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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 9 |
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Volume 9 Suppl 12
Proceedings
Taipei, Taiwan. 20 23 October 2008
Volume 9 Suppl 11
Research
Columbus, OH, USA. 19 June 2008
Volume 9 Suppl 10
Meeting abstracts
Toronto, Canada. 18 July 2008
more supplements 
Software
  
WGCNA: an R package for weighted correlation network analysis
Peter Langfelder, Steve Horvath
BMC Bioinformatics 2008, 9:559 (29December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Software
SPRINT: A new parallel framework for R
Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence M Sloan, Florian Scharinger, Arthur Trew, Peter Ghazal
BMC Bioinformatics 2008, 9:558 (29December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SimHap GUI: An intuitive graphical user interface for genetic association analysis
Kim W Carter, Pamela A McCaskie, Lyle J Palmer
BMC Bioinformatics 2008, 9:557 (25December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The meaning of alignment: lessons from structural diversity
Walter Pirovano, K Anton Feenstra, Jaap Heringa
BMC Bioinformatics 2008, 9:556 (23December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays
Romesh Stanislaus, Mark Carey, Helena F Deus, Kevin Coombes, Bryan T Hennessy, Gordon B Mills, Jonas S Almeida
BMC Bioinformatics 2008, 9:555 (22December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family
Alberto I Roca, Albert E Almada, Aaron C Abajian
BMC Bioinformatics 2008, 9:554 (22December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Prediction of protein-protein binding site by using core interface residue and support vector machine
Nan Li, Zhonghua Sun, Fan Jiang
BMC Bioinformatics 2008, 9:553 (22December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments
Andreas Keller, Christina Backes, Maher Al-Awadhi, Andreas Gerasch, Jan K ntzer, Oliver Kohlbacher, Michael Kaufmann, Hans-Peter Lenhof
BMC Bioinformatics 2008, 9:552 (22December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network
Matteo Brilli, Alessio Mengoni, Marco Fondi, Marco Bazzicalupo, Pietro Li , Renato Fani
BMC Bioinformatics 2008, 9:551 (21December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [1 comment]
Research article
Pathological rate matrices: from primates to pathogens
Harold W Schranz, Von Bing Yap, Simon Easteal, Rob Knight, Gavin A Huttley
BMC Bioinformatics 2008, 9:550 (19December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
nGASP the nematode genome annotation assessment project
Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar, the nGASP Consortium, Lincoln D Stein
BMC Bioinformatics 2008, 9:549 (19December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J Butte
BMC Bioinformatics 2008, 9:548 (18December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Prediction of regulatory elements in mammalian genomes using chromatin signatures
Kyoung-Jae Won, Iouri Chepelev, Bing Ren, Wei Wang
BMC Bioinformatics 2008, 9:547 (18December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Barcodes for genomes and applications
Fengfeng Zhou, Victor Olman, Ying Xu
BMC Bioinformatics 2008, 9:546 (17December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Examining the significance of fingerprint-based classifiers
Brian T Luke, Jack R Collins
BMC Bioinformatics 2008, 9:545 (17December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
AnEnPi: identification and annotation of analogous enzymes
Thomas D Otto, Ana Carolina R Guimar es, Wim M Degrave, Antonio B de Miranda
BMC Bioinformatics 2008, 9:544 (17December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
PocketMatch: A new algorithm to compare binding sites in protein structures
Kalidas Yeturu, Nagasuma Chandra
BMC Bioinformatics 2008, 9:543 (17December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
Mi-Youn Brusniak, Bernd Bodenmiller, David Campbell, Kelly Cooke, James Eddes, Andrew Garbutt, Hollis Lau, Simon Letarte, Lukas N Mueller, Vagisha Sharma, Olga Vitek, Ning Zhang, Ruedi Aebersold, Julian D Watts
BMC Bioinformatics 2008, 9:542 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
GeNESiS: gene network evolution simulation software
Anton Kratz, Masaru Tomita, Arun Krishnan
BMC Bioinformatics 2008, 9:541 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Shape-IT: new rapid and accurate algorithm for haplotype inference
Olivier Delaneau, C dric Coulonges, Jean-Fran ois Zagury
BMC Bioinformatics 2008, 9:540 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
Jukka Corander, Pekka Marttinen, Jukka Sirn, Jing Tang
BMC Bioinformatics 2008, 9:539 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis
Yan Xin Huang, Yong Li Bao, Shu Yan Guo, Yan Wang, Chun Guang Zhou, Yu Xin Li
BMC Bioinformatics 2008, 9:538 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
Fan Mo, Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbert S Omenn, Biaoyang Lin
BMC Bioinformatics 2008, 9:537 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes
Frdric Lemoine, Bernard Labedan, Olivier Lespinet
BMC Bioinformatics 2008, 9:536 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites
Evert-Jan Blom, Sacha AFT van Hijum, Klaas J Hofstede, Remko Silvis, Jos BTM Roerdink, Oscar P Kuipers
BMC Bioinformatics 2008, 9:535 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Optimal neighborhood indexing for protein similarity search
Pierre Peterlongo, Laurent No, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud
BMC Bioinformatics 2008, 9:534 (16December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
GPAT: Retrieval of genomic annotation from large genomic position datasets
Arnaud Krebs, Mattia Frontini, L szl Tora
BMC Bioinformatics 2008, 9:533 (15December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Correspondence
Extended Newick: it is time for a standard representation of phylogenetic networks
Gabriel Cardona, Francesc Rossell , Gabriel Valiente
BMC Bioinformatics 2008, 9:532 (15December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
Shashi Bhushan Pandit, Jeffrey Skolnick
BMC Bioinformatics 2008, 9:531 (12December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data
Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi, David M Gilbert
BMC Bioinformatics 2008, 9:530 (10December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results
John C Braisted, Srilatha Kuntumalla, Christine Vogel, Edward M Marcotte, Alan R Rodrigues, Rong Wang, Shih-Ting Huang, Erik S Ferlanti, Alexander I Saeed, Robert D Fleischmann, Scott N Peterson, Rembert Pieper
BMC Bioinformatics 2008, 9:529 (9December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Gene Prospector: An evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases
Wei Yu, Anja Wulf, Tiebin Liu, Muin J Khoury, Marta Gwinn
BMC Bioinformatics 2008, 9:528 (8December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Compo: composite motif discovery using discrete models
Geir Kjetil Sandve, Osman Abul, Finn Drabl s
BMC Bioinformatics 2008, 9:527 (8December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
SNPFile A software library and file format for large scale association mapping and population genetics studies
Jesper Nielsen, Thomas Mailund
BMC Bioinformatics 2008, 9:526 (8December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Multi-label literature classification based on the Gene Ontology graph
Bo Jin, Brian Muller, Chengxiang Zhai, Xinghua Lu
BMC Bioinformatics 2008, 9:525 (8December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
IDEA: Interactive Display for Evolutionary Analyses
Amy Egan, Anup Mahurkar, Jonathan Crabtree, Jonathan H Badger, Jane M Carlton, Joana C Silva
BMC Bioinformatics 2008, 9:524 (8December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
David A Nix, Samir J Courdy, Kenneth M Boucher
BMC Bioinformatics 2008, 9:523 (5December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Systematic identification of yeast cell cycle transcription factors using multiple data sources
Wei-Sheng Wu, Wen-Hsiung Li
BMC Bioinformatics 2008, 9:522 (5December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast
Akito Taneda
BMC Bioinformatics 2008, 9:521 (5December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data
Carl R Pelz, Molly Kulesz-Martin, Grover Bagby, Rosalie C Sears
BMC Bioinformatics 2008, 9:520 (4December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Integrated multi-level quality control for proteomic profiling studies using mass spectrometry
David A Cairns, David N Perkins, Anthea J Stanley, Douglas Thompson, Jennifer H Barrett, Peter J Selby, Rosamonde E Banks
BMC Bioinformatics 2008, 9:519 (4December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Algorithm of OMA for large-scale orthology inference
Alexander CJ Roth, Gaston H Gonnet, Christophe Dessimoz
BMC Bioinformatics 2008, 9:518 (4December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Detection of protein catalytic residues at high precision using local network properties
Patrick Slama, Ioannis Filippis, Michael Lappe
BMC Bioinformatics 2008, 9:517 (4December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions
Martin Bader, Mohamed I Abouelhoda, Enno Ohlebusch
BMC Bioinformatics 2008, 9:516 (4December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Improved machine learning method for analysis of gas phase chemistry of peptides
Allison Gehrke, Shaojun Sun, Lukasz Kurgan, Natalie Ahn, Katheryn Resing, Karen Kafadar, Krzysztof Cios
BMC Bioinformatics 2008, 9:515 (3December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
ElliPro: a new structure-based tool for the prediction of antibody epitopes
Julia Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E Bourne, Alessandro Sette, Bjoern Peters
BMC Bioinformatics 2008, 9:514 (2December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions
Shu-Yi Su, Jonathan White, David J Balding, Lachlan JM Coin
BMC Bioinformatics 2008, 9:513 (1December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips
Marta Blangiardo, Sylvia Richardson
BMC Bioinformatics 2008, 9:512 (1December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Comparison of methods for estimating the nucleotide substitution matrix
Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A Huttley, Manuel E Lladser, Rob Knight
BMC Bioinformatics 2008, 9:511 (1December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis
Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong, Xuan Wang
BMC Bioinformatics 2008, 9:510 (1December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Position dependent mismatch discrimination on DNA microarrays experiments and model
Thomas Naiser, Jona Kayser, Timo Mai, Wolfgang Michel, Albrecht Ott
BMC Bioinformatics 2008, 9:509 (1December2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method
Joseph W Foley, Fumiaki Katagiri
BMC Bioinformatics 2008, 9:508 (29November2008)
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Research article
MetaboMiner semi-automated identification of metabolites from 2D NMR spectra of complex biofluids
Jianguo Xia, Trent C Bjorndahl, Peter Tang, David S Wishart
BMC Bioinformatics 2008, 9:507 (28November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression
Katerina Kechris, Hao Li
BMC Bioinformatics 2008, 9:506 (28November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Use of normalization methods for analysis of microarrays containing a high degree of gene effects
Terri T Ni, William J Lemon, Yu Shyr, Tao P Zhong
BMC Bioinformatics 2008, 9:505 (28November2008)
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Research article
Highly sensitive feature detection for high resolution LC/MS
Ralf Tautenhahn, Christoph B ttcher, Steffen Neumann
BMC Bioinformatics 2008, 9:504 (28November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins
Aarti Garg, Gajendra PS Raghava
BMC Bioinformatics 2008, 9:503 (28November2008)
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Methodology article
Microarray-based gene set analysis: a comparison of current methods
Sarah Song, Michael A Black
BMC Bioinformatics 2008, 9:502 (27November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features
Derek Huntley, Y Amy Tang, Tatyana B Nesterova, Sarah Butcher, Neil Brockdorff
BMC Bioinformatics 2008, 9:501 (27November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Prediction of glycosylation sites using random forests
Stephen E Hamby, Jonathan D Hirst
BMC Bioinformatics 2008, 9:500 (27November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Natural computation meta-heuristics for the in silico optimization of microbial strains
Miguel Rocha, Paulo Maia, Rui Mendes, Jos P Pinto, Eugnio C Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha
BMC Bioinformatics 2008, 9:499 (27November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level
Hl ne Chiapello, Annie Gendrault, Christophe Caron, Jrome Blum, Marie-Agns Petit, Meriem El Karoui
BMC Bioinformatics 2008, 9:498 (27November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Clustering cancer gene expression data: a comparative study
Marcilio CP de Souto, Ivan G Costa, Daniel SA de Araujo, Teresa B Ludermir, Alexander Schliep
BMC Bioinformatics 2008, 9:497 (27November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes
Josephine F Reyes, Andrew R Francis, Mark M Tanaka
BMC Bioinformatics 2008, 9:496 (27November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes
Matthew S Hestand, Michiel van Galen, Michel P Villerius, Gert-Jan B van Ommen, Johan T den Dunnen, Peter AC 't Hoen
BMC Bioinformatics 2008, 9:495 (26November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
ExonMiner: Web service for analysis of GeneChip Exon array data
Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano
BMC Bioinformatics 2008, 9:494 (26November2008)
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Software
EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management
G Barton, J Abbott, N Chiba, DW Huang, Y Huang, M Krznaric, J Mack-Smith, A Saleem, BT Sherman, B Tiwari, C Tomlinson, T Aitman, J Darlington, L Game, MJE Sternberg, SA Butcher
BMC Bioinformatics 2008, 9:493 (25November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
Structural descriptor database: a new tool for sequence-based functional site prediction
Juliana S Bernardes, Jorge H Fernandez, Ana Tereza R Vasconcelos
BMC Bioinformatics 2008, 9:492 (25November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Prediction of specificity-determining residues for small-molecule kinase inhibitors
Daniel R Caffrey, Elizabeth A Lunney, Deborah J Moshinsky
BMC Bioinformatics 2008, 9:491 (25November2008)
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Research article
A comparison of four clustering methods for brain expression microarray data
Alexander L Richards, Peter Holmans, Michael C O'Donovan, Michael J Owen, Lesley Jones
BMC Bioinformatics 2008, 9:490 (25November2008)
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Methodology article
Determining gene expression on a single pair of microarrays
Robert W Reid, Anthony A Fodor
BMC Bioinformatics 2008, 9:489 (21November2008)
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Methodology article
Identifying differential correlation in gene/pathway combinations
Rosemary Braun, Leslie Cope, Giovanni Parmigiani
BMC Bioinformatics 2008, 9:488 (18November2008)
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Research article
Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable
Myron Peto, Andrzej Kloczkowski, Vasant Honavar, Robert L Jernigan
BMC Bioinformatics 2008, 9:487 (18November2008)
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Research article
Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification
Michael Gormley, Aydin Tozeren
BMC Bioinformatics 2008, 9:486 (17November2008)
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Software
CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments
Paolo Uva, Emanuele de Rinaldis
BMC Bioinformatics 2008, 9:485 (17November2008)
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Research article
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne, Jan Komorowski
BMC Bioinformatics 2008, 9:484 (17November2008)
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Software
mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences
Hwan Young Lee, Injee Song, Eunho Ha, Sung-Bae Cho, Woo Ick Yang, Kyoung-Jin Shin
BMC Bioinformatics 2008, 9:483 (17November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
CellProfiler Analyst: data exploration and analysis software for complex image-based screens
Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist, Adam Papallo, David M Sabatini, Polina Golland, Anne E Carpenter
BMC Bioinformatics 2008, 9:482 (15November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Gene set enrichment analysis for non-monotone association and multiple experimental categories
Rongheng Lin, Shuangshuang Dai, Richard D Irwin, Alexandra N Heinloth, Gary A Boorman, Leping Li
BMC Bioinformatics 2008, 9:481 (14November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data
Luca Corradi, Marco Fato, Ivan Porro, Silvia Scaglione, Livia Torterolo
BMC Bioinformatics 2008, 9:480 (13November2008)
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Database
Extension of the COG and arCOG databases by amino acid and nucleotide sequences
Florian Meereis, Michael Kaufmann
BMC Bioinformatics 2008, 9:479 (13November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences
James K Hane, Richard P Oliver
BMC Bioinformatics 2008, 9:478 (12November2008)
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Research article
Improved identification of conserved cassette exons using Bayesian networks
Rileen Sinha, Michael Hiller, Rainer Pudimat, Ulrike Gausmann, Matthias Platzer, Rolf Backofen
BMC Bioinformatics 2008, 9:477 (12November2008)
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Software
CoCoNUT: an efficient system for the comparison and analysis of genomes
Mohamed I Abouelhoda, Stefan Kurtz, Enno Ohlebusch
BMC Bioinformatics 2008, 9:476 (12November2008)
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Software
Standardized high-throughput evaluation of cell-based compound screens
Peter Frommolt, Roman K Thomas
BMC Bioinformatics 2008, 9:475 (12November2008)
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Methodology article
RNAalifold: improved consensus structure prediction for RNA alignments
Stephan H Bernhart, Ivo L Hofacker, Sebastian Will, Andreas R Gruber, Peter F Stadler
BMC Bioinformatics 2008, 9:474 (11November2008)
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Methodology article
Nuclear staining and relative distance for quantifying epidermal differentiation in biomarker expression profiling
Thora Pommerencke, Thorsten Steinberg, Hartmut Dickhaus, Pascal Tomakidi, Niels Grabe
BMC Bioinformatics 2008, 9:473 (6November2008)
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Research article
Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data
Tao Xu, LinFang Du, Yan Zhou
BMC Bioinformatics 2008, 9:472 (6November2008)
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Research article
Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes
Inna Myslyuk, Tirza Doniger, Yair Horesh, Avraham Hury, Ran Hoffer, Yaara Ziporen, Shulamit Michaeli, Ron Unger
BMC Bioinformatics 2008, 9:471 (5November2008)
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Software
MetaFIND: A feature analysis tool for metabolomics data
Kenneth Bryan, Lorraine Brennan, P draig Cunningham
BMC Bioinformatics 2008, 9:470 (5November2008)
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Methodology article
Gene set analyses for interpreting microarray experiments on prokaryotic organisms
Nathan L Tintle, Aaron A Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron, Steffen Porwollik, Ronald C Taylor
BMC Bioinformatics 2008, 9:469 (5November2008)
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Methodology article
A relation based measure of semantic similarity for Gene Ontology annotations
Brendan Sheehan, Aaron Quigley, Benoit Gaudin, Simon Dobson
BMC Bioinformatics 2008, 9:468 (4November2008)
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Research article
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
Weijun Luo, Kurt D Hankenson, Peter J Woolf
BMC Bioinformatics 2008, 9:467 (3November2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central] [1 comment]
Research article
Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats
Vladimir Paar, Nenad Pavin, Ivan Basar, Marija Rosandi , Matko Glun i, Nils Paar
BMC Bioinformatics 2008, 9:466 (3November2008)
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Software
QuantPrime a flexible tool for reliable high-throughput primer design for quantitative PCR
Samuel Arvidsson, Miroslaw Kwasniewski, Diego Mauricio Ria o-Pachn, Bernd Mueller-Roeber
BMC Bioinformatics 2008, 9:465 (1November2008)
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Neutral network sizes of biological RNA molecules can be computed and are not atypically small
Thomas Jrg, Olivier C Martin, Andreas Wagner
BMC Bioinformatics 2008, 9:464 (30October2008)
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Information-based methods for predicting gene function from systematic gene knock-downs
Matthew T Weirauch, Christopher K Wong, Alexandra B Byrne, Joshua M Stuart
BMC Bioinformatics 2008, 9:463 (29October2008)
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Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer
Raffaele Giancarlo, Davide Scaturro, Filippo Utro
BMC Bioinformatics 2008, 9:462 (29October2008)
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Patrick E Meyer, Frdric Lafitte, Gianluca Bontempi
BMC Bioinformatics 2008, 9:461 (29October2008)
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A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics
Sabine Prs, Laurence Molina, Nicolas Salvetat, Claude Granier, Franck Molina
BMC Bioinformatics 2008, 9:460 (28October2008)
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