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In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: In their article entitled ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’ de Figueiredo and co-authors assess the performance of three pathway prediction tools (METATOOL, PathFinding and Pathway Hunter Tool) using the synthesis of glucose-6-phosphate (G6P) from acetyl-CoA in humans as a test case. We think that this article is biased for three reasons: (i) the metabolic networks used as input for the respective tools were of very different sizes; (ii) the ‘assessment’ is restricted to two study cases; (iii) developers are inherently more skilled to use t...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Faust, K., Croes, D., van Helden, J. Tags: SYSTEMS BIOLOGY Source Type: journals

ncRNAppi--a tool for identifying disease-related miRNA and siRNA targeting pathwaysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Currently, there are a number of databases which store microRNA (miRNA) information, and tools available which provide miRNA target prediction. In this article, we describe a novel web-based tool that integrate the miRNA-targeted mRNA data, protein–protein interactions (PPI) records, tissues, biochemical pathways, human disease and gene function information to establish a disease-related miRNA target pathway database. This database is unique in the sense that it links miRNA target genes with their PPI partners according to being tissue- and diseases-specific or both. The same approach is also applied to siRN...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Ng, K.-L., Liu, H.-C., Lee, S.-C. Tags: DATABASES AND ONTOLOGIES Source Type: journals

SimCT: a generic tool to visualize ontology-based relationships for biological objectsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant features. Unlike the numerous tools that search for overrepresented terms, SimCT draws a simplified representation of biological terms present in the set of objects, and can be applied to any ontology for which annotation data is available. Being web-based, it does not require prior i...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Herrmann, C., Berard, S., Tichit, L. Tags: DATABASES AND ONTOLOGIES Source Type: journals

Client-side integration of life science literature resourcesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The online resources in the life sciences are characterized by a great fragmentation and one of the pressing issues of bioinformatics is making the integration of these resources a smoother and more flexible process than it is currently. Here we present i-cite, a browser extension, which implements a client-side model of integration which improves the navigation within the rapidly increasing life science literature and links terms from it to corresponding non-textual data. Availability: http://i-cite.org. Contact: nan23@cam.ac.uk (Source: Bioinformatics)
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Easty, R., Nikolov, N. Tags: DATABASES AND ONTOLOGIES Source Type: journals

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: W-ChIPMotifs is a web application tool that provides a user friendly interface for de novo motif discovery. The web tool is based on our previous ChIPMotifs program which is a de novo motif finding tool developed for ChIP-based high-throughput data and incorporated various ab initio motif discovery tools such as MEME, MaMF, Weeder and optimized the significance of the detected motifs by using a bootstrap resampling statistic method and a Fisher test. Use of a randomized statistical model like bootstrap resampling can significantly increase the accuracy of the detected motifs. In our web tool, we have modified the ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Jin, V. X., Apostolos, J., Nagisetty, N. S. V. R., Farnham, P. J. Tags: SYSTEMS BIOLOGY Source Type: journals

Processing and population genetic analysis of multigenic datasets with ProSeq3 softwareEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The current tendency in molecular population genetics is to use increasing numbers of genes in the analysis. Here I describe a program for handling and population genetic analysis of DNA polymorphism data collected from multiple genes. The program includes a sequence/alignment editor and an internal relational database that simplify the preparation and manipulation of multigenic DNA polymorphism datasets. The most commonly used DNA polymorphism analyses are implemented in ProSeq3, facilitating population genetic analysis of large multigenic datasets. Extensive input/output options make ProSeq3 a convenient hub ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Filatov, D. A. Tags: GENETICS AND POPULATION ANALYSIS Source Type: journals

VDNA: The virtual DNA plug-in for VMDEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: The DNA inter base pair step parameters (Tilt, Roll, Twist, Shift, Slide, Rise) are a standard internal coordinate representation of DNA. In the absence of bend and shear, it is relatively easy to mentally visualize how Twist and Rise generate the familiar double helix. More complex structures do not readily yield to such intuition. For this reason, we developed a plug-in for VMD that accepts a set of mathematical expressions as input and generates a coarse-grained model of DNA as output. This feature of VDNA appears to provide a unique approach to DNA modeling. Predefined expressions include: linear, sheared, ben...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Bishop, T. C. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: SiteHound uses Molecular Interaction Fields (MIFs) produced by EasyMIFs to identify protein structure regions that show a high propensity for interaction with ligands. The type of binding site identified depends on the probe atom used in the MIF calculation. The input to EasyMIFs is a PDB file of a protein structure; the output MIF serves as input to SiteHound, which in turn produces a list of putative binding sites. Extensive testing of SiteHound for the detection of binding sites for drug-like molecules and phosphorylated ligands has been carried out. Availability: EasyMIFs and SiteHound executables for Linux, M...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Ghersi, D., Sanchez, R. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: The increasing number of available atomic 3D structures of transmembrane channel proteins represents a valuable resource for better understanding their structure–function relationships and to eventually predict their selectivity. Herein, we present PoreLogo, an automatic tool for analysing, visualizing and comparing the amino acid composition of transmembrane channels and its conservation across the corresponding protein family. Availability: PoreLogo is accessible as a public web server at http://www.ebi.ac.uk/thornton-srv/software/PoreLogo/. Contacts: marial@ebi.ac.uk; romina.oliva@uniparthenope.it. (Source: Bioinformatics)
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Oliva, R., Thornton, J. M., Pellegrini-Calace, M. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

MOODS: fast search for position weight matrix matches in DNA sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library. Availability: The package with documentation and examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The source co...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Korhonen, J., Martinmaki, P., Pizzi, C., Rastas, P., Ukkonen, E. Tags: SEQUENCE ANALYSIS Source Type: journals

Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and DiscussionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Discussion (IMRAD). Classifying sentences into these categories can benefit many other text-mining tasks. Although many studies have applied different approaches for automatically classifying sentences in MEDLINE abstracts into the IMRAD categories, few have explored the classification of sentences that appear in full-text biomedical articles. We first evaluated whether sentences in full-text biomedical articles could be reliably annotated into the IMRAD format and then explored different approaches for automatically classifying these sentences into the IMRAD categories. Our results show an overall annotation agreement of ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Agarwal, S., Yu, H. Tags: DATA AND TEXT MINING Source Type: journals

Functionally guided alignment of protein interaction networks for module detectionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Functional module detection within protein interaction networks is a challenging problem due to the sparsity of data and presence of errors. Computational techniques for this task range from purely graph theoretical approaches involving single networks to alignment of multiple networks from several species. Current network alignment methods all rely on protein sequence similarity to map proteins across species. Results: Here we carry out network alignment using a protein functional similarity measure. We show that using functional similarity to map proteins across species improves network alignment in terms of ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Ali, W., Deane, C. M. Tags: SYSTEMS BIOLOGY Source Type: journals

Computing the shortest elementary flux modes in genome-scale metabolic networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity. Results: In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic net...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: de Figueiredo, L. F., Podhorski, A., Rubio, A., Kaleta, C., Beasley, J. E., Schuster, S., Planes, F. J. Tags: SYSTEMS BIOLOGY Source Type: journals

Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, a systematic method is proposed for identifying metabolic biomarkers in urine samples by selecting candidate biomarkers from altered genome-wide gene expression signatures of cancer cells. Biomarkers identified by the present study have increased coherence and robustness because the significances of biomarkers are validated in both gene expression profiles and metabolic profiles. Results: The proposed method was applied to the gene expression profiles and urine samples of 50 breast cancer patients and 50 normal persons. Nine altered metabolic pathways were identified from the breast cancer gene expression si...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Nam, H., Chung, B. C., Kim, Y., Lee, K., Lee, D. Tags: SYSTEMS BIOLOGY Source Type: journals

How and when should interactome-derived clusters be used to predict functional modules and protein function?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Clustering of protein–protein interaction networks is one of the most common approaches for predicting functional modules, protein complexes and protein functions. But, how well does clustering perform at these tasks? Results: We develop a general framework to assess how well computationally derived clusters in physical interactomes overlap functional modules derived via the Gene Ontology (GO). Using this framework, we evaluate six diverse network clustering algorithms using Saccharomyces cerevisiae and show that (i) the performances of these algorithms can differ substantially when run on the same networ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Song, J., Singh, M. Tags: SYSTEMS BIOLOGY Source Type: journals

Automatic assignment of reaction operators to enzymatic reactionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The analysis and comparison of enzymatic reactions according to their electron shift patterns is defining enzyme groups characterised by unique reaction cores. Our results demonstrate the applicability of the Dugundji–Ugi model as a reasonable pre-classification system allowing an objective and rational view on biochemical reactions. Availability: The program to generate reaction matrix descriptors is available upon request. Contact: d.schomburg@tu-bs.de (Source: Bioinformatics)
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Leber, M., Egelhofer, V., Schomburg, I., Schomburg, D. Tags: SYSTEMS BIOLOGY Source Type: journals

Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experimentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The goal of present -omics sciences is to understand biological systems as a whole in terms of interactions of the individual cellular components. One of the main building blocks in this field of study is proteomics where tandem mass spectrometry (LC-MS/MS) in combination with isotopic labelling techniques provides a common way to obtain a direct insight into regulation at the protein level. Methods to identify and quantify the peptides contained in a sample are well established, and their output usually results in lists of identified proteins and calculated relative abundance values. The next step is to move a...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Albaum, S. P., Neuweger, H., Franzel, B., Lange, S., Mertens, D., Trotschel, C., Wolters, D., Kalinowski, J., Nattkemper, T. W., Goesmann, A. Tags: GENE EXPRESSION Source Type: journals

Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistanceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project (DGAP) was launched to profile gene expression in a variety of related animal models and human subjects. We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance. Results: We perform integrative analysis of the 16 DGAP data sets that span multiple tissues, conditions, array types, laboratories, species, genetic b...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Park, P. J., Kong, S. W., Tebaldi, T., Lai, W. R., Kasif, S., Kohane, I. S. Tags: GENE EXPRESSION Source Type: journals

Bayesian detection of non-sinusoidal periodic patterns in circadian expression dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present an analysis of variance (ANOVA) periodicity detector and its Bayesian extension that can be used to discover periodic transcripts of arbitrary shapes from replicated gene expression profiles. The models are applicable when the profiles are collected at comparable time points for at least two cycles. We provide an empirical Bayes procedure for estimating parameters of the prior distributions and derive closed-form expressions for the posterior probability of periodicity, enabling efficient computation. The model is applied to two datasets profiling circadian regulation in murine liver and skeletal muscle, reveali...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Chudova, D., Ihler, A., Lin, K. K., Andersen, B., Smyth, P. Tags: GENE EXPRESSION Source Type: journals

The interwinding nature of protein-protein interfaces and its implication for protein complex formationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Structural features at protein–protein interfaces can be studied to understand protein–protein interactions. It was noticed that in a dataset of 45 multimeric proteins the interface could either be described as flat against flat or protruding/interwound. In the latter, residues within one chain were surrounded by those in other chains, whereas in the former they were not. Results: A simple method was developed that could distinguish between these two types with results that matched those made by a human annotator. Applying this automatic method to a large dataset of 888 structures, chains at interfa...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Yura, K., Hayward, S. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue predictionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Identifying residues that interact with ligands is useful as a first step to understanding protein function and as an aid to designing small molecules that target the protein for interaction. Several studies have shown that sequence features are very informative for this type of prediction, while structure features have also been useful when structure is available. We develop a sequence-based method, called LIBRUS, that combines homology-based transfer and direct prediction using machine learning and compare it to previous sequence-based work and current structure-based methods. Results: Our analysis shows that...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Kauffman, C., Karypis, G. Tags: STRUCTURAL BIOINFORMATICS Source Type: journals

Reproducing the manual annotation of multiple sequence alignments using a SVM classifierEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present here an automated editing method based on the classification of ‘valid’ and ‘invalid’ sites. Results: A support vector machine (SVM) classifier is trained to reproduce the decisions made during manual editing with an accuracy of 95.0%. This implies that manual editing can be made reproducible and applied to large-scale analyses. We further demonstrate that it is possible to retrain/extend the training of the classifier by providing examples of multiple sequence alignment (MSA) annotation. Near optimal training can be achieved with only 1000 annotated sites, or roughly three samples of pro...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Blouin, C., Perry, S., Lavell, A., Susko, E., Roger, A. J. Tags: PHYLOGENETICS Source Type: journals

Adaptive multi-agent architecture for functional sequence motifs recognitionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Accurate genome annotation or protein function prediction requires precise recognition of functional sequence motifs. Many computational motif prediction models have been proposed. Due to the complexity of the biological data, it may be desirable to apply an integrated approach that uses multiple models for analysis. Results: In this article, we propose a novel multi-agent architecture for the general purpose of functional sequence motif recognition. The approach takes advantage of the synergy provided by multiple agents through the employment of different agents equipped with distinctive problem solving skills...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Zeng, J., Alhajj, R., Demetrick, D. Tags: SEQUENCE ANALYSIS Source Type: journals

Detection of new protein domains using co-occurrence: application to Plasmodium falciparumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Hidden Markov models (HMMs) have proved to be a powerful tool for protein domain identification in newly sequenced organisms. However, numerous domains may be missed in highly divergent proteins. This is the case for Plasmodium falciparum proteins, the main causal agent of human malaria. Results: We propose a method to improve the sensitivity of HMM domain detection by exploiting the tendency of the domains to appear preferentially with a few other favorite domains in a protein. When sequence information alone is not sufficient to warrant the presence of a particular domain, our method enables its detection on ...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Terrapon, N., Gascuel, O., Marechal, E., Breehelin, L. Tags: SEQUENCE ANALYSIS Source Type: journals

HHsvm: fast and accurate classification of profile-profile matches identified by HHsearchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Recently developed profile–profile methods rival structural comparisons in their ability to detect homology between distantly related proteins. Despite this tremendous progress, many genuine relationships between protein families cannot be recognized as comparisons of their profiles result in scores that are statistically insignificant. Results: Using known evolutionary relationships among protein superfamilies in SCOP database, support vector machines were trained on four sets of discriminatory features derived from the output of HHsearch. Upon validation, it was shown that the automatic classification o...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Dlakic, M. Tags: SEQUENCE ANALYSIS Source Type: journals

Genome analysis with inter-nucleotide distancesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objective of this work was to find a mapping scheme directly related to DNA characteristics and that would be useful in discriminating between different species. Mathematical models to explore DNA correlation structures may contribute to a better knowledge of the DNA and to find a concise DNA description. Results: We developed a methodology to process DNA sequences based on inter-nucleotide distances. Our main contribution is a method to obtain genomic signatures for complete genomes, based on the inter-nucleotide distances, that are able to discriminate between different species. Using these signatures and hierarchica...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Afreixo, V., Bastos, C. A. C., Pinho, A. J., Garcia, S. P., Ferreira, P. J. S. G. Tags: SEQUENCE ANALYSIS Source Type: journals

Quantitative measurement of aging using image texture entropyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: A key element in understanding the aging of Caenorhabditis elegans is objective quantification of the morphological differences between younger and older animals. Here we propose to use the image texture entropy as an objective measurement that reflects the structural deterioration of the C.elegans muscle tissues during aging. Results: The texture entropy and directionality of the muscle microscopy images were measured using 50 animals on Days 0, 2, 4, 6, 8, 10 and 12 of adulthood. Results show that the entropy of the C.elegans pharynx tissues increases as the animal ages, but a sharper increase was measured be...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Shamir, L., Wolkow, C. A., Goldberg, I. G. Tags: DATA AND TEXT MINING Source Type: journals

Identifiability of isoform deconvolution from junction arrays and RNA-SeqEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Splice junction microarrays and RNA-seq are two popular ways of quantifying splice variants within a cell. Unfortunately, isoform expressions cannot always be determined from the expressions of individual exons and splice junctions. While this issue has been noted before, the extent of the problem on various platforms has not yet been explored, nor have potential remedies been presented. Results: We propose criteria that will guarantee identifiability of an isoform deconvolution model on exon and splice junction arrays and in RNA-Seq. We show that up to 97% of 2256 alternatively spliced human genes selected fro...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Hiller, D., Jiang, H., Xu, W., Wong, W. H. Tags: GENE EXPRESSION Source Type: journals

Lost in translation: an assessment and perspective for computational microRNA target identificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs (miRNAs) are a class of short endogenously expressed RNA molecules that regulate gene expression by binding directly to the messenger RNA of protein coding genes. They have been found to confer a novel layer of genetic regulation in a wide range of biological processes. Computational miRNA target prediction remains one of the key means used to decipher the role of miRNAs in development and disease. Here we introduce the basic idea behind the experimental identification of miRNA targets and present some of the most widely used computational miRNA target identification programs. The review includes an assessment of...
Source: Bioinformatics - November 17, 2009 Category: Bioinformatics Authors: Alexiou, P., Maragkakis, M., Papadopoulos, G. L., Reczko, M., Hatzigeorgiou, A. G. Tags: GENE EXPRESSION Source Type: journals

Rapid detection, classification and accurate alignment of up to a million or more related protein sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Bioinformatics)
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Neuwald, A. F. Tags: CORRIGENDUM Source Type: journals

QuickGO: a web-based tool for Gene Ontology searchingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. Availability and Implementation: QuickGO has implemented in JavaScript, Ajax and HTML, with all major browsers supported. It can be queried online at ht...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Binns, D., Dimmer, E., Huntley, R., Barrell, D., O'Donovan, C., Apweiler, R. Tags: DATABASES AND ONTOLOGIES Source Type: journals

Next generation software for functional trend analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with a new interface and several new features. For example, enrichment analysis can now be performed within multiple gene- and protein-naming systems. This feature avoids potentially serious translation artifacts to which other enrichment analysis strategies are subject. Availability: The FuncAssociate web application is freely available to all users at http://llama.med.harvard.edu/funcassociate. Contact: fritz_roth@hms.harvard.edu...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Berriz, G. F., Beaver, J. E., Cenik, C., Tasan, M., Roth, F. P. Tags: DATABASES AND ONTOLOGIES Source Type: journals

CMap 1.01: a comparative mapping application for the InternetEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary:CMap is a web-based tool for displaying and comparing maps of any type and from any species. A user can compare an unlimited number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession. CMap is freely available, can run on a variety of database engines and uses only free and open software components. Availability: http://www.gmod.org/cmap Contact: kclark@cshl.edu (Source: Bioinformatics)
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Youens-Clark, K., Faga, B., Yap, I. V., Stein, L., Ware, D. Tags: DATABASES AND ONTOLOGIES Source Type: journals

Identifying related journals through log analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data. Availability: http://www.ncbi.nlm.nih.gov/IRET/Journals Contact: luzh@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatic...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Lu, Z., Xie, N., Wilbur, W. J. Tags: DATA AND TEXT MINING Source Type: journals

UniMaP: finding unique mass and peptide signatures in the human proteomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a publicly available web application that offers information concerning the uniqueness of one or more molecular masses and one or more peptide sequences in the human proteome. When a sequence is found to be unique in humans, the application is able to search across all species querying whether this sequence is unique, not only in humans but also in other species found in the Swiss-Prot Database. The application is also able to search for unique protein fragments derived computationally from enzymatic digestion driven by certain enzymes. Furthermore, the application can list all the unique masses and peptides of ...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Alexandridou, A., Tsangaris, G. Th., Vougas, K., Nikita, K., Spyrou, G. Tags: DATA AND TEXT MINING Source Type: journals

digeR: a graphical user interface R package for analyzing 2D-DIGE dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We report on an R package, digeR, with an easy to use graphical user interface for analyzing 2D-DIGE (2D gel) data. It provides a tool for visually looking for potential PTM changes from different biological states and support biomarker discovery through multivariate analysis techniques. Availability: digeR package is freely available from the CRAN: http://cran.r-project.org/web/packages/digeR/index.html. Contact: yue.fan@ucd.ie Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Fan, Y., Murphy, T. B., Watson, R. W. G. Tags: DATA AND TEXT MINING Source Type: journals

PubMed-EX: a web browser extension to enhance PubMed search with text mining featuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources. Availability: PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/. Contact: thtsai@saturn.yzu.edu.tw Supplementary information: Supplementary data are available at Bioinform...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Tsai, R. T.-H., Dai, H.-J., Lai, P.-T., Huang, C.-H. Tags: DATA AND TEXT MINING Source Type: journals

CellClassifier: supervised learning of cellular phenotypesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary:CellClassifier is a tool for classifying single-cell phenotypes in microscope images. It includes several unique and user-friendly features for classification using multiclass support vector machines Availability: Source code, user manual and SaveObjectSegmentation CellProfiler module available for download at www.cellclassifier.ethz.ch under the GPL license (implemented in Matlab). Contact: pelkmans@imsb.biol.ethz.ch Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Ramo, P., Sacher, R., Snijder, B., Begemann, B., Pelkmans, L. Tags: SYSTEMS BIOLOGY Source Type: journals

Saint: a lightweight integration environment for model annotationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources. Availability and Implementation: Saint is freely available for use on the web at http://www.cisban.ac.uk/saint. The web application is implemented in Google Web Toolkit and Tomcat, with all major browsers supported. The Java source code is freely available for download at http://saint-annotate.sourceforge.net. The Saint web server requires an installation of libSBML and ...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Lister, A. L., Pocock, M., Taschuk, M., Wipat, A. Tags: SYSTEMS BIOLOGY Source Type: journals

Comparative analysis and unification of domain-domain interaction networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Certain protein domains are known to preferentially interact with other domains. Several approaches have been proposed to predict domain–domain interactions, and over nine datasets are available. Our aim is to analyse the coverage and quality of the existing resources, as well as the extent of their overlap. With this knowledge, we have the opportunity to merge individual domain interaction networks to construct a comprehensive and reliable database. Results: In this article we introduce a new approach towards comparing domain–domain interaction networks. This approach is used to compare nine predic...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Bjorkholm, P., Sonnhammer, E. L. L. Tags: DATABASES AND ONTOLOGIES Source Type: journals

A method for visualizing CellML modelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article presents a framework that combines a visual language, together with CellML ontologies, to support the visualization of the underlying physical and biological concepts described by the mathematical model and also their relationships with the CellML model. Automated CellML model visualization assists in the interpretation of model concepts and facilitates model communication and exchange between different communities. Contact: sarala.dissanayake@auckland.ac.nz Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Wimalaratne, S. M., Halstead, M. D. B., Lloyd, C. M., Cooling, M. T., Crampin, E. J., Nielsen, P. F. Tags: DATABASES AND ONTOLOGIES Source Type: journals

Mobyle: a new full web bioinformatics frameworkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally, given that scientific tools can be difficult to install, it is particularly helpful for biologists to be able to use these tools through a web user interface. However, providing a web interface for a set of tools raises the problem that a single web portal cannot offer all the existing and possible services...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Neron, B., Menager, H., Maufrais, C., Joly, N., Maupetit, J., Letort, S., Carrere, S., Tuffery, P., Letondal, C. Tags: DATABASES AND ONTOLOGIES Source Type: journals

Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The highly coordinated expression of thousands of genes in an organism is regulated by the concerted action of transcription factors, chromatin proteins and epigenetic mechanisms. High-throughput experimental data for genome wide in vivo protein–DNA interactions and epigenetic marks are becoming available from large projects, such as the model organism ENCyclopedia Of DNA Elements (modENCODE) and from individual labs. Dissemination and visualization of these datasets in an explorable form is an important challenge. Results: To support research on Drosophila melanogaster transcription regulation and make t...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Tian, F., Shah, P. K., Liu, X., Negre, N., Chen, J., Karpenko, O., White, K. P., Grossman, R. L. Tags: DATABASES AND ONTOLOGIES Source Type: journals

Characterization of 1H NMR spectroscopic data and the generation of synthetic validation setsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Common contemporary practice within the nuclear magnetic resonance (NMR) metabolomics community is to evaluate and validate novel algorithms on empirical data or simplified simulated data. Empirical data captures the complex characteristics of experimental data, but the optimal or most correct analysis is unknown a priori; therefore, researchers are forced to rely on indirect performance metrics, which are of limited value. In order to achieve fair and complete analysis of competing techniques more exacting metrics are required. Thus, metabolomics researchers often evaluate their algorithms on simplified simula...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Anderson, P. E., Raymer, M. L., Kelly, B. J., Reo, N. V., DelRaso, N. J., Doom, T. E. Tags: DATA AND TEXT MINING Source Type: journals

A dictionary to identify small molecules and drugs in free textEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers. Results: We developed a dictionary for the identification of small molecules and drugs in text, combining information from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB and ChemIDplus. Rule-based term filtering, manual check of h...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Hettne, K. M., Stierum, R. H., Schuemie, M. J., Hendriksen, P. J. M., Schijvenaars, B. J. A., Mulligen, E. M. v., Kleinjans, J., Kors, J. A. Tags: DATA AND TEXT MINING Source Type: journals

Metabolite and reaction inference based on enzyme specificitiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Many enzymes are not absolutely specific, or even promiscuous: they can catalyze transformations of more compounds than the traditional ones as listed in, e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity database. In this article, we propose to model enzyme aspecificity by predicting whether an input compound is likely to be transformed by a certain enzyme. Such a predictor has many applications, for example, to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. Results: We have dev...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: de Groot, M. J. L., van Berlo, R. J. P., van Winden, W. A., Verheijen, P. J. T., Reinders, M. J. T., de Ridder, D. Tags: DATA AND TEXT MINING Source Type: journals

Improving peptide identification with single-stage mass spectrum peaksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Database searching is the major peptide identification method in shotgun proteomics. It searches tandem mass spectrometry (MS/MS) spectra against a protein database to identify target peptides. The success of such a database searching method relies on a scoring algorithm that can evaluate the quality of peptide-spectrum matches (PSMs) accurately. However, current scoring algorithms frequently generate inaccurate assignments due to variations and noises in the MS/MS spectra. To address this issue, we like to improve peptide identification by using additional information from other data sources. Results: Single-s...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: He, Z., Yu, W. Tags: DATA AND TEXT MINING Source Type: journals

Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The existing supervised methods for biological network inference work on each of the networks individually based only on intra-species information such as gene expression data. We believe that it will be more effective to use genomic data and cross-species evolutionary information from different species simultaneously, rather than to use the genomic data alone. Results: We created a new semi-supervised learning method called Link Propagation for inferring biological networks of multiple species based on genome-wide data and evolutionary information. The new method was applied to simultaneous reconstruction of t...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Kashima, H., Yamanishi, Y., Kato, T., Sugiyama, M., Tsuda, K. Tags: DATA AND TEXT MINING Source Type: journals

Mining gene functional networks to improve mass-spectrometry-based protein identificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: High-throughput protein identification experiments based on tandem mass spectrometry (MS/MS) often suffer from low sensitivity and low-confidence protein identifications. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other evidence to suggest that a protein is present and confidence in individual protein identification can be updated accordingly. Results: We develop a method that analyzes MS/MS experiments in the larger context of the biological processes active in a cell. Our method, MSNet, improves protein identification i...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Ramakrishnan, S. R., Vogel, C., Kwon, T., Penalva, L. O., Marcotte, E. M., Miranker, D. P. Tags: DATA AND TEXT MINING Source Type: journals

Identification of genes involved in the same pathways using a Hidden Markov Model-based approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The sequencing of whole genomes from various species has provided us with a wealth of genetic information. To make use of the vast amounts of data available today it is necessary to devise computer-based analysis techniques. Results: We propose a Hidden Markov Model (HMM) based algorithm to detect groups of genes functionally similar to a set of input genes from microarray expression data. A subset of experiments from a microarray is selected based on a set of related input genes. HMMs are trained from the input genes and a group of random gene input sets to provide significance estimates. Every gene in the mic...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Senf, A., Chen, X.-w. Tags: SYSTEMS BIOLOGY Source Type: journals