Elisabeth RM Tillier BMC Bioinformatics 2005, 6:236 (27 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    An analysis of extensible modelling for functional genomics data Andrew R Jones, Norman W Paton BMC Bioinformatics 2005, 6:235 (27 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Quality determination and the repair of poor quality spots in array experiments Brian DM Tom, Walter R Gilks, Elizabeth T Brooke-Powell, James W Ajioka BMC Bioinformatics 2005, 6:234 (26 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     GeneRank: Using search engine technology for the analysis of microarray experiments Julie L Morrison, Rainer Breitling, Desmond J Higham, David R Gilbert BMC Bioinformatics 2005, 6:233 (21 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
     EXPANDER an integrative program suite for microarray data analysis Ron Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosef Shiloh, Ran Elkon BMC Bioinformatics 2005, 6:232 (21 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    A linear memory algorithm for Baum-Welch training Istv n Mikl s, Irmtraud M Meyer BMC Bioinformatics 2005, 6:231 (19 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Chromosomal clustering of a human transcriptome reveals regulatory background Jan H Vogel, Anja von Heydebreck, Antje Purmann, Silke Sperling BMC Bioinformatics 2005, 6:230 (19 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    ProbeMaker: an extensible framework for design of sets of oligonucleotide probes Johan Stenberg, Mats Nilsson, Ulf Landegren BMC Bioinformatics 2005, 6:229 (19 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
    Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software H di Soula, C line Robardet, Fran ois Perrin, S bastien Gripon, Guillaume Beslon, Olivier Gandrillon BMC Bioinformatics 2005, 6:228 (19 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks Cecily J Wolfe, Isaac S Kohane, Atul J Butte BMC Bioinformatics 2005, 6:227 (14 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    Assessing local structural perturbations in proteins Martin A Lema, Julian Echave BMC Bioinformatics 2005, 6:226 (13 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    Pathway level analysis of gene expression using singular value decomposition John Tomfohr, Jun Lu, Thomas B Kepler BMC Bioinformatics 2005, 6:225 (12 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
     Versatile and declarative dynamic programming using pair algebras Peter Steffen, Robert Giegerich BMC Bioinformatics 2005, 6:224 (12 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    SUPERFICIAL Surface mapping of proteins via structure-based peptide library design Andrean Goede, Ines S Jaeger, Robert Preissner BMC Bioinformatics 2005, 6:223 (9 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Database
    Micro-Mar: a database for dynamic representation of marine microbial biodiversity Ravindra Pushker, Giuseppe D'Auria, Jose Carlos Alba-Casado, Francisco Rodr guez-Valera BMC Bioinformatics 2005, 6:222 (9 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
    GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures Daron M Standley, Hiroyuki Toh, Haruki Nakamura BMC Bioinformatics 2005, 6:221 (8 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage Jianmin Wang, Xiaoqiu Huang BMC Bioinformatics 2005, 6:220 (7 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Software
     Generalizations of Markov model to characterize biological sequences Junwen Wang, Sridhar Hannenhalli BMC Bioinformatics 2005, 6:219 (6 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Database
    TmaDB: a repository for tissue microarray data Archana Sharma-Oates, Philip Quirke, David R Westhead BMC Bioinformatics 2005, 6:218 (1 September 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Automation of gene assignments to metabolic pathways using high-throughput expression data Liviu Popescu, Golan Yona BMC Bioinformatics 2005, 6:217 (31 August 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] Methodology article
    JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture Peter Sperisen, Marco Pagni BMC Bioinformatics 2005, 6:216 (31 August 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
    Dynamic covariation between gene expression and proteome characteristics Mansour Taghavi Azar Sharabiani, Markku Siermala, Tommi O Lehtinen, Mauno Vihinen BMC Bioinformatics 2005, 6:215 (30 August 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Research article
     Sources of variation in Affymetrix microarray experiments Stanislav O Zakharkin, Kyoungmi Kim, Tapan Mehta, Lang Chen, Stephen Barnes, Katherine E Scheirer, Rudolph S Parrish, David B Allison, Grier P Page BMC Bioinformatics 2005, 6:214 (29 August 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    Improved prediction of critical residues for protein function based on network and phylogenetic analyses Boris Thibert, Dale E Bredesen, Gabriel del Rio BMC Bioinformatics 2005, 6:213 (26 August 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Methodology article
    A new dynamical layout algorithm for complex biochemical reaction networks Katja Wegner, Ursula Kummer BMC Bioinformatics 2005, 6:212 (26 August 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] Software
    stam a Bioconductor compliant R package for structured analysis of microarray data Claudio Lottaz, Rainer Spang BMC Bioinformatics 2005, 6:211 (25 August 2005) [Abstract] [Full text] [PDF] [PubMed] [Related articles]
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