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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 8 |
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Volume 8 Suppl 10
Proceedings
Whistler, Canada. 8 December 2006
Volume 8 Suppl 9
Proceedings
Arlington, VA, USA. 10 November 2006
Volume 8 Suppl 8
Meeting abstracts  A single PDF containing all abstracts in this Supplement is available here
Vienna, Austria. 21 July 2007
more supplements 
Research article
  
Background frequencies for residue variability estimates: BLOSUM revisited
I Mihalek, I Re , O Lichtarge
BMC Bioinformatics 2007, 8:488 (27December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Userscripts for the Life Sciences
Egon L Willighagen, Noel M O'Boyle, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, Christoph Steinbeck, David J Wild
BMC Bioinformatics 2007, 8:487 (21December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data
Yvonne E Pittelkow, Susan R Wilson
BMC Bioinformatics 2007, 8:486 (20December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Characterization and simulation of cDNA microarray spots using a novel mathematical model
Hye Young Kim, Seo Eun Lee, Min Jung Kim, Jin Il Han, Bo Kyung Kim, Yong Sung Lee, Young Seek Lee, Jin Hyuk Kim
BMC Bioinformatics 2007, 8:485 (20December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Effective selection of informative SNPs and classification on the HapMap genotype data
Nina Zhou, Lipo Wang
BMC Bioinformatics 2007, 8:484 (20December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system
Arnaud Droit, Joanna M Hunter, Mich le Rouleau, Chantal Ethier, Aude Picard-Cloutier, David Bourgais, Guy G Poirier
BMC Bioinformatics 2007, 8:483 (19December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identifying protein complexes directly from high-throughput TAP data with Markov random fields
Wasinee Rungsarityotin, Roland Krause, Arno Sch dl, Alexander Schliep
BMC Bioinformatics 2007, 8:482 (19December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
Victor G Levitsky, Elena V Ignatieva, Elena A Ananko, Igor I Turnaev, Tatyana I Merkulova, Nikolay A Kolchanov, TC Hodgman
BMC Bioinformatics 2007, 8:481 (19December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
TABASCO: A single molecule, base-pair resolved gene expression simulator
Sriram Kosuri, Jason R Kelly, Drew Endy
BMC Bioinformatics 2007, 8:480 (19December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases
Scott A Givan, Christopher M Sullivan, James C Carrington
BMC Bioinformatics 2007, 8:479 (18December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Ab initio identification of human microRNAs based on structure motifs
Markus Brameier, Carsten Wiuf
BMC Bioinformatics 2007, 8:478 (18December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve
Jingjing Ye, Hao Liu, Crystal Kirmiz, Carlito B Lebrilla, David M Rocke
BMC Bioinformatics 2007, 8:477 (12December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries
Corinne Dahinden, Giovanni Parmigiani, Mark C Emerick, Peter B hlmann
BMC Bioinformatics 2007, 8:476 (11December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting gene ontology functions from protein's regional surface structures
Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Luonan Chen, Xiang-Sun Zhang
BMC Bioinformatics 2007, 8:475 (11December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
High-throughput sequence alignment using Graphics Processing Units
Michael C Schatz, Cole Trapnell, Arthur L Delcher, Amitabh Varshney
BMC Bioinformatics 2007, 8:474 (10December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A systematic approach to detecting transcription factors in response to environmental stresses
Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen
BMC Bioinformatics 2007, 8:473 (8December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Direct maximum parsimony phylogeny reconstruction from genotype data
Srinath Sridhar, Fumei Lam, Guy E Blelloch, R Ravi, Russell Schwartz
BMC Bioinformatics 2007, 8:472 (5December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting and improving the protein sequence alignment quality by support vector regression
Minho Lee, Chan-seok Jeong, Dongsup Kim
BMC Bioinformatics 2007, 8:471 (3December2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Domain motions of Argonaute, the catalytic engine of RNA interference
Dengming Ming, Michael E Wall, Kevin Y Sanbonmatsu
BMC Bioinformatics 2007, 8:470 (30November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A structural analysis of in vitro catalytic activities of hammerhead ribozymes
Yu Shao, Susan Wu, Chi Yu Chan, Jessie R Klapper, Erasmus Schneider, Ye Ding
BMC Bioinformatics 2007, 8:469 (30November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics
Nico Pfeifer, Andreas Leinenbach, Christian G Huber, Oliver Kohlbacher
BMC Bioinformatics 2007, 8:468 (30November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Generating confidence intervals on biological networks
Thomas Thorne, Michael PH Stumpf
BMC Bioinformatics 2007, 8:467 (30November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition
Takeyuki Tamura, Tatsuya Akutsu
BMC Bioinformatics 2007, 8:466 (30November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SAT, a flexible and optimized Web application for SSR marker development
Alexis Dereeper, Xavier Argout, Claire Billot, Jean-Fran ois Rami, Manuel Ruiz
BMC Bioinformatics 2007, 8:465 (29November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences
St fan Engelen, Fariza Tahi
BMC Bioinformatics 2007, 8:464 (28November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identification of DNA-binding proteins using support vector machines and evolutionary profiles
Manish Kumar, Michael M Gromiha, Gajendra PS Raghava
BMC Bioinformatics 2007, 8:463 (27November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Dynamic simulation of regulatory networks using SQUAD
Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios, Luis Mendoza
BMC Bioinformatics 2007, 8:462 (26November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
Tineke Casneuf, Yves Van de Peer, Wolfgang Huber
BMC Bioinformatics 2007, 8:461 (26November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Dendroscope: An interactive viewer for large phylogenetic trees
Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz, Regula Rupp
BMC Bioinformatics 2007, 8:460 (22November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms
Menaka Rajapakse, Bertil Schmidt, Lin Feng, Vladimir Brusic
BMC Bioinformatics 2007, 8:459 (22November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography
Miguel Arenas, David Posada
BMC Bioinformatics 2007, 8:458 (20November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
GEDI: a user-friendly toolbox for analysis of large-scale gene expression data
Andr Fujita, Jo o R Sato, Carlos E Ferreira, Mari C Sogayar
BMC Bioinformatics 2007, 8:457 (19November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
J Christopher Bare, Paul T Shannon, Amy K Schmid, Nitin S Baliga
BMC Bioinformatics 2007, 8:456 (19November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA a Bayesian approach
Carmen Pin, Mark Reuter
BMC Bioinformatics 2007, 8:455 (19November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana
Henning Redestig, Daniel Weicht, Joachim Selbig, Matthew A Hannah
BMC Bioinformatics 2007, 8:454 (18November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu, Myeong Ho Jung
BMC Bioinformatics 2007, 8:453 (17November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Inferring activity changes of transcription factors by binding association with sorted expression profiles
Chao Cheng, Xiting Yan, Fengzhu Sun, Lei M Li
BMC Bioinformatics 2007, 8:452 (16November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Peptide ligand screening of  -synuclein aggregation modulators by in silico panning
Koichi Abe, Natsuki Kobayashi, Koji Sode, Kazunori Ikebukuro
BMC Bioinformatics 2007, 8:451 (16November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines
Jian Tian, Ningfeng Wu, Xuexia Guo, Jun Guo, Juhua Zhang, Yunliu Fan
BMC Bioinformatics 2007, 8:450 (16November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A comparison of Affymetrix gene expression arrays
Mark D Robinson, Terence P Speed
BMC Bioinformatics 2007, 8:449 (15November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
PedGenie: meta genetic association testing in mixed family and case-control designs
Karen Curtin, Jathine Wong, Kristina Allen-Brady, Nicola J Camp
BMC Bioinformatics 2007, 8:448 (15November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Application of a correlation correction factor in a microarray cross-platform reproducibility study
Kellie J Archer, Catherine I Dumur, G Scott Taylor, Michael D Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T Garrett
BMC Bioinformatics 2007, 8:447 (15November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Novel definition files for human GeneChips based on GeneAnnot
Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian Antonio Danieli, Silvio Bicciato
BMC Bioinformatics 2007, 8:446 (15November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining
Xochitl C Morgan, Shulin Ni, Daniel P Miranker, Vishwanath R Iyer
BMC Bioinformatics 2007, 8:445 (15November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions
Haiyan Jiang, Christian Blouin
BMC Bioinformatics 2007, 8:444 (15November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Correction
Ringo an R/Bioconductor package for analyzing ChIP-chip readouts
Joern Toedling, Oleg Skylar, Tammo Krueger, Jenny J Fischer, Silke Sperling, Wolfgang Huber
BMC Bioinformatics 2007, 8:443 (15November2007)
[Abstract] [Full text] [PDF]
Methodology article
A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification
Antonio Marco, Ignacio Mar n
BMC Bioinformatics 2007, 8:442 (15November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures
Konstantin Yu Popadin, Leila A Mamirova, Fyodor A Kondrashov
BMC Bioinformatics 2007, 8:441 (14November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL
Francois Besnier,  rjan Carlborg
BMC Bioinformatics 2007, 8:440 (13November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips
Ernest Turro, Natalia Bochkina, Anne-Mette K Hein, Sylvia Richardson
BMC Bioinformatics 2007, 8:439 (12November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Glycosylation site prediction using ensembles of Support Vector Machine classifiers
Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, Vasant Honavar
BMC Bioinformatics 2007, 8:438 (9November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
Xueping Yu, Jimmy Lin, Donald J Zack, Jiang Qian
BMC Bioinformatics 2007, 8:437 (9November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology
Wei Yu, Ajay Yesupriya, Anja Wulf, Junfeng Qu, Muin J Khoury, Marta Gwinn
BMC Bioinformatics 2007, 8:436 (9November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Improving model construction of profile HMMs for remote homology detection through structural alignment
Juliana S Bernardes, Alberto MR D vila, Vtor S Costa, Gerson Zaverucha
BMC Bioinformatics 2007, 8:435 (9November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays
Philippe Lamy, Claus L Andersen, Lars Dyrskjot, Niels Torring, Carsten Wiuf
BMC Bioinformatics 2007, 8:434 (9November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Incremental and unifying modelling formalism for biological interaction networks
Anastasia Yartseva, Hanna Klaudel, Raymond Devillers, Franois Kps
BMC Bioinformatics 2007, 8:433 (8November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila
Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li
BMC Bioinformatics 2007, 8:432 (8November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Comparative evaluation of gene-set analysis methods
Qi Liu, Irina Dinu, Adeniyi J Adewale, John D Potter, Yutaka Yasui
BMC Bioinformatics 2007, 8:431 (7November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Analysis of feedback loops and robustness in network evolution based on Boolean models
Yung-Keun Kwon, Kwang-Hyun Cho
BMC Bioinformatics 2007, 8:430 (7November2007)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
CoryneRegNet 4.0 A reference database for corynebacterial gene regulatory networks
Jan Baumbach
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