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SitesIdentify: a protein functional site prediction toolEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at www.manchester.ac.uk/bioinformatics/sitesidentify/ (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 18, 2009 Category: Bioinformatics Authors: Tracey BrayPedro ChanSalim BougouffaRichard GreavesAndrew DoigJim Warwicker Source Type: journals

The ontology of biological sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 18, 2009 Category: Bioinformatics Authors: Robert HoehndorfJanet KelsoHeinrich Herre Source Type: journals

Nonlinear preprocessing method for detecting peaks from gas chromatogramsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results demonstrate that the proposed method can achieve near perfect peak detection performance while maintaining very small false alarm probabilities in case of gas chromatograms. Given the fact that biological signals appear in the form of peaks in various experimental data and that the propose method can easily be extended to such data, our approach will be a useful and robust tool that can help researchers highlight valid signals in their noisy measurements. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 18, 2009 Category: Bioinformatics Authors: Byonghyo ShimHyeyoung MinSungroh Yoon Source Type: journals

Algorithms for effective querying of compound graph-based pathway databasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The PATIKA Project Web site is http://www.patika.org.PATIKAweb version 2.1 is available at http://web.patika.org. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 16, 2009 Category: Bioinformatics Authors: Ugur DogrusozAhmet CetintasEmek DemirOzgun Babur Source Type: journals

Linguistic feature analysis for protein interaction extractionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our findings suggest that grammatical relations play an important role in the interaction extraction task. Moreover, the net advantage of adding lexical and shallow syntactic features is small related to the number of added features. This implies that efficient classifiers can be built by using only a small fraction of the features that are typically being used in recent approaches. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 12, 2009 Category: Bioinformatics Authors: Timur FayruzovMartine De CockChris CornelisVeronique Hoste Source Type: journals

An empirical Bayesian approach for model-based inference of cellular signaling networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: In summary, an empirical Bayesian approach was developed for inferring the confidence that one can place in a particular model that describes signal transduction mechanisms and for inferring inconsistencies in experimental measurements. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 9, 2009 Category: Bioinformatics Authors: David Klinke Source Type: journals

RNA folding on the 3D triangular latticeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Folding simulation on the 3D triangular lattice is effective method for RNA secondary structure prediction and lattice conformation reconstruction. The visualization software for the lattice conformations of RNA structures is a valuable tool for the study of RNA folding and is a great pedagogic device. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 5, 2009 Category: Bioinformatics Authors: Joel GillespieMartin MayneMinghui Jiang Source Type: journals

A biosegmentation benchmark for evaluation of bioimage analysis methodsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This online benchmark will facilitate integration and comparison of image analysis methods for bioimages. While the primary focus is on biological images, we believe that the dataset and infrastructure will be of interest to researchers and developers working with biological image analysis, image segmentation and object tracking in general. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - November 1, 2009 Category: Bioinformatics Authors: Elisa Drelie GelascaBoguslaw ObaraDmitry FedorovKristian KvilekvalB. Manjunath Source Type: journals

Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methodsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have developed an hybrid scheme in which energy terms are used as input features of machine learning models. This strategy combines the strengths of machine learning and energy-based methods. Although so far these two types of approaches have mainly been applied separately to biomolecular problems, the results of our investigation indicate that there are substantial benefits to be gained by their integration. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 30, 2009 Category: Bioinformatics Authors: Stefano LiseCedric ArchambeauMassimiliano PontilDavid Jones Source Type: journals

multiplierz: an extensible API based desktop environment for proteomics data analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 29, 2009 Category: Bioinformatics Authors: Jignesh ParikhManor AskenaziScott FicarroTanya CashoraliJames WebberNathaniel BlankYi ZhangJarrod Marto Source Type: journals

A novel R-package graphic user interface for the analysis of metabonomic profilesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We made complex multivariate analysis user-friendly for both experienced and novice users, which could help to expand the use of NMR-based metabonomics. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 29, 2009 Category: Bioinformatics Authors: Jose Izquierdo-GarciaIgnacio RodriguezAngelos KyriazisPalmira VillaPilar BarreiroManuel DescoJesus Ruiz-Cabello Source Type: journals

Inferring within-patient HIV-1 evolutionary dynamics under anti-HIV therapy using serial virus samples with vSPAEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Given that many new anti-HIV drugs will be available in the near future, vSPA may be useful for quickly providing information on the acquisition of HIV drug-resistant mutations by monitoring the within-patient HIV evolution under anti-HIV therapy as a computational approach. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 29, 2009 Category: Bioinformatics Authors: Naoki HasegawaWataru SugiuraJunko ShibataMasakazu MatsudaFengrong RenHiroshi Tanaka Source Type: journals

BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Barcrawl and bartab can benefit researchers who are engaged in metagenomic projects that employ multiplexed specimen processing. The source code is released under the GNU general public license and can be accessed at http://www.phyloware.com. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 29, 2009 Category: Bioinformatics Authors: Daniel Frank Source Type: journals

Analysis and comparison of very large metagenomes with fast clustering and functional annotationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: RAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from http://tools.camera.calit2.net/camera/rammcap/. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 28, 2009 Category: Bioinformatics Authors: Weizhong Li Source Type: journals

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalizationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 28, 2009 Category: Bioinformatics Authors: Enrico GlaabJonathan GaribaldiNatalio Krasnogor Source Type: journals

phyloXML: XML for evolutionary biology and comparative genomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at http://www.phyloxml.org. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 27, 2009 Category: Bioinformatics Authors: Mira HanChristian Zmasek Source Type: journals

Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLABEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Gene ARMADA provides a highly adaptable, integrative, yet flexible tool, which can be used for automated quality control, analysis, annotation and visualization of microarray data constituting a starting point for further data interpretation and integration with numerous other tools. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 27, 2009 Category: Bioinformatics Authors: Aristotelis ChatziioannouPanagiotis MoulosFragiskos Kolisis Source Type: journals

Bayesian modeling of ChIP-chip data using latent variablesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The Bayesian latent method is successfully applied to real andten simulated datasets, with comparisons with some of the existing Bayesian methods, hidden Markov model methods, and sliding window methods. The numerical results indicate that the Bayesian latent method can outperform other methods, especially when the data contain outliers. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 26, 2009 Category: Bioinformatics Authors: Mingqi WuFaming LiangYanan Tian Source Type: journals

Time warping of evolutionary distant temporal gene expression data based on noise suppressionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our alignment-based predictions of differences in the cell cycle phases between the two yeast species were in a good agreement with the existing data, thus supporting the computational strategy adopted in this study. We propose that the existence of the alternative alignments, specific to distinct groups of genes, suggests presence of different synchronization modes between the two organisms and possible functional decoupling of particular physiological gene networks in the course of evolution. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 26, 2009 Category: Bioinformatics Authors: Yury GoltsevDmitri Papatsenko Source Type: journals

A structure filter for the Eukaryotic Linear Motif ResourceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: New occurrences of known linear motifs require experimental validation as the bioinformatics tools currently have limited reliability. The ELM structure filter will aid users assessing candidate motifs presenting in globular structural regions. Most importantly, it will help users to decide whether to expend their valuable time and resources on experimental testing of interesting motif candidates. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 23, 2009 Category: Bioinformatics Authors: Allegra ViaCathryn GouldChristine GemundToby GibsonManuela Helmer-Citterich Source Type: journals

Direct calibration of PICKY-designed microarraysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 22, 2009 Category: Bioinformatics Authors: Hui-Hsien ChouArunee TrisirirojSunyoung ParkYue-Ie HsingPamela RonaldPatrick Schnable Source Type: journals

Arabidopsis gene co-expression network and its functional modulesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study reveals new insight into the topological properties of biological networks. The preferential hub-hub connections might be necessary for the formation of modular structure in gene co-expression networks. The study also reveals new insight into the organization of gene functional modules. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 20, 2009 Category: Bioinformatics Authors: Linyong MaoJohn Van HemertSudhansu DashJulie Dickerson Source Type: journals

iQuantitator: A tool for protein expression inference using iTRAQEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: iQuantitator's process-based modeling approach overcomes limitations in current methods and allows for application in a variety of experimental designs. Additionally, hypertext-linked documents produced by the tool aid in the interpretation and exploration of results. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 17, 2009 Category: Bioinformatics Authors: John SchwackeElizabeth HillEdward KrugSusana Comte-WaltersKevin Schey Source Type: journals

Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Many different protein structure prediction methods exist and each uses different tools and auxiliary predictions to help determine the native structure. In this work the sequence is used to predict local context dependent dihedral angle propensities in coil-regions. This predicted distribution can potentially improve tertiary structure prediction methods that are based on sampling the backbone dihedral angles of individual amino acids. The predicted distribution may also help predict local structure fragments used in fragment assembly methods. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 15, 2009 Category: Bioinformatics Authors: Glennie HellesRasmus Fonseca Source Type: journals

A Permutation-Based Multiple Testing Method for Time-Course Microarray ExperimentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our method is computationally efficient and applicable for identifying genes whose expression levels are time-dependent in a single biological group and for identifying the genes for which the time-profile depends on the group in a multi-group setting. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 14, 2009 Category: Bioinformatics Authors: Insuk SohnKouros OwzarStephen GeorgeSujong KimSin-Ho Jung Source Type: journals

Classification and biomarker identification using gene network modules and support vector machinesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: More than 90% accuracy can be obtained in classification of selected microarray datasets by integrating the interaction network information with the gene expression information from the microarrays.AvailabilityThe Matlab version of SVM-RCE can be downloaded from http://web.macam.ac.il/~myousef (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 14, 2009 Category: Bioinformatics Authors: Malik YousefMohamed KetanyLarry ManevitzLouise ShoweMichael Showe Source Type: journals

Magallanes: a web services discovery and automatic workflow composition toolEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Different implementations of the same client (web-based, desktop applications, etc.) have been deployed and are currently in use in real installations such as the National Institute of Bioinformatics, Spain and ACGT-EU project, showing the potential utility and versatility of the software library, including the integration of novel tools in the domain and with strong evidences in the line of facilitate the automatic discovering and composition of workflows. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 14, 2009 Category: Bioinformatics Authors: Javier RiosJohan KarlssonOswaldo Trelles Source Type: journals

StarNet 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: StarNet 2 is a useful tool for developing new hypotheses about regulatory relationships between genes and gene products, and has coverage for 10 species. Interpretation of the correlation networks is supported with a database of previously documented interactions, a test for enrichment of Gene Ontology terms, and heat maps of correlation distances that may be used to compare two networks. The list of genes in a StarNet network may be useful in developing a list of candidate genes to use for the inference of causal networks. The tool is freely available at http://vanburenlab.medicine.tamhsc.edu/starnet2.html, a...
Source: BMC Bioinformatics - Latest articles - October 13, 2009 Category: Bioinformatics Authors: Daniel JupiterHailin ChenVincent VanBuren Source Type: journals

Phylogenetic analysis of modularity in protein interaction networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These results establish modularity and network proximity as useful features in comparative network analysis and motivate detailed studies of the evolutionary histories of network modules. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 13, 2009 Category: Bioinformatics Authors: Sinan ErtenXin LiGurkan BebekJing LiMehmet Koyuturk Source Type: journals

ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discoveryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The ConservedPrimers 2.0 pipeline for designing intron-flanking primers was developed and its utility demonstrated. The tool can be used for SNP discovery, genetic variation assays and marker development for any target genome that has abundant ESTs and a related reference genome that has been fully sequenced. The ConservedPrimers 2.0 pipeline has been implemented as a command-line tool as well as a web application. Both versions are freely available at http://wheat.pw.usda.gov/demos/ConservedPrimers/. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 12, 2009 Category: Bioinformatics Authors: Frank YouNaxin HuoYong GuGerard LazoJan DvorakOlin Anderson Source Type: journals

BASE - 2nd generation software for microarray data management and analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 11, 2009 Category: Bioinformatics Authors: Johan Vallon-ChristerssonNicklas NordborgMartin SvenssonJari Hakkinen Source Type: journals

VANLO - Interactive visual exploration of aligned biological networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our system provides an intuitive global understanding of aligned PPI networks and it allows theinvestigation of key biological questions. We evaluate our system by applying it to real-world examplesdocumenting how our system can be used to investigate the data with respect to these key questions. Our toolVANLO (Visualization of Aligned Networks with Layout Optimization) can be accessed athttp://www.math-inf.uni-greifswald.de/VANLO. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 11, 2009 Category: Bioinformatics Authors: Steffen BraschLars LinsenGeorg Fuellen Source Type: journals

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expressionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 11, 2009 Category: Bioinformatics Authors: Wei-Chi WangFeng-Mao LinWen-Chi ChangKuan-Yu LinHsien-Da HuangNa-Sheng Lin Source Type: journals

PLAST: parallel local alignment search tool for database comparisonEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A parallel algorithmic approach driven by the knowledge of the internal microprocessor architecture allows significant speedup to be obtained while preserving standard sensitivity for similarity search problems. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 11, 2009 Category: Bioinformatics Authors: Van Hoa NguyenDominique Lavenier Source Type: journals

A stochastic context free grammar based framework for analysis of protein sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A new Stochastic Context Free Grammar based framework has been introduced allowing the detection of binding site patterns in protein sequences. Experiments have shown that not only is this new approach valid, but has the potential to produce human-readable descriptors for binding sites which have been beyond the capability of current machine learning techniques. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 7, 2009 Category: Bioinformatics Authors: Witold DyrkaJean-Christophe Nebel Source Type: journals

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: KEGGconverter is capable of producing integrated analogues of metabolic pathways appropriate for simulation tasks, by inputting only KGML files. The web application acts as a user friendly shell which transparently enables the automated biochemically correct pathway merging, conversion to SBML format, proper renaming of the species, and insertion of default kinetic properties for the pertaining reactions. The tool is available at: http://www.grissom.gr/keggconverter (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 7, 2009 Category: Bioinformatics Authors: Konstantinos MoutselosIoannis KanarisAristotelis ChatziioannouIlias MaglogiannisFragiskos Kolisis Source Type: journals

Riboswitch detection using profile Hidden Markov ModelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Riboswitches play a crucial role in controlling the expression of several prokaryotic genes involved in metabolism and transport processes. As more and more new classes of riboswitches are being discovered, it is important to understand the patterns of their intra and inter genomic distribution. Understanding such patterns will enable us to better understand the evolutionary history of these genetic regulatory elements. However, a complete picture of the distribution pattern of riboswitches will emerge only after accurate identification of riboswitches across genomes. We believe that the riboswitch detection m...
Source: BMC Bioinformatics - Latest articles - October 7, 2009 Category: Bioinformatics Authors: Payal SinghPradipta BandyopadhyaySudha BhattacharyaA KrishnamachariSupratim Sengupta Source Type: journals

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This text-mining project is unique in its integration of existing tools into a single workflow with direct application to CTD. We performed a baseline assessment of the inter-curator consistency and coverage in CTD, which allowed us to measure the potential of these integrated tools to improve prioritization of journal articles for manual curation. Our study presents a feasible and cost-effective approach for developing a text mining solution to enhance manual curation throughput and efficiency. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 7, 2009 Category: Bioinformatics Authors: Thomas WiegersAllan DavisK. CohenLynette HirschmanCarolyn Mattingly Source Type: journals

Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: DEPNs offer a robust, efficient and simple approach to infer protein signaling networks from multiple interventions. The method as well as the data have been made part of the latest version of the R package "nem" available as a supplement to this paper and via the Bioconductor repository. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 7, 2009 Category: Bioinformatics Authors: Holger FroehlichOezguer SahinDorit ArltChristian BenderTim Beissbarth Source Type: journals

Generation of Gene Ontology benchmark datasets with various types of positive signalEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present the use of the effective number and various normalizations while embedding the signal to a selected class or classes and the use of binary correlation to ensure that the selected signal classes are independent with each other. The usefulness of generated datasets is demonstrated by comparing different GO class ranking and GO clustering methods.DiscussionThe presented methods aid the development and evaluation of GO analysis methods as they enable thorough testing with different signal types and different signal levels. As an example, our comparisons reveal clear differences between compared GO clustering and GO ...
Source: BMC Bioinformatics - Latest articles - October 6, 2009 Category: Bioinformatics Authors: Petri ToronenPetri PehkonenLiisa Holm Source Type: journals

BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literatureEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These experiments suggest the feasibility of our approach for automatically discovering and indexing current and future bioinformatics resources. Given the domain-independent characteristics of this tool, it is currently being applied by the authors in other areas, such as medical nanoinformatics. BIRI is available at http://edelman.dia.fi.upm.es/biri/. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 6, 2009 Category: Bioinformatics Authors: Guillermo de la CalleMiguel Garcia-RemesalStefano ChiesaDiana de la IglesiaVictor Maojo Source Type: journals

Unsupervised statistical clustering of environmental shotgun sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: An unsupervised binning method based on statistical signatures of short environmental sequences is a viable stand-alone binning method for low complexity samples. For medium and high complexity samples, we discuss the possibility of combining the current method with other methods as part of an iterative process to enhance the resolving power of sorting reads into taxonomic and/or functional bins. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 1, 2009 Category: Bioinformatics Authors: Andrey KislyukSrijak BhatnagarJonathan DushoffJoshua Weitz Source Type: journals

Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We concluded that penalized canonical correlation analysis is a powerful tool to identify candidate genes in pathway analysis. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - September 27, 2009 Category: Bioinformatics Authors: Sandra WaaijenborgAeilko Zwinderman Source Type: journals

MetaTM - A consensus method for transmembrane protein topology predictionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Combining several TM predictors in a consensus prediction framework improves overall accuracy compared to any of the individual methods. Our proposed SVM-based system also has higher accuracy than a previous consensus predictor. MetaTM is made available both as downloadable source code and as a DAS server at http://MetaTM.sbc.su.se (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - September 27, 2009 Category: Bioinformatics Authors: Martin KlammerDavid MessinaThomas SchmittErik Sonnhammer Source Type: journals

Challenges for automatically extracting molecular interactions from full-text articlesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We introduce the MIM corpus, a unique resource that maps interaction facts in a MIM to annotated passages within full-text articles. It is an invaluable case study providing guidance to developers of biomedical IR and IE systems, and can be used as a gold-standard evaluation set for full-text IR tasks. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - September 23, 2009 Category: Bioinformatics Authors: Tara McIntoshJames Curran Source Type: journals

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring functionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: GSZ and improved versions of earlier methods are a useful contribution to the analysis of differential gene expression. The methods and supplementary material are available from the website (http://ekhidna.biocenter.helsinki.fi/users/petri/public/GSZ/GSZscore.html). (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - September 22, 2009 Category: Bioinformatics Authors: Petri ToronenPauli OjalaPekka MarttinenLiisa Holm Source Type: journals

Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriouslyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These methods represent a qualitative advance in the location of recurrent CNA regions, highlight the relevance of population heterogeneity for definitions of recurrence, and can facilitate the clustering of samples with respect to patterns of CNA. Ultimately, the methods developed can become important tools in the search for genomic regions harboring disease-critical genes. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - September 22, 2009 Category: Bioinformatics Authors: Oscar RuedaRamon Diaz-Uriarte Source Type: journals

Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We conclude that 2D LC MALDI-MS/MS is a powerful, rapid and economical tool to aid in the annotation of fungal genomic assemblies. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - September 21, 2009 Category: Bioinformatics Authors: Scott BringansJames HaneTammy CaseyKar-Chun TanRichard LipscombePeter SolomonRichard Oliver Source Type: journals