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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Danielle Burgess PhD
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| | BMC Bioinformatics, Volume 9 |
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Software
  
MetaMine  A tool to detect and analyse gene patterns in their environmental context
Uta Bohnebeck, Thierry Lombardot, Renzo Kottmann, Frank O Gl ckner
BMC Bioinformatics 2008, 9:459 (28October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
Peter A DiMaggio Jr, Scott R McAllister, Christodoulos A Floudas, Xiao-Jiang Feng, Joshua D Rabinowitz, Herschel A Rabitz
BMC Bioinformatics 2008, 9:458 (27October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles
Hailong Meng, Edward L Murrelle, Guoya Li
BMC Bioinformatics 2008, 9:457 (27October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
FUNYBASE: a FUNgal phYlogenomic dataBASE
Sylvain Marthey, Gabriela Aguileta, Fran ois Rodolphe, Annie Gendrault, Tatiana Giraud, Elisabeth Fournier, Manuela Lopez-Villavicencio, Ang lique Gautier, Marc-Henri Lebrun, Hl ne Chiapello
BMC Bioinformatics 2008, 9:456 (27October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Software
CompMoby: Comparative MobyDick for detection of cis-regulatory motifs
Christina Chaivorapol, Collin Melton, Grace Wei, Ru-Fang Yeh, Miguel Ramalho-Santos, Robert Blelloch, Hao Li
BMC Bioinformatics 2008, 9:455 (27October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites
Mohd Zeeshan Ansari, Jyoti Sharma, Rajesh S Gokhale, Debasisa Mohanty
BMC Bioinformatics 2008, 9:454 (25October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Probe signal correction for differential methylation hybridization experiments
Dustin P Potter, Pearlly Yan, Tim HM Huang, Shili Lin
BMC Bioinformatics 2008, 9:453 (23October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Background correction using dinucleotide affinities improves the performance of GCRMA
Raad Z Gharaibeh, Anthony A Fodor, Cynthia J Gibas
BMC Bioinformatics 2008, 9:452 (23October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Feature selection environment for genomic applications
Fabr cio Martins Lopes, David Corr a Martins Jr, Roberto M Cesar Jr
BMC Bioinformatics 2008, 9:451 (22October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking
Jung Soh, Paul MK Gordon, Morgan L Taschuk, Anguo Dong, Andrew C Ah-Seng, Andrei L Turinsky, Christoph W Sensen
BMC Bioinformatics 2008, 9:450 (22October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification
Ning Wei, Erwin Flaschel, Karl Friehs, Tim Wilhelm Nattkemper
BMC Bioinformatics 2008, 9:449 (21October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces
Salim Bougouffa, Jim Warwicker
BMC Bioinformatics 2008, 9:448 (21October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Identification of hot-spot residues in protein-protein interactions by computational docking
Solne Grosdidier, Juan Fern ndez-Recio
BMC Bioinformatics 2008, 9:447 (21October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Envelope: interactive software for modeling and fitting complex isotope distributions
Michael T Sykes, James R Williamson
BMC Bioinformatics 2008, 9:446 (20October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
An incremental approach to automated protein localisation
Marko Tscherepanow, Nickels Jensen, Franz Kummert
BMC Bioinformatics 2008, 9:445 (20October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Assessment of protein set coherence using functional annotations
Monica Chagoyen, Jose M Carazo, Alberto Pascual-Montano
BMC Bioinformatics 2008, 9:444 (20October2008)
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Methodology article
Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics
Wiebke Timm, Alexandra Scherbart, Sebastian Bcker, Oliver Kohlbacher, Tim W Nattkemper
BMC Bioinformatics 2008, 9:443 (20October2008)
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Methodology article
Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data
Michael J Gilchrist, Mikkel B Christensen, Richard Harland, Nicolas Pollet, James C Smith, Naoto Ueno, Nancy Papalopulu
BMC Bioinformatics 2008, 9:442 (17October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Structural assembly of two-domain proteins by rigid-body docking
Tammy MK Cheng, Tom L Blundell, Juan Fernandez-Recio
BMC Bioinformatics 2008, 9:441 (16October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data
Laurent Brhlin, Jean-Franois Dufayard, Olivier Gascuel
BMC Bioinformatics 2008, 9:440 (16October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
CMA a comprehensive Bioconductor package for supervised classification with high dimensional data
M Slawski, M Daumer, A-L Boulesteix
BMC Bioinformatics 2008, 9:439 (16October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O Villoutreix, Maria A Miteva
BMC Bioinformatics 2008, 9:438 (16October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
OntoDas a tool for facilitating the construction of complex queries to the Gene Ontology
Kieran O'Neill, Alexander Garcia, Anita Schwegmann, Rafael C Jimenez, Dan Jacobson, Henning Hermjakob
BMC Bioinformatics 2008, 9:437 (16October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Prediction of TF target sites based on atomistic models of protein-DNA complexes
Vladimir Espinosa Angarica, Abel Gonzlez Prez, Ana T Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira
BMC Bioinformatics 2008, 9:436 (16October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Multi-agent systems in epidemiology: a first step for computational biology in the study of vector-borne disease transmission
Benjamin Roche, Jean-Franois Gugan, Franois Bousquet
BMC Bioinformatics 2008, 9:435 (15October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Comparative optimism in models involving both classical clinical and gene expression information
Caroline Truntzer, Delphine Maucort-Boulch, Pascal Roy
BMC Bioinformatics 2008, 9:434 (15October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Reranking candidate gene models with cross-species comparison for improved gene prediction
Qian Liu, Koby Crammer, Fernando CN Pereira, David S Roos
BMC Bioinformatics 2008, 9:433 (14October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
easyExon A Java-based GUI tool for processing and visualization of Affymetrix exon array data
Ting-Yu Chang, Yin-Yi Li, Chih-Hung Jen, Tsun-Po Yang, Chi-Hung Lin, Ming-Ta Hsu, Hsei-Wei Wang
BMC Bioinformatics 2008, 9:432 (14October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Probabilistic base calling of Solexa sequencing data
Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef
BMC Bioinformatics 2008, 9:431 (13October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments
Ce Zheng, Lukasz Kurgan
BMC Bioinformatics 2008, 9:430 (10October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure
Christopher Bystroff, Bobbie-Jo Webb-Robertson
BMC Bioinformatics 2008, 9:429 (10October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access
Jorge Amigo, Antonio Salas, Christopher Phillips,  ngel Carracedo
BMC Bioinformatics 2008, 9:428 (10October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations
Guillaume Launay, Thomas Simonson
BMC Bioinformatics 2008, 9:427 (9October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Mining protein networks for synthetic genetic interactions
Sri R Paladugu, Shan Zhao, Animesh Ray, Alpan Raval
BMC Bioinformatics 2008, 9:426 (9October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems
Yu-Shuen Tsai, Chin-Teng Lin, George C Tseng, I-Fang Chung, Nikhil Ranjan Pal
BMC Bioinformatics 2008, 9:425 (9October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks
Iaroslav Ispolatov, Sergei Maslov
BMC Bioinformatics 2008, 9:424 (8October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
LC-MSsim a simulation software for liquid chromatography mass spectrometry data
Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Grpl, Oliver Kohlbacher, Knut Reinert
BMC Bioinformatics 2008, 9:423 (8October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Software
SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes
Raj Chari, Bradley P Coe, Craig Wedseltoft, Marie Benetti, Ian M Wilson, Emily A Vucic, Calum MacAulay, Raymond T Ng, Wan L Lam
BMC Bioinformatics 2008, 9:422 (7October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Bayesian modeling of recombination events in bacterial populations
Pekka Marttinen, Adam Baldwin, William P Hanage, Chris Dowson, Eshwar Mahenthiralingam, Jukka Corander
BMC Bioinformatics 2008, 9:421 (7October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
Daniel N Frank
BMC Bioinformatics 2008, 9:420 (7October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Database
A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
Sheila Podell, Terry Gaasterland, Eric E Allen
BMC Bioinformatics 2008, 9:419 (7October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
Automatically extracting functionally equivalent proteins from SwissProt
Lisa EM McMillan, Andrew CR Martin
BMC Bioinformatics 2008, 9:418 (6October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A method for analyzing censored survival phenotype with gene expression data
Tongtong Wu, Wei Sun, Shinsheng Yuan, Chun-Houh Chen, Ker-Chau Li
BMC Bioinformatics 2008, 9:417 (6October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Knowledge-guided multi-scale independent component analysis for biomarker identification
Li Chen, Jianhua Xuan, Chen Wang, Ie-Ming Shih, Yue Wang, Zhen Zhang, Eric Hoffman, Robert Clarke
BMC Bioinformatics 2008, 9:416 (6October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments
Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky
BMC Bioinformatics 2008, 9:415 (6October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach
Firoz Anwar, Syed Murtuza Baker, Taskeed Jabid, Md Mehedi Hasan, Mohammad Shoyaib, Haseena Khan, Ray Walshe
BMC Bioinformatics 2008, 9:414 (4October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
PhySIC_IST: cleaning source trees to infer more informative supertrees
Celine Scornavacca, Vincent Berry, Vincent Lefort, Emmanuel JP Douzery, Vincent Ranwez
BMC Bioinformatics 2008, 9:413 (4October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Gene and pathway identification with Lp penalized Bayesian logistic regression
Zhenqiu Liu, Ronald B Gartenhaus, Ming Tan, Feng Jiang, Xiaoli Jiao
BMC Bioinformatics 2008, 9:412 (3October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Classification of drug molecules considering their IC50 values using mixed-integer linear programming based hyper-boxes method
Pelin Armutlu, Muhittin E Ozdemir, Fadime Uney-Yuksektepe, I Halil Kavakli, Metin Turkay
BMC Bioinformatics 2008, 9:411 (3October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments
Stefano Parodi, Vito Pistoia, Marco Muselli
BMC Bioinformatics 2008, 9:410 (3October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
Johan Staaf, Johan Vallon-Christersson, David Lindgren, Gunnar Juliusson, Richard Rosenquist, Mattias Hglund,  ke Borg, Markus Ringnr
BMC Bioinformatics 2008, 9:409 (2October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools
Kevin Bleakley, Marie-Paule Lefranc, Grard Biau
BMC Bioinformatics 2008, 9:408 (2October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Towards a lightweight generic computational grid framework for biological research
Mark D Halling-Brown, David S Moss, Adrian J Shepherd
BMC Bioinformatics 2008, 9:407 (2October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
BibGlimpse: The case for a light-weight reprint manager in distributed literature research
Thomas T chler, Golda Velez, Alexandra Graf, David P Kreil
BMC Bioinformatics 2008, 9:406 (1October2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
iRefIndex: A consolidated protein interaction database with provenance
Sabry Razick, George Magklaras, Ian M Donaldson
BMC Bioinformatics 2008, 9:405 (30September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
Atsushi Niida, Andrew D Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q Zhang, Tetsu Akiyama
BMC Bioinformatics 2008, 9:404 (29September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
MetaMQAP: A meta-server for the quality assessment of protein models
Marcin Pawlowski, Michal J Gajda, Ryszard Matlak, Janusz M Bujnicki
BMC Bioinformatics 2008, 9:403 (29September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Abbreviation definition identification based on automatic precision estimates
Sunghwan Sohn, Donald C Comeau, Won Kim, W John Wilbur
BMC Bioinformatics 2008, 9:402 (25September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Developing and validating predictive decision tree models from mining chemical structural fingerprints and highthroughput screening data in PubChem
Lianyi Han, Yanli Wang, Stephen H Bryant
BMC Bioinformatics 2008, 9:401 (25September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction
Stefan Kuhn, Bjrn Egert, Steffen Neumann, Christoph Steinbeck
BMC Bioinformatics 2008, 9:400 (25September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Presenting and exploring biological pathways with PathVisio
Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, Chris Evelo
BMC Bioinformatics 2008, 9:399 (25September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
Min Li, Jian-er Chen, Jian-xin Wang, Bin Hu, Gang Chen
BMC Bioinformatics 2008, 9:398 (25September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Predicting protein linkages in bacteria: Which method is best depends on task
Anis Karimpour-Fard, Sonia M Leach, Ryan T Gill, Lawrence E Hunter
BMC Bioinformatics 2008, 9:397 (24September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects
David Lagorce, Olivier Sperandio, Herv Galons, Maria A Miteva, Bruno O Villoutreix
BMC Bioinformatics 2008, 9:396 (24September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach
Li Shen, Jie Liu, Wei Wang
BMC Bioinformatics 2008, 9:395 (24September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'
Qi Dai, Tianming Wang
BMC Bioinformatics 2008, 9:394 (23September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
HECTAR: A method to predict subcellular targeting in heterokonts
Bernhard Gschloessl, Yann Guermeur, J Mark Cock
BMC Bioinformatics 2008, 9:393 (23September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
PredGPI: a GPI-anchor predictor
Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio
BMC Bioinformatics 2008, 9:392 (23September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase
Fabrice PA David, Yum L Yip
BMC Bioinformatics 2008, 9:391 (23September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
R/parallel speeding up bioinformatics analysis with R
Gonzalo Vera, Ritsert C Jansen, Remo L Suppi
BMC Bioinformatics 2008, 9:390 (22September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Combining classifiers for improved classification of proteins from sequence or structure
Iain Melvin, Jason Weston, Christina S Leslie, William S Noble
BMC Bioinformatics 2008, 9:389 (22September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Sequence based residue depth prediction using evolutionary information and predicted secondary structure
Hua Zhang, Tuo Zhang, Ke Chen, Shiyi Shen, Jishou Ruan, Lukasz Kurgan
BMC Bioinformatics 2008, 9:388 (20September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
"TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis
Pornpat Nikamanon, Elroy Pun, Wayne Chou, Marek D Koter, Paul D Gershon
BMC Bioinformatics 2008, 9:387 (20September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
The metagenomics RAST server a public resource for the automatic phylogenetic and functional analysis of metagenomes
F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, RA Edwards
BMC Bioinformatics 2008, 9:386 (19September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Research article
Improving peptide-MHC class I binding prediction for unbalanced datasets
Ana Paula Sales, Georgia D Tomaras, Thomas B Kepler
BMC Bioinformatics 2008, 9:385 (19September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
GlycomeDB integration of open-access carbohydrate structure databases
Ren Ranzinger, Stephan Herget, Thomas Wetter, Claus-Wilhelm von der Lieth
BMC Bioinformatics 2008, 9:384 (19September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
caBIG VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data
Yitan Zhu, Huai Li, David J Miller, Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric P Hoffman, Yue Wang
BMC Bioinformatics 2008, 9:383 (18September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge
Young-Rae Cho, Lei Shi, Murali Ramanathan, Aidong Zhang
BMC Bioinformatics 2008, 9:382 (18September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
MetWAMer: eukaryotic translation initiation site prediction
Michael E Sparks, Volker Brendel
BMC Bioinformatics 2008, 9:381 (18September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A Population Proportion approach for ranking differentially expressed genes
Mugdha Gadgil
BMC Bioinformatics 2008, 9:380 (18September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
MiMiR an integrated platform for microarray data sharing, mining and analysis
Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Tim Aitman, Laurence Game
BMC Bioinformatics 2008, 9:379 (18September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
SQUAT: A web tool to mine human, murine and avian SAGE data
Johan Leyritz, Stphane Schicklin, Sylvain Blachon, Cline Keime, Cline Robardet, Jean-Franois Boulicaut, Jrmy Besson, Ruggero G Pensa, Olivier Gandrillon
BMC Bioinformatics 2008, 9:378 (18September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
CBESW: Sequence Alignment on the Playstation 3
Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, Bertil Schmidt
BMC Bioinformatics 2008, 9:377 (17September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Software
GenomeMatcher: A graphical user interface for DNA sequence comparison
Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata, Masataka Tsuda
BMC Bioinformatics 2008, 9:376 (16September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Research article
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
Eva Lange, Ralf Tautenhahn, Steffen Neumann, Clemens Grpl
BMC Bioinformatics 2008, 9:375 (15September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Large-scale identification of polymorphic microsatellites using an in silico approach
Jifeng Tang, Samantha J Baldwin, Jeanne ME Jacobs, C Gerard van der Linden, Roeland E Voorrips, Jack AM Leunissen, Herman van Eck, Ben Vosman
BMC Bioinformatics 2008, 9:374 (15September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy
Marco AJ Iafolla, Guang Qiang Dong, David R McMillen
BMC Bioinformatics 2008, 9:373 (12September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast
Uri Keich, Hong Gao, Jeffrey S Garretson, Anand Bhaskar, Ivan Liachko, Justin Donato, Bik K Tye
BMC Bioinformatics 2008, 9:372 (12September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Kismeth: Analyzer of plant methylation states through bisulfite sequencing
Eyal Gruntman, Yijun Qi, R Keith Slotkin, Ted Roeder, Robert A Martienssen, Ravi Sachidanandam
BMC Bioinformatics 2008, 9:371 (11September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Mixture models for analysis of melting temperature data
Christoffer Nell ker, Fredrik Uhrzander, Joanna Tyrcha, Hkan Karlsson
BMC Bioinformatics 2008, 9:370 (11September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Automatic detection of exonic splicing enhancers (ESEs) using SVMs
Britta Mersch, Alexander Gepperth, Sndor Suhai, Agnes Hotz-Wagenblatt
BMC Bioinformatics 2008, 9:369 (10September2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens
Wah Heng Lee, Christopher W Wong, Wan Yee Leong, Lance D Miller, Wing Kin Sung
BMC Bioinformatics 2008, 9:368 (10September2008)
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BMC Bioinformatics 2008, 9:367 (10September2008)
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BMC Bioinformatics 2008, 9:366 (9September2008)
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Marc Chadeau-Hyam, Clive J Hoggart, Paul F O'Reilly, John C Whittaker, Maria De Iorio, David J Balding
BMC Bioinformatics 2008, 9:364 (8September2008)
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BMC Bioinformatics 2008, 9:363 (6September2008)
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BMC Bioinformatics 2008, 9:362 (2September2008)
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BMC Bioinformatics 2008, 9:361 (2September2008)
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