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The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The field of synthetic biology holds an inspiring vision for the future; it integrates computational analysis, biological data and the systems engineering paradigm in the design of new biological machines and systems. These biological machines are built from basic biomolecular components analogous to electrical devices, and the information flow among these components requires the augmentation of biological insight with the power of a formal approach to information management. Here we review the informatics challenges in synthetic biology along three dimensions: in silico, in vitro and in vivo. First, we describe state ...
Source: Briefings in Bioinformatics - November 11, 2009 Category: Bioinformatics Authors: Alterovitz G, Muso T, Ramoni MF Tags: Brief Bioinform Source Type: journals

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called 'next-generation' sequencing platforms, with several others anticipated to become available shortly. The previously unimaginable scale and economy of these methods, coupled with their enthusiastic uptake by the scientific community and the potential for further improvements in accuracy and read length, suggest that these technologies are destined...
Source: Briefings in Bioinformatics - October 27, 2009 Category: Bioinformatics Authors: Horner DS, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G Tags: Brief Bioinform Source Type: journals

Knowledge-based data analysis comes of age.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The emergence of high-throughput technologies for measuring biological systems has introduced problems for data interpretation that must be addressed for proper inference. First, analysis techniques need to be matched to the biological system, reflecting in their mathematical structure the underlying behavior being studied. When this is not done, mathematical techniques will generate answers, but the values and reliability estimates may not accurately reflect the biology. Second, analysis approaches must address the vast excess in variables measured (e.g. transcript levels of genes) over the number of samples (e.g. tum...
Source: Briefings in Bioinformatics - October 23, 2009 Category: Bioinformatics Authors: Ochs MF Tags: Brief Bioinform Source Type: journals

Gene association analysis: a survey of frequent pattern mining from gene expression data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Establishing an association between variables is always of interest in genomic studies. Generation of DNA microarray gene expression data introduces a variety of data analysis issues not encountered in traditional molecular biology or medicine. Frequent pattern mining (FPM) has been applied successfully in business and scientific data for discovering interesting association patterns, and is becoming a promising strategy in microarray gene expression analysis. We review the most relevant FPM strategies, as well as surrounding main issues when devising efficient and practical methods for gene association analysis (GAA). ...
Source: Briefings in Bioinformatics - October 7, 2009 Category: Bioinformatics Authors: Alves R, Rodriguez-Baena DS, Aguilar-Ruiz JS Tags: Brief Bioinform Source Type: journals

Advances in metaheuristics for gene selection and classification of microarray data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene selection aims at identifying a (small) subset of informative genes from the initial data in order to obtain high predictive accuracy for classification. Gene selection can be considered as a combinatorial search problem and thus be conveniently handled with optimization methods. In this article, we summarize some recent developments of using metaheuristic-based methods within an embedded approach for gene selection. In particular, we put forward the importance and usefulness of integrating problem-specific knowledge into the search operators of such a method. To illustrate the point, we explain how ranking coeffi...
Source: Briefings in Bioinformatics - September 28, 2009 Category: Bioinformatics Authors: Duval B, Hao JK Tags: Brief Bioinform Source Type: journals

Bioinformatics in the orphan crops.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Orphan crops are those which are grown as food, animal feed or other crops of some importance in agriculture, but which have not yet received the investment of research effort or funding required to develop significant public bioinformatics resources. Where an orphan crop is related to a well-characterised model plant species, comparative genomics and bioinformatics can often, though not always, be exploited to assist research and crop improvement. This review addresses some challenges and opportunities presented by bioinformatics in the orphan crops, using three examples: forage grasses from the genera Lolium and Fest...
Source: Briefings in Bioinformatics - September 3, 2009 Category: Bioinformatics Authors: Armstead I, Huang L, Ravagnani A, Robson P, Ougham H Tags: Brief Bioinform Source Type: journals

Stability and aggregation of ranked gene lists.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ranked gene lists are highly instable in the sense that similar measures of differential gene expression may yield very different rankings, and that a small change of the data set usually affects the obtained gene list considerably. Stability issues have long been under-considered in the literature, but they have grown to a hot topic in the last few years, perhaps as a consequence of the increasing skepticism on the reproducibility and clinical applicability of molecular research findings. In this article, we review existing approaches for the assessment of stability of ranked gene lists and the related problem of aggr...
Source: Briefings in Bioinformatics - August 16, 2009 Category: Bioinformatics Authors: Boulesteix AL, Slawski M Tags: Brief Bioinform Source Type: journals

Biological knowledge management: the emerging role of the Semantic Web technologies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
New knowledge is produced at a continuously increasing speed, and the list of papers, databases and other knowledge sources that a researcher in the life sciences needs to cope with is actually turning into a problem rather than an asset. The adequate management of knowledge is therefore becoming fundamentally important for life scientists, especially if they work with approaches that thoroughly depend on knowledge integration, such as systems biology. Several initiatives to organize biological knowledge sources into a readily exploitable resourceome are presently being carried out. Ontologies and Semantic Web technolo...
Source: Briefings in Bioinformatics - June 13, 2009 Category: Bioinformatics Authors: Antezana E, Kuiper M, Mironov V Tags: Brief Bioinform Source Type: journals

Genome assembly reborn: recent computational challenges.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological landscape leads to the need for continued research. In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings. For example, the new field of metagenomics relies on large-scale sequencing of entire microbial communities instead of isolate genomes, lead...
Source: Briefings in Bioinformatics - June 13, 2009 Category: Bioinformatics Authors: Pop M Tags: Brief Bioinform Source Type: journals

Briefings in bioinformatics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19505887 [PubMed - in process] (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - June 13, 2009 Category: Bioinformatics Authors: Dubitzky W Tags: Brief Bioinform Source Type: journals

Approaches to neuroscience data integration.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
As the number of neuroscience databases increases, the need for neuroscience data integration grows. This paper reviews and compares several approaches, including the Neuroscience Database Gateway (NDG), Neuroscience Information Framework (NIF) and Entrez Neuron, which enable neuroscience database annotation and integration. These approaches cover a range of activities spanning from registry, discovery and integration of a wide variety of neuroscience data sources. They also provide different user interfaces for browsing, querying and displaying query results. In Entrez Neuron, for example, four different facets or tre...
Source: Briefings in Bioinformatics - June 13, 2009 Category: Bioinformatics Authors: Cheung KH, Lim E, Samwald M, Chen H, Marenco L, Holford ME, Morse TM, Mutalik P, Shepherd GM, Miller PL Tags: Brief Bioinform Source Type: journals

Computational methods for discovering gene networks from expression data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Designing and conducting experiments are routine practices for modern biologists. The real challenge, especially in the post-genome era, usually comes not from acquiring data, but from subsequent activities such as data processing, analysis, knowledge generation and gaining insight into the research question of interest. The approach of inferring gene regulatory networks (GRNs) has been flourishing for many years, and new methods from mathematics, information science, engineering and social sciences have been applied. We review different kinds of computational methods biologists use to infer networks of varying levels ...
Source: Briefings in Bioinformatics - June 13, 2009 Category: Bioinformatics Authors: Lee WP, Tzou WS Tags: Brief Bioinform Source Type: journals

Computational methods for the detection of cis-regulatory modules.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Metazoan transcription regulation occurs through the concerted action of multiple transcription factors that bind co-operatively to cis-regulatory modules (CRMs). The annotation of these key regulators of transcription is lagging far behind the annotation of the transcriptome itself. Here, we give an overview of existing computational methods to detect these CRMs in metazoan genomes. We subdivide these methods into three classes: CRM scanners screen sequences for CRMs based on predefined models that often consist of multiple position weight matrices (PWMs). CRM builders construct models of similar CRMs controlling a se...
Source: Briefings in Bioinformatics - June 4, 2009 Category: Bioinformatics Authors: Loo PV, Marynen P Tags: Brief Bioinform Source Type: journals

Recent advances in computer-aided drug design.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Modern drug discovery is characterized by the production of vast quantities of compounds and the need to examine these huge libraries in short periods of time. The need to store, manage and analyze these rapidly increasing resources has given rise to the field known as computer-aided drug design (CADD). CADD represents computational methods and resources that are used to facilitate the design and discovery of new therapeutic solutions. Digital repositories, containing detailed information on drugs and other useful compounds, are goldmines for the study of chemical reactions capabilities. Design libraries, with the pote...
Source: Briefings in Bioinformatics - May 11, 2009 Category: Bioinformatics Authors: Song CM, Lim SJ, Tong JC Tags: Brief Bioinform Source Type: journals

2D molecular graphics: a flattened world of chemistry and biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Molecular graphics provides an intuitive way for representation, modeling and analysis of complex chemical and biological systems. It is now widely used in the theoretical chemistry, structural biology, molecular modeling and drug design communities. Traditional molecular graphics techniques mainly dedicate to showing molecular architectures at three-dimensional (3D) level. However, in some occasions the two-dimensional (2D) representation of molecular configurations, profiles, behaviors and interactions may be more readily acceptable for audiences, especially when we need to describe abstract information in a straight...
Source: Briefings in Bioinformatics - May 1, 2009 Category: Bioinformatics Authors: Zhou P, Shang Z Tags: Brief Bioinform Source Type: journals

Taming the complexity of biological pathways through parallel computing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Biological systems are characterised by a large number of interacting entities whose dynamics is described by a number of reaction equations. Mathematical methods for modelling biological systems are mostly based on a centralised solution approach: the modelled system is described as a whole and the solution technique, normally the integration of a system of ordinary differential equations (ODEs) or the simulation of a stochastic model, is commonly computed in a centralised fashion. In recent times, research efforts moved towards the definition of parallel/distributed algorithms as a means to tackle the complexity of b...
Source: Briefings in Bioinformatics - May 1, 2009 Category: Bioinformatics Authors: Ballarini P, Guido R, Mazza T, Prandi D Tags: Brief Bioinform Source Type: journals

Progress and challenges in predicting protein-protein interaction sites.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The identification of protein-protein interaction sites is an essential intermediate step for mutant design and the prediction of protein networks. In recent years a significant number of methods have been developed to predict these interface residues and here we review the current status of the field. Progress in this area requires a clear view of the methodology applied, the data sets used for training and testing the systems, and the evaluation procedures. We have analysed the impact of a representative set of features and algorithms and highlighted the problems inherent in generating reliable protein data sets and ...
Source: Briefings in Bioinformatics - May 1, 2009 Category: Bioinformatics Authors: Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML Tags: Brief Bioinform Source Type: journals

Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The reliable interpretation of Affymetrix GeneChip data is a multi-faceted problem. The interplay between biophysics, bioinformatics and mining of GeneChip surveys is leading to new insights into how best to analyse the data. Many of the molecular processes occurring on the surfaces of GeneChips result from the high surface density of probes. Interactions between neighbouring adjacent probes affect their rate and strength of hybridization to targets. Competing targets may hybridize to the same probe, and targets may partially bind to more than one probe. The formation of these partial hybrids results in a number of pro...
Source: Briefings in Bioinformatics - May 1, 2009 Category: Bioinformatics Authors: Langdon WB, Upton GJ, Harrison AP Tags: Brief Bioinform Source Type: journals

ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
c V Vaccine research is a combinatorial science requiring computational analysis of vaccine components, formulations and optimization. We have developed a framework that combines computational tools for the study of immune function and vaccine development. This framework, named ImmunoGrid combines conceptual models of the immune system, models of antigen processing and presentation, system-level models of the immune system, Grid computing, and database technology to facilitate discovery, formulation and optimization of vaccines. ImmunoGrid modules share common conceptual models and ontologies. The ImmunoGrid portal off...
Source: Briefings in Bioinformatics - May 1, 2009 Category: Bioinformatics Authors: Pappalardo F, Halling-Brown MD, Rapin N, Zhang P, Alemani D, Emerson A, Paci P, Duroux P, Pennisi M, Palladini A, Miotto O, Churchill D, Rossi E, Shepherd AJ, Moss DS, Castiglione F, Bernaschi M, Lefranc MP, Brunak S, Motta S, Lollini PL, Basford KE, Brus Tags: Brief Bioinform Source Type: journals

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Non-protein coding RNAs (ncRNAs) have emerged as a vast and heterogeneous portion of eukaryotic transcriptomes. Several ncRNA families, either short (<200 nucleotides, nt) or long (>200 nt), have been described and implicated in a variety of biological processes, from translation to gene expression regulation and nuclear trafficking. Most probably, other families are still to be discovered. Computational methods for ncRNA research require different approaches from the ones normally used in the prediction of protein-coding genes. Indeed, primary sequence alone is often insufficient to infer ncRNA functionality, wh...
Source: Briefings in Bioinformatics - April 21, 2009 Category: Bioinformatics Authors: Soldà G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A Tags: Brief Bioinform Source Type: journals

Development of biomarker classifiers from high-dimensional data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article reviews and evaluates some important aspects and key issues in the development of biomarker classifiers. Development of a biomarker classifier for high-throughput data involves two components: (i) model building and (ii) performance assessment. This article focuses on feature selection in model building and cross validation for performance assessment. A 'frequency' approach to feature selection is presented and compared to the 'conventional' approach in terms of the predictive accuracy and stability of the selected feature set. The two approaches are compared based on four biomarker classifiers, each with a di...
Source: Briefings in Bioinformatics - April 3, 2009 Category: Bioinformatics Authors: Baek S, Tsai CA, Chen JJ Tags: Brief Bioinform Source Type: journals

Expression profiling of microRNAs by deep sequencing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
MicroRNAs are short non-coding RNAs that regulate the stability and translation of mRNAs. Profiling experiments, using microarray or deep sequencing technology, have identified microRNAs that are preferentially expressed in certain tissues, specific stages of development, or disease states such as cancer. Deep sequencing utilizes massively parallel sequencing, generating millions of small RNA sequence reads from a given sample. Profiling of microRNAs by deep sequencing measures absolute abundance and allows for the discovery of novel microRNAs that have eluded previous cloning and standard sequencing efforts. Public da...
Source: Briefings in Bioinformatics - March 30, 2009 Category: Bioinformatics Authors: Creighton CJ, Reid JG, Gunaratne PH Tags: Brief Bioinform Source Type: journals

FINDSITE: a combined evolution/structure-based approach to protein function prediction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A key challenge of the post-genomic era is the identification of the function(s) of all the molecules in a given organism. Here, we review the status of sequence and structure-based approaches to protein function inference and ligand screening that can provide functional insights for a significant fraction of the approximately 50% of ORFs of unassigned function in an average proteome. We then describe FINDSITE, a recently developed algorithm for ligand binding site prediction, ligand screening and molecular function prediction, which is based on binding site conservation across evolutionary distant proteins identified ...
Source: Briefings in Bioinformatics - March 26, 2009 Category: Bioinformatics Authors: Skolnick J, Brylinski M Tags: Brief Bioinform Source Type: journals

An introduction to artificial neural networks in bioinformatics--application to complex microarray and mass spectrometry datasets in cancer studies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Applications of genomic and proteomic technologies have seen a major increase, resulting in an explosion in the amount of highly dimensional and complex data being generated. Subsequently this has increased the effort by the bioinformatics community to develop novel computational approaches that allow for meaningful information to be extracted. This information must be of biological relevance and thus correlate to disease phenotypes of interest. Artificial neural networks are a form of machine learning from the field of artificial intelligence with proven pattern recognition capabilities and have been utilized in many ...
Source: Briefings in Bioinformatics - March 23, 2009 Category: Bioinformatics Authors: Lancashire LJ, Lemetre C, Ball GR Tags: Brief Bioinform Source Type: journals

The virtual cell--a candidate co-ordinator for 'middle-out' modelling of biological systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Understanding the functioning of biological systems depends on tackling complexity spanning spatial scales from genome to organ to whole organism. The basic unit of life, the cell, acts to co-ordinate information received across these scales and processes the myriad of signals to produce an integrated cellular response. Cells interact with and respond to other cells through direct or indirect contact, resulting in emergent structure and function of tissues and organs. Systems biology has traditionally used either a 'top-down' or 'bottom-up' approach. However, neither approach takes account of heterogeneity or 'noise', ...
Source: Briefings in Bioinformatics - March 17, 2009 Category: Bioinformatics Authors: Walker DC, Southgate J Tags: Brief Bioinform Source Type: journals

Flux balance analysis of biological systems: applications and challenges.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article reviews the usefulness of FBA as a tool for gaining biological insights, advances in methodology enabling integration of regulatory information and thermodynamic constraints, and finally addresses the challenges that lie ahead. Various use scenarios and biological insights obtained from FBA, and applications in fields such metabolic engineering and drug target identification, are also discussed. Genome-scale constraint-based models have an immense potential for building and testing hypotheses, as well as to guide experimentation. PMID: 19287049 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - March 15, 2009 Category: Bioinformatics Authors: Raman K, Chandra N Tags: Brief Bioinform Source Type: journals

Life sciences on the Semantic Web: the Neurocommons and beyond.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present the Neurocommons prototype knowledge base, a demonstration intended to show the feasibility and benefits of using these technologies. The prototype knowledge base can be used to experiment with and assess the scalability of current tools and methods for creating such a resource, and to elicit issues that will need to be addressed in order to expand the scope and use of it. We demonstrate the utility of the knowledge base by reviewing a few example queries that provide answers to precise questions relevant to the understanding of disease. All components of the knowledge base are freely available at http://neuroco...
Source: Briefings in Bioinformatics - March 12, 2009 Category: Bioinformatics Authors: Ruttenberg A, Rees JA, Samwald M, Marshall MS Tags: Brief Bioinform Source Type: journals

Potential Bias in Go::TermFinder.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The increased need for multiple statistical comparisons under conditions of non-independence in bioinformatics applications, such as DNA microarray data analysis, has led to the development of alternatives to the conventional Bonferroni correction for adjusting P-values. The use of the false discovery rate (FDR), in particular, has grown considerably. However, the calculation of the FDR frequently depends on drawing random samples from a population, and inappropriate sampling will result in a bias in the calculated FDR. In this work, we demonstrate a bias due to incorrect random sampling in the widely used GO::TermFind...
Source: Briefings in Bioinformatics - March 11, 2009 Category: Bioinformatics Authors: Flight RM, Wentzell PD Tags: Brief Bioinform Source Type: journals

Computational biology for cardiovascular biomarker discovery.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article introduces key computational approaches and applications to biomarker discovery based on different types of 'omic' data. Although we emphasize applications in cardiovascular research, the computational requirements and advances discussed here are also relevant to other domains. We will start by introducing some of the contributions of computational biology to translational research, followed by an overview of methods and technologies used for the identification of biomarkers with predictive or classification value. The main types of 'omic' approaches to biomarker discovery will be presented with specific examp...
Source: Briefings in Bioinformatics - March 10, 2009 Category: Bioinformatics Authors: Azuaje F, Devaux Y, Wagner D Tags: Brief Bioinform Source Type: journals

Exploring autonomy through computational biomodelling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The question of whether living organisms possess autonomy of action is tied up with the nature of causal efficacy. Yet the nature of organisms is such that they frequently defy conventional causal language. Did the fig wasp select the fig, or vice versa? Is this an epithelial cell because of its genetic structure, or because it develops within the epithelium? The intimate coupling of biological levels of organisation leads developmental systems theory to deconstruct the biological organism into a life-cycle process which constitutes itself from the resources available within a complete developmental system. This radica...
Source: Briefings in Bioinformatics - March 10, 2009 Category: Bioinformatics Authors: Palfreyman N Tags: Brief Bioinform Source Type: journals

Computational systems biology of the cell cycle.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
One of the early success stories of computational systems biology was the work done on cell-cycle regulation. The earliest mathematical descriptions of cell-cycle control evolved into very complex, detailed computational models that describe the regulation of cell division in many different cell types. On the way these models predicted several dynamical properties and unknown components of the system that were later experimentally verified/identified. Still, research on this field is far from over. We need to understand how the core cell-cycle machinery is controlled by internal and external signals, also in yeast cell...
Source: Briefings in Bioinformatics - March 6, 2009 Category: Bioinformatics Authors: Csikász-Nagy A Tags: Brief Bioinform Source Type: journals

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The unanimous agreement that cellular processes are (largely) governed by interactions between proteins has led to enormous community efforts culminating in overwhelming information relating to these proteins; to the regulation of their interactions, to the way in which they interact and to the function which is determined by these interactions. These data have been organized in databases and servers. However, to make these really useful, it is essential not only to be aware of these, but in particular to have a working knowledge of which tools to use for a given problem; what are the tool advantages and drawbacks; and...
Source: Briefings in Bioinformatics - February 24, 2009 Category: Bioinformatics Authors: Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R Tags: Brief Bioinform Source Type: journals

A roadmap of clustering algorithms: finding a match for a biomedical application.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Clustering is ubiquitously applied in bioinformatics with hierarchical clustering and k-means partitioning being the most popular methods. Numerous improvements of these two clustering methods have been introduced, as well as completely different approaches such as grid-based, density-based and model-based clustering. For improved bioinformatics analysis of data, it is important to match clusterings to the requirements of a biomedical application. In this article, we present a set of desirable clustering features that are used as evaluation criteria for clustering algorithms. We review 40 different clustering algorithm...
Source: Briefings in Bioinformatics - February 24, 2009 Category: Bioinformatics Authors: Andreopoulos B, An A, Wang X, Schroeder M Tags: Brief Bioinform Source Type: journals

Towards pharmacogenomics knowledge discovery with the semantic web.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Pharmacogenomics aims to understand pharmacological response with respect to genetic variation. Essential to the delivery of better health care is the use of pharmacogenomics knowledge to answer questions about therapeutic, pharmacological or genetic aspects. Several XML markup languages have been developed to capture pharmacogenomic and related information so as to facilitate data sharing. However, recent advances in semantic web technologies have presented exciting new opportunities for pharmacogenomics knowledge discovery by representing the information with machine understandable semantics. Progress in this area is...
Source: Briefings in Bioinformatics - February 24, 2009 Category: Bioinformatics Authors: Dumontier M, Villanueva-Rosales N Tags: Brief Bioinform Source Type: journals

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Computer simulations have become an invaluable tool to study the sometimes counterintuitive temporal dynamics of (bio-)chemical systems. In particular, stochastic simulation methods have attracted increasing interest recently. In contrast to the well-known deterministic approach based on ordinary differential equations, they can capture effects that occur due to the underlying discreteness of the systems and random fluctuations in molecular numbers. Numerous stochastic, approximate stochastic and hybrid simulation methods have been proposed in the literature. In this article, they are systematically reviewed in order t...
Source: Briefings in Bioinformatics - January 16, 2009 Category: Bioinformatics Authors: Pahle J Tags: Brief Bioinform Source Type: journals

Domain mobility in proteins: functional and evolutionary implications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A substantial fraction of eukaryotic proteins contains multiple domains, some of which show a tendency to occur in diverse domain architectures and can be considered mobile (or 'promiscuous'). These promiscuous domains are typically involved in protein-protein interactions and play crucial roles in interaction networks, particularly those contributing to signal transduction. They also play a major role in creating diversity of protein domain architecture in the proteome. It is now apparent that promiscuity is a volatile and relatively fast-changing feature in evolution, and that only a few domains retain their promiscu...
Source: Briefings in Bioinformatics - January 16, 2009 Category: Bioinformatics Authors: Basu MK, Poliakov E, Rogozin IB Tags: Brief Bioinform Source Type: journals

Moby and Moby 2: Creatures of the Deep (Web).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Facile and meaningful integration of data from disparate resources is the 'holy grail' of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized 'semantic warehouses' that collect public data from third parties, integrate it, translate it ...
Source: Briefings in Bioinformatics - January 16, 2009 Category: Bioinformatics Authors: Vandervalk BP, McCarthy EL, Wilkinson MD Tags: Brief Bioinform Source Type: journals

Simulation of DNA sequence evolution under models of recent directional selection.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Computer simulation is an essential tool in the analysis of DNA sequence variation for mapping events of recent adaptive evolution in the genome. Various simulation methods are employed to predict the signature of selection in sequence variation. The most informative and efficient method currently in use is coalescent simulation. However, this method is limited to simple models of directional selection. Whole-population forward-in-time simulations are the alternative to coalescent simulations for more complex models. The notorious problem of excessive computational cost in forward-in-time simulations can be overcome by...
Source: Briefings in Bioinformatics - December 24, 2008 Category: Bioinformatics Authors: Kim Y, Wiehe T Tags: Brief Bioinform Source Type: journals

Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To handle changing environmental surroundings and to manage unfavorable conditions, microbial organisms have evolved complex transcriptional regulatory networks. To comprehensively analyze these gene regulatory networks, several online available databases and analysis platforms have been implemented and established. In this article, we address the typical cycle of scientific knowledge exploration and integration in the area of procaryotic transcriptional gene regulation. We briefly review five popular, publicly available systems that support (i) the integration of existing knowledge, (ii) visualization capabilities and...
Source: Briefings in Bioinformatics - December 12, 2008 Category: Bioinformatics Authors: Baumbach J, Tauch A, Rahmann S Tags: Brief Bioinform Source Type: journals

Building a knowledge base for systems pathology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Translating the exponentially growing amount of omics data into knowledge usable for a personalized medicine approach poses a formidable challenge. In this article-taking diabetes as a use case-we present strategies for developing data repositories into computer-accessible knowledge sources that can be used for a systemic view on the molecular causes of diseases, thus laying the foundation for systems pathology. PMID: 19073714 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - December 10, 2008 Category: Bioinformatics Authors: Michael H, Hogan J, Kel A, Kel-Margoulis O, Schacherer F, Voss N, Wingender E Tags: Brief Bioinform Source Type: journals

Building biomedical web communities using a semantically aware content management system.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Web-based biomedical communities are becoming an increasingly popular vehicle for sharing information amongst researchers and are fast gaining an online presence. However, information organization and exchange in such communities is usually unstructured, rendering interoperability between communities difficult. Furthermore, specialized software to create such communities at low cost-targeted at the specific common information requirements of biomedical researchers-has been largely lacking. At the same time, a growing number of biological knowledge bases and biomedical resources are being structured for the Semantic Web...
Source: Briefings in Bioinformatics - December 6, 2008 Category: Bioinformatics Authors: Das S, Girard L, Green T, Weitzman L, Lewis-Bowen A, Clark T Tags: Brief Bioinform Source Type: journals

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The biomedical literature can be seen as a large integrated, but unstructured data repository. Extracting facts from literature and making them accessible is approached from two directions: manual curation efforts develop ontologies and vocabularies to annotate gene products based on statements in papers. Text mining aims to automatically identify entities and their relationships in text using information retrieval and natural language processing techniques. Manual curation is highly accurate but time consuming, and does not scale with the ever increasing growth of literature. Text mining as a high-throughput computati...
Source: Briefings in Bioinformatics - December 6, 2008 Category: Bioinformatics Authors: Winnenburg R, Wächter T, Plake C, Doms A, Schroeder M Tags: Brief Bioinform Source Type: journals

Data curation + process curation=data integration + science.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article will brief the community on the current state of the art and the current challenges for process curation, both within and without the Life Sciences. PMID: 19060304 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - December 6, 2008 Category: Bioinformatics Authors: Goble C, Stevens R, Hull D, Wolstencroft K, Lopez R Tags: Brief Bioinform Source Type: journals

A pitfall of wiki solution for biological databases.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Not a few biologists tend to consider wiki as a solution to manage and reorganize data by a community. However, in its basic functionality, wiki lacks a measure to check data consistency and is not suitable for a database. To circumvent this pitfall, installation of page dependency through in-line page searches is necessary. We also introduce two existing approaches that support in-line queries. PMID: 19060305 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - December 6, 2008 Category: Bioinformatics Authors: Arita M Tags: Brief Bioinform Source Type: journals

Linked data and provenance in biological data webs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article presents design patterns for representing and querying provenance information relating to mapping links between heterogeneous data from sources in the domain of functional genomics. We illustrate the use of named resource description framework (RDF) graphs at different levels of granularity to make provenance assertions about linked data, and demonstrate that these assertions are sufficient to support requirements including data currency, integrity, evidential support and historical queries. PMID: 19060306 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - December 6, 2008 Category: Bioinformatics Authors: Zhao J, Miles A, Klyne G, Shotton D Tags: Brief Bioinform Source Type: journals

Data and knowledge integration in the life sciences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 18980960 [PubMed - as supplied by publisher] (Source: Briefings in Bioinformatics)
Source: Briefings in Bioinformatics - November 2, 2008 Category: Bioinformatics Authors: Philippi S Tags: Brief Bioinform Source Type: journals

Models of coding sequence evolution.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Probabilistic models of sequence evolution are in widespread use in phylogenetics and molecular sequence evolution. These models have become increasingly sophisticated and combined with statistical model comparison techniques have helped to shed light on how genes and proteins evolve. Models of codon evolution have been particularly useful, because, in addition to providing a significant improvement in model realism for protein-coding sequences, codon models can also be designed to test hypotheses about the selective pressures that shape the evolution of the sequences. Such models typically assume a phylogeny and can b...
Source: Briefings in Bioinformatics - October 29, 2008 Category: Bioinformatics Authors: Delport W, Scheffler K, Seoighe C Tags: Brief Bioinform Source Type: journals

Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The traditional approach to bioinformatics analyses relies on independent task-specific services and applications, using different input and output formats, often idiosyncratic, and frequently not designed to inter-operate. In general, such analyses were performed by experts who manually verified the results obtained at each step in the process. Today, the amount of bioinformatics information continuously being produced means that handling the various applications used to study this information presents a major data management and analysis challenge to researchers. It is now impossible to manually analyse all this info...
Source: Briefings in Bioinformatics - October 29, 2008 Category: Bioinformatics Authors: Aniba MR, Siguenza S, Friedrich A, Plewniak F, Poch O, Marchler-Bauer A, Thompson JD Tags: Brief Bioinform Source Type: journals

Bringing Web 2.0 to bioinformatics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collabo...
Source: Briefings in Bioinformatics - October 8, 2008 Category: Bioinformatics Authors: Zhang Z, Cheung KH, Townsend JP Tags: Brief Bioinform Source Type: journals

Gene-set analysis and reduction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene-set analysis aims to identify differentially expressed gene sets (pathways) by a phenotype in DNA microarray studies. We review here important methodological aspects of gene-set analysis and illustrate them with varying performance of several methods proposed in the literature. We emphasize the importance of distinguishing between 'self-contained' versus 'competitive' methods, following Goeman and Bühlmann. We also discuss reducing a gene set to its subset, consisting of 'core members' that chiefly contribute to the statistical significance of the differential expression of the initial gene set by phenotype. ...
Source: Briefings in Bioinformatics - October 4, 2008 Category: Bioinformatics Authors: Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, Yasui Y Tags: Brief Bioinform Source Type: journals