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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 9 |
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Volume 9 Suppl 8
Proceedings
Evry, France. 25 27 June 2008
Volume 9 Suppl 7
Meeting abstracts
Cadiz, KY, USA. 2830 March 2008
Volume 9 Suppl 6
Research
Iowa City, Iowa, USA. 1315 August 2007
more supplements 
Research article
 
Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements
Qingwu Yang, Sing-Hoi Sze
BMC Bioinformatics 2008, 9:320 (23July2008)
[Abstract] [Provisional PDF]
Research article
A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification
Alexander Statnikov, Lily Wang, Constantin F Aliferis
BMC Bioinformatics 2008, 9:319 (22July2008)
[Abstract] [Provisional PDF]
Methodology article
Directed acyclic graph kernels for structural RNA analysis
Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
BMC Bioinformatics 2008, 9:318 (22July2008)
[Abstract] [Provisional PDF]
Software
Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis.
Angela P Presson, Eric M Sobel, Paivi Pajukanta, Christopher Plaisier, Daniel E Weeks, Karolina Aberg, Jeanette C Papp
BMC Bioinformatics 2008, 9:317 (21July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
PatternLab for proteomics: a tool for differential shotgun proteomics
Paulo C Carvalho, Juliana SG Fischer, Emily I Chen, John R Yates III, Valmir C Barbosa
BMC Bioinformatics 2008, 9:316 (21July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies
Li Ma, H. BIRALI Runesha, Daniel Dvorkin, John R Garbe, Yang Da
BMC Bioinformatics 2008, 9:315 (21July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Assessing probe-specific dye and slide biases in two-color microarray Data
Ruixiao Lu, Geun-Cheol Lee, Michael Shultz, Chris Dardick, Kihong Jung, Jirapa Phetsom, Yi Jia, Robert H Rice, Zelanna Goldberg, Patrick S Schnable, Pamela Ronald, David M Rocke
BMC Bioinformatics 2008, 9:314 (19July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Database
SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.
Michael C Ryan, Barry R Zeeberg, Natash J Caplen, James A Cleland, Ari B Kahn, Hongfang Liu, John N Weinstein
BMC Bioinformatics 2008, 9:313 (18July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
MSDmotif: exploring protein sites and motifs
Adel Golovin, Kim Henrick
BMC Bioinformatics 2008, 9:312 (17July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
Function2Gene: a gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge
Don L Armstrong, Chaim O Jacob, Raphael Zidovetzki
BMC Bioinformatics 2008, 9:311 (17July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Computational identification of ubiquitylation sites from protein sequences
Chun-Wei Tung, Shinn-Ying Ho
BMC Bioinformatics 2008, 9:310 (15July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software
PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies
Brian L Browning
BMC Bioinformatics 2008, 9:309 (13July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords
Zhong-Xi Huang, Hui-Yong Tian, Zhen-Fu Hu, Yi-Bo Zhou, Jin Zhao, Kai-Tai Yao
BMC Bioinformatics 2008, 9:308 (13July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
Conditional Variable Importance for Random Forests
Carolin Strobl, Anne-Laure Boulesteix, Thomas Kneib, Thomas Augustin, Achim Zeileis
BMC Bioinformatics 2008, 9:307 (11July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Grammar-based distance in progressive multiple sequence alignment
David J Russell, Hasan H Otu, Khalid Sayood
BMC Bioinformatics 2008, 9:306 (10July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
MAID : An effect size based model for microarray data integration across laboratories and platforms
Ivan Borozan, Limin Chen, Bryan Paeper, Jenny E. Heathcote, Aled M. Edwards, Michael Katze, Zhaolei Zhang, Ian D. McGilvray
BMC Bioinformatics 2008, 9:305 (10July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Investigating selection on viruses: a statistical alignment approach
Saskia de Groot, Thomas Mailund, Gerton Lunter, Jotun Hein
BMC Bioinformatics 2008, 9:304 (10July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A unified approach to false discovery rate estimation
Korbinian Strimmer
BMC Bioinformatics 2008, 9:303 (9July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments
Jens Allmer, Sebastian Kuhlgert, Michael Hippler
BMC Bioinformatics 2008, 9:302 (7July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Deducing topology of protein-protein interaction networks from experimentally measured sub-networks
Ling Yang, Thomas M Vondriska, Zhangang Han, W Robb MacLellan, James N Weiss, Zhilin Qu
BMC Bioinformatics 2008, 9:301 (3July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A novel application of quantile regression for identification of biomarkers exemplified by equine cartilage microarray data
Liping Huang, Wenying Zhu, Christopher P Saunders, James N MacLeod, Mai Zhou, Arnold J Stromberg, Arne C Bathke
BMC Bioinformatics 2008, 9:300 (2July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
PseudoGeneQuest Service for identification of different pseudogene types in the human genome
Csaba Ortutay, Mauno Vihinen
BMC Bioinformatics 2008, 9:299 (2July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection
Inkyung Jung, Jaehyung Lee, Soo-Young Lee, Dongsup Kim
BMC Bioinformatics 2008, 9:298 (1July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information
Jing Hu, Changhui Yan
BMC Bioinformatics 2008, 9:297 (27June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Re-searcher: a system for recurrent detection of homologous protein sequences
Valdemaras Rep ys, Mindaugas Margelevi ius,  eslovas Venclovas
BMC Bioinformatics 2008, 9:296 (27June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Systems biology driven software design for the research enterprise
John Boyle, Christopher Cavnor, Sarah Killcoyne, Ilya Shmulevich
BMC Bioinformatics 2008, 9:295 (25June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Relating gene expression data on two-component systems to functional annotations in Escherichia coli
Anne M Denton, Jianfei Wu, Megan K Townsend, Preeti Sule, Birgit M Pr 
BMC Bioinformatics 2008, 9:294 (25June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins
Michael Hsing, Artem Cherkasov
BMC Bioinformatics 2008, 9:293 (25June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models
Dawei Liu, Debashis Ghosh, Xihong Lin
BMC Bioinformatics 2008, 9:292 (24June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease
Rob Jelier, Peter AC 't Hoen, Ellen Sterrenburg, Johan T den Dunnen, Gert-Jan B van Ommen, Jan A Kors, Barend Mons
BMC Bioinformatics 2008, 9:291 (24June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis
Jinho Yoo, Youngbok Lee, Yujung Kim, Sun Young Rha, Yangseok Kim
BMC Bioinformatics 2008, 9:290 (23June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Stability of gene contributions and identification of outliers in multivariate analysis of microarray data
Florent Baty, Daniel Jaeger, Frank Preiswerk, Martin M Schumacher, Martin H Brutsche
BMC Bioinformatics 2008, 9:289 (20June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient
Jianchao Yao, Chunqi Chang, Mari L Salmi, Yeung Sam Hung, Ann Loraine, Stanley J Roux
BMC Bioinformatics 2008, 9:288 (18June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Partial mixture model for tight clustering of gene expression time-course
Yinyin Yuan, Chang-Tsun Li, Roland Wilson
BMC Bioinformatics 2008, 9:287 (18June2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Precise detection of rearrangement breakpoints in mammalian chromosomes
Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot
BMC Bioinformatics 2008, 9:286 (18June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
Ryosuke LA Watanabe, Enrique Morett, Edgar E Vallejo
BMC Bioinformatics 2008, 9:285 (17June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Methods for evaluating gene expression from Affymetrix microarray datasets
Ning Jiang, Lindsey J Leach, Xiaohua Hu, Elena Potokina, Tianye Jia, Arnis Druka, Robbie Waugh, Michael J Kearsey, Zewei W Luo
BMC Bioinformatics 2008, 9:284 (17June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions
Ki-Yeol Kim, Dong Hyuk Ki, Hei-Cheul Jeung, Hyun Cheol Chung, Sun Young Rha
BMC Bioinformatics 2008, 9:283 (16June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor
Guangyong Zheng, Ziliang Qian, Qing Yang, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li
BMC Bioinformatics 2008, 9:282 (16June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
PURE: A webserver for the prediction of domains in unassigned regions in proteins
Chilamakuri CS Reddy, Khader Shameer, Bernard O Offmann, Ramanathan Sowdhamini
BMC Bioinformatics 2008, 9:281 (14June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification
Manli Zhu, Aleix M Martinez
BMC Bioinformatics 2008, 9:280 (14June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping
Guohui Lin, Zhipeng Cai, Junfeng Wu, Xiu-Feng Wan, Lizhe Xu, Randy Goebel
BMC Bioinformatics 2008, 9:279 (13June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar, Stephan Waack
BMC Bioinformatics 2008, 9:278 (13June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Semantic role labeling for protein transport predicates
Steven Bethard, Zhiyong Lu, James H Martin, Lawrence Hunter
BMC Bioinformatics 2008, 9:277 (11June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Discovering functional interaction patterns in protein-protein interaction networks
Mehmet E Turanalp, Tolga Can
BMC Bioinformatics 2008, 9:276 (11June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles
Guangtao Ge, G William Wong
BMC Bioinformatics 2008, 9:275 (11June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins
Armita Sheari, Mehdi Kargar, Ali Katanforoush, Shahriar Arab, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi, Sayed-Amir Marashi
BMC Bioinformatics 2008, 9:274 (11June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
AMYPdb: A database dedicated to amyloid precursor proteins
Sandrine Pawlicki, Antony Le B chec, Christian Delamarche
BMC Bioinformatics 2008, 9:273 (10June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles
Paul D Yoo, Yung Shwen Ho, Bing Bing Zhou, Albert Y Zomaya
BMC Bioinformatics 2008, 9:272 (10June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
TiGER: A database for tissue-specific gene expression and regulation
Xiong Liu, Xueping Yu, Donald J Zack, Heng Zhu, Jiang Qian
BMC Bioinformatics 2008, 9:271 (9June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval
Jimmy Lin
BMC Bioinformatics 2008, 9:270 (6June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Flexible boosting of accelerated failure time models
Matthias Schmid, Torsten Hothorn
BMC Bioinformatics 2008, 9:269 (6June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures
Meng P Tan, Erin N Smith, James R Broach, Christodoulos A Floudas
BMC Bioinformatics 2008, 9:268 (6June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Principal components analysis based methodology to identify differentially expressed genes in time-course microarray data
Sudhakar Jonnalagadda, Rajagopalan Srinivasan
BMC Bioinformatics 2008, 9:267 (6June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen
BMC Bioinformatics 2008, 9:266 (6June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
StAR: a simple tool for the statistical comparison of ROC curves
Ismael A Vergara, Tom s Norambuena, Evandro Ferrada, Alex W Slater, Francisco Melo
BMC Bioinformatics 2008, 9:265 (5June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens
Zheng Yin, Xiaobo Zhou, Chris Bakal, Fuhai Li, Youxian Sun, Norbert Perrimon, Stephen TC Wong
BMC Bioinformatics 2008, 9:264 (5June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors
Chiara Parravicini, Graziella Ranghino, Maria P Abbracchio, Piercarlo Fantucci
BMC Bioinformatics 2008, 9:263 (4June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Mari o-Ram rez, John L Spouge
BMC Bioinformatics 2008, 9:262 (4June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)
Juan R Gonzalez, Josep L Carrasco, Lluis Armengol, Sergi Vilaroto, Lluis Jover, Yutaka Yasui, Xavier Estivill
BMC Bioinformatics 2008, 9:261 (4June2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Database
GMDD: a database of GMO detection methods
Wei Dong, Litao Yang, Kailin Shen, Banghyun Kim, Gijs A Kleter, Hans JP Marvin, Rong Guo, Wanqi Liang, Dabing Zhang
BMC Bioinformatics 2008, 9:260 (4June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Word correlation matrices for protein sequence analysis and remote homology detection
Thomas Lingner, Peter Meinicke
BMC Bioinformatics 2008, 9:259 (3June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A simple and robust method for connecting small-molecule drugs using gene-expression signatures
Shu-Dong Zhang, Timothy W Gant
BMC Bioinformatics 2008, 9:258 (2June2008)
[Abstract] [Full text |
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