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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 7 |
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Volume 7 Suppl 5
Proceedings
New Delhi, India. 18 20 December 2006
Volume 7 Suppl 4
Research
Hangzhou, China. June 2024, 2006
Volume 7 Suppl 3
Proceedings
Jena, Germany. 912 April 2006
more supplements 
Software
  
The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy
Arnim Jenett, Johannes E Schindelin, Martin Heisenberg
BMC Bioinformatics 2006, 7:544 (29December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE
Satoshi Niijima, Satoru Kuhara
BMC Bioinformatics 2006, 7:543 (25December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
HaploRec: efficient and accurate large-scale reconstruction of haplotypes
Lauri Eronen, Floris Geerts, Hannu Toivonen
BMC Bioinformatics 2006, 7:542 (22December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
How repetitive are genomes?
Bernhard Haubold, Thomas Wiehe
BMC Bioinformatics 2006, 7:541 (22December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics
I Emrah Nikerel, Wouter A van Winden, Walter M van Gulik, Joseph J Heijnen
BMC Bioinformatics 2006, 7:540 (21December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors
Andreas Keller, Nicole Ludwig, Nicole Comtesse, Andreas Hildebrandt, Eckart Meese, Hans-Peter Lenhof
BMC Bioinformatics 2006, 7:539 (21December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Maureen A Sartor, Craig R Tomlinson, Scott C Wesselkamper, Siva Sivaganesan, George D Leikauf, Mario Medvedovic
BMC Bioinformatics 2006, 7:538 (19December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Empirical study of supervised gene screening
Shuangge Ma
BMC Bioinformatics 2006, 7:537 (18December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
TaxMan: a taxonomic database manager
Martin Jones, Mark Blaxter
BMC Bioinformatics 2006, 7:536 (18December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments
Bj rn Usadel, Axel Nagel, Dirk Steinhauser, Yves Gibon, Oliver E Bl sing, Henning Redestig, Nese Sreenivasulu, Leonard Krall, Matthew A Hannah, Fabien Poree, Alisdair R Fernie, Mark Stitt
BMC Bioinformatics 2006, 7:535 (18December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website
Benjamin M Good, Edward A Kawas, Byron Yu-Lin Kuo, Mark D Wilkinson
BMC Bioinformatics 2006, 7:534 (15December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Effect of various normalization methods on Applied Biosystems expression array system data
Catalin C Barbacioru, Yulei Wang, Roger D Canales, Yongming A Sun, David N Keys, Frances Chan, Karen A Poulter, Raymond R Samaha
BMC Bioinformatics 2006, 7:533 (15December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it
Kevin Garwood, Christopher Garwood, Cornelia Hedeler, Tony Griffiths, Neil Swainston, Stephen G Oliver, Norman W Paton
BMC Bioinformatics 2006, 7:532 (14December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases
Gully APC Burns, Wei-Cheng Cheng, Richard H Thompson, Larry W Swanson
BMC Bioinformatics 2006, 7:531 (13December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
MathDAMP: a package for differential analysis of metabolite profiles
Richard Baran, Hayataro Kochi, Natsumi Saito, Makoto Suematsu, Tomoyoshi Soga, Takaaki Nishioka, Martin Robert, Masaru Tomita
BMC Bioinformatics 2006, 7:530 (13December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
Christophe Dessimoz, Manuel Gil, Adrian Schneider, Gaston H Gonnet
BMC Bioinformatics 2006, 7:529 (5December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
A specialized learner for inferring structured cis-regulatory modules
Keith Noto, Mark Craven
BMC Bioinformatics 2006, 7:528 (5December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Logarithmic gap costs decrease alignment accuracy
Reed A Cartwright
BMC Bioinformatics 2006, 7:527 (5December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas
Federico E Turkheimer, Federico Roncaroli, Benoit Hennuy, Christian Herens, Minh Nguyen, Didier Martin, Annick Evrard, Vincent Bours, Jacques Boniver, Manuel Deprez
BMC Bioinformatics 2006, 7:526 (1December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
iHAP integrated haplotype analysis pipeline for characterizing the haplotype structure of genes
Chun Meng Song, Boon Huat Yeo, Erwin Tantoso, Yuchen Yang, Yun Ping Lim, Kuo-Bin Li, Gunaretnam Rajagopal
BMC Bioinformatics 2006, 7:525 (1December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost
Shinsuke Yamada, Osamu Gotoh, Hayato Yamana
BMC Bioinformatics 2006, 7:524 (1December2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
BioMoby extensions to the Taverna workflow management and enactment software
Edward Kawas, Martin Senger, Mark D Wilkinson
BMC Bioinformatics 2006, 7:523 (30November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Research article
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves
Kenneth W Berendzen, Kurt St ber, Klaus Harter, Dierk Wanke
BMC Bioinformatics 2006, 7:522 (30November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Dynamic variable selection in SNP genotype autocalling from APEX microarray data
Mohua Podder, William J Welch, Ruben H Zamar, Scott J Tebbutt
BMC Bioinformatics 2006, 7:521 (30November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
An accurate and interpretable model for siRNA efficacy prediction
Jean-Philippe Vert, Nicolas Foveau, Christian Lajaunie, Yves Vandenbrouck
BMC Bioinformatics 2006, 7:520 (30November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Inferring topology from clustering coefficients in protein-protein interaction networks
Caroline C Friedel, Ralf Zimmer
BMC Bioinformatics 2006, 7:519 (30November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
Pufeng Du, Yanda Li
BMC Bioinformatics 2006, 7:518 (30November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
Correcting ligands, metabolites, and pathways
Martin A Ott, Gert Vriend
BMC Bioinformatics 2006, 7:517 (28November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Integrated siRNA design based on surveying of features associated with high RNAi effectiveness
Wuming Gong, Yongliang Ren, Qiqi Xu, Yejun Wang, Dong Lin, Haiyan Zhou, Tongbin Li
BMC Bioinformatics 2006, 7:516 (27November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
SigFlux: A novel network feature to evaluate the importance of proteins in signal transduction networks
Wei Liu, Dong Li, Jiyang Zhang, Yunping Zhu, Fuchu He
BMC Bioinformatics 2006, 7:515 (27November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A hierarchical Na ve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays
Francesca Demichelis, Paolo Magni, Paolo Piergiorgi, Mark A Rubin, Riccardo Bellazzi
BMC Bioinformatics 2006, 7:514 (24November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow
Mariano Latorre, Herman Silva, Juan Saba, Carito Guziolowski, Paula Vizoso, Veronica Martinez, Jonathan Maldonado, Andrea Morales, Rodrigo Caroca, Veronica Cambiazo, Reinaldo Campos-Vargas, Mauricio Gonzalez, Ariel Orellana, Julio Retamales, Lee A Meisel
BMC Bioinformatics 2006, 7:513 (23November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Systematic assignment of thermodynamic constraints in metabolic network models
Anne Kmmel, Sven Panke, Matthias Heinemann
BMC Bioinformatics 2006, 7:512 (23November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis
Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David DL Bowtell, Gordon K Smyth
BMC Bioinformatics 2006, 7:511 (22November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Connectivity independent protein-structure alignment: a hierarchical approach
Bjoern Kolbeck, Patrick May, Tobias Schmidt-Goenner, Thomas Steinke, Ernst-Walter Knapp
BMC Bioinformatics 2006, 7:510 (21November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
CoXpress: differential co-expression in gene expression data
Michael Watson
BMC Bioinformatics 2006, 7:509 (20November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model
Kai Xia, Dong Dong, Jing-Dong J Han
BMC Bioinformatics 2006, 7:508 (18November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Novel methods for secondary structure determination using low wavelength (VUV) circular dichroism spectroscopic data
Jonathan G Lees, Andrew J Miles, Robert W Janes, B A Wallace
BMC Bioinformatics 2006, 7:507 (17November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Visual setup of logical models of signaling and regulatory networks with ProMoT
Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst Dieter Gilles, Martin Ginkel
BMC Bioinformatics 2006, 7:506 (17November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Using local gene expression similarities to discover regulatory binding site modules
Bartek Wilczy ski, Torgeir R Hvidsten, Andriy Kryshtafovych, Jerzy Tiuryn, Jan Komorowski, Krzysztof Fidelis
BMC Bioinformatics 2006, 7:505 (17November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A comparative analysis of the information content in long and short SAGE libraries
Yi-Ju Li, Puting Xu, Xuejun Qin, Donald E Schmechel, Christine M Hulette, Jonathan L Haines, Margaret A Pericak-Vance, John R Gilbert
BMC Bioinformatics 2006, 7:504 (16November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives
Petras J Kundrotas, Emil G Alexov
BMC Bioinformatics 2006, 7:503 (16November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
A correlated motif approach for finding short linear motifs from protein interaction networks
Soon-Heng Tan, Willy Hugo, Wing-Kin Sung, See-Kiong Ng
BMC Bioinformatics 2006, 7:502 (16November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores
Jesper Salomon, Darren R Flower
BMC Bioinformatics 2006, 7:501 (14November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens
Sreedevi Thiyagarajan, Miloslav Karhanek, Michael Akhras, Ronald W Davis, Nader Pourmand
BMC Bioinformatics 2006, 7:500 (14November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
State of the art: refinement of multiple sequence alignments
Saikat Chakrabarti, Christopher J Lanczycki, Anna R Panchenko, Teresa M Przytycka, Paul A Thiessen, Stephen H Bryant
BMC Bioinformatics 2006, 7:499 (14November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
4SALE A tool for synchronous RNA sequence and secondary structure alignment and editing
Philipp N Seibel, Tobias Mller, Thomas Dandekar, Jrg Schultz, Matthias Wolf
BMC Bioinformatics 2006, 7:498 (13November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
cPath: open source software for collecting, storing, and querying biological pathways
Ethan G Cerami, Gary D Bader, Benjamin E Gross, Chris Sander
BMC Bioinformatics 2006, 7:497 (13November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
methBLAST and methPrimerDB: web-tools for PCR based methylation analysis
Filip Pattyn, Jasmien Hoebeeck, Piet Robbrecht, Evi Michels, Anne De Paepe, Guy Bottu, David Coornaert, Robert Herzog, Frank Speleman, Jo Vandesompele
BMC Bioinformatics 2006, 7:496 (9November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
DWARF a data warehouse system for analyzing protein families
Markus Fischer, Quan K Thai, Melanie Grieb, Jrgen Pleiss
BMC Bioinformatics 2006, 7:495 (9November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Time scale and dimension analysis of a budding yeast cell cycle model
Anna Lovrics, Attila Csik sz-Nagy, Istvn Gy Zs ly, Judit Zdor, Tams Turnyi, Bla Novk
BMC Bioinformatics 2006, 7:494 (9November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A method for rapid similarity analysis of RNA secondary structures
Na Liu, Tianming Wang
BMC Bioinformatics 2006, 7:493 (8November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Automated recognition of malignancy mentions in biomedical literature
Yang Jin, Ryan T McDonald, Kevin Lerman, Mark A Mandel, Steven Carroll, Mark Y Liberman, Fernando C Pereira, Raymond S Winters, Peter S White
BMC Bioinformatics 2006, 7:492 (7November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction
Zhengdeng Lei, Yang Dai
BMC Bioinformatics 2006, 7:491 (7November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
XML schemas for common bioinformatic data types and their application in workflow systems
Philipp N Seibel, Jan Krger, Sven Hartmeier, Knut Schwarzer, Kai Lwenthal, Henning Mersch, Thomas Dandekar, Robert Giegerich
BMC Bioinformatics 2006, 7:490 (6November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Commentary
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Tim F Rayner, Philippe Rocca-Serra, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, Junmin Liu, Donald S Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J Stoeckert Jr, Joseph White, Patricia L Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A Ball, Alvis Brazma
BMC Bioinformatics 2006, 7:489 (6November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Evaluation of clustering algorithms for protein-protein interaction networks
Sylvain Brohe, Jacques van Helden
BMC Bioinformatics 2006, 7:488 (6November2006)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
Rodrigo Malig, Cristian Varela, Eduardo Agosin, Francisco Melo
BMC Bioinformatics 2006, 7:487 (4 |
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