Bioinformatics Research 
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This page shows you the most recent publications within this specialty of the MedWorm directory. This is page number 34.
Learning from our GWAS mistakes: from experimental design to scientific method
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Many public and private genome-wide association studies that we have analyzed include flaws in design, with avoidable confounding appearing as a norm rather than the exception. Rather than recognizing flawed research design and addressing that, a category of quality-control statistical methods has arisen to treat only the symptoms. Reflecting more deeply, we examine elements of current genomic research in light of the traditional scientific method and find that hypotheses are often detached from data collection, experimental design, and causal theories. Association studies independent of causal theories, along with multipl...
Source: Biostatistics - March 9, 2012 Category: Bioinformatics Authors: Lambert, C. G., Black, L. J. Tags: Articles Source Type: research
Proteomic analysis of soybean defense response induced by cotton worm (prodenia litura, fabricius) feedingEmail this article to a colleague.
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Conclusion:
This is the first proteomic analysis of the soybean defense response induced by cotton worm. The differentially expressed proteins could work together to play a major role in the induced defense response. PAL and SAMS were up-regulated at both the protein and mRNA levels. These genes can be strongest candidates for further functional research.
Source: Proteome Science - March 8, 2012 Category: Bioinformatics Authors: Rui FanHui WangYongli WangDeyue Yu Source Type: research
Non-negative Matrix Factorisation methods for the spectral decomposition of MRS data from human brain tumoursEmail this article to a colleague.
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Conclusions:
The unsupervised properties of Convex-NMF place this approach one step ahead of classical label-requiring supervised methods for the discrimination of brain tumour types, as it accounts for their increasingly recognised molecular subtype heterogeneity. The application of Convex-NMF in computer assisted decision support systems is expected to facilitate further improvements in the uptake of MRS-derived information by clinicians.
Source: BMC Bioinformatics - Latest articles - March 8, 2012 Category: Bioinformatics Authors: Sandra Ortega-MartorellPaulo LisboaAlfredo VellidoMargarida Julia-SapeCarles Arus Source Type: research
Molecular dynamics studies of β-hairpin folding with the presence of the sodium ion.Email this article to a colleague.
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Abstract
Metal ions are ubiquitous in protein systems and play a significant role during their folding processes. Nineteen independent structures were determined for the Na(+)/β-hairpin interacting systems, and their folding pathways are different. (i) For Na(S47), the turn is rapidly shaped with the help of Na(+) and acts as the folding nucleus for the rest regions. Two intermediate states are observed and the resulted structure is the most folded. (ii) For Na(B41), Na(B52), Na(B54), Na(S55) and Na(B56), the inclusive Na(+) ions are anchored by β-strands. The local structures around the Na(+) ions and the turn r...
Source: Computational Biology and Chemistry - March 7, 2012 Category: Bioinformatics Authors: Wu X, Yang G, Zu Y, Zhou L Tags: Comput Biol Chem Source Type: research
A dynamic framework for quantifying the genetic architecture of phenotypic plasticity.Email this article to a colleague.
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Abstract
Despite its central role in the adaptation and microevolution of traits, the genetic architecture of phenotypic plasticity, i.e. multiple phenotypes produced by a single genotype in changing environments, remains elusive. We know little about the genes that underlie the plastic response of traits to the environment, their number, chromosomal locations and genetic interactions as well as environment impact on their effects. Here we review key statistical approaches for analyzing the genetic variation of phenotypic plasticity due to genotype-environment interactions and describe the implementation of a dynam...
Source: Briefings in Bioinformatics - March 6, 2012 Category: Bioinformatics Authors: Wang Z, Pang X, Lv Y, Xu F, Zhou T, Li X, Feng S, Li J, Li Z, Wu R Tags: Brief Bioinform Source Type: research
Adjusting confounders in ranking biomarkers: a model-based ROC approach.Email this article to a colleague.
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Abstract
High-throughput studies have been extensively conducted in the research of complex human diseases. As a representative example, consider gene-expression studies where thousands of genes are profiled at the same time. An important objective of such studies is to rank the diagnostic accuracy of biomarkers (e.g. gene expressions) for predicting outcome variables while properly adjusting for confounding effects from low-dimensional clinical risk factors and environmental exposures. Existing approaches are often fully based on parametric or semi-parametric models and target evaluating estimation significance as...
Source: Briefings in Bioinformatics - March 6, 2012 Category: Bioinformatics Authors: Yu T, Li J, Ma S Tags: Brief Bioinform Source Type: research
Network biology methods integrating biological data for translational science.Email this article to a colleague.
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Abstract
The explosion of biomedical data, both on the genomic and proteomic side as well as clinical data, will require complex integration and analysis to provide new molecular variables to better understand the molecular basis of phenotype. Currently, much data exist in silos and is not analyzed in frameworks where all data are brought to bear in the development of biomarkers and novel functional targets. This is beginning to change. Network biology approaches, which emphasize the interactions between genes, proteins and metabolites provide a framework for data integration such that genome, proteome, metabolome ...
Source: Briefings in Bioinformatics - March 5, 2012 Category: Bioinformatics Authors: Bebek G, Koyutürk M, Price ND, Chance MR Tags: Brief Bioinform Source Type: research
Identifying malignant transformations in recurrent low grade gliomas using high resolution magic angle spinning spectroscopyEmail this article to a colleague.
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Conclusions: This study demonstrates the feasibility of using quantitative pattern recognition methods for the analysis of metabolic data from brain tissue obtained during the surgical resection of gliomas. All pattern recognition techniques provided good diagnostic accuracies, though logistic regression and decision stump boosting slightly outperform the other classifiers. These methods identified biomarkers that can be used to detect malignant transformations in individual low grade gliomas, and can lead to a timely change in treatment for each patient.
Source: Artificial Intelligence in Medicine - March 5, 2012 Category: Bioinformatics Authors: Alexandra Constantin, Adam Elkhaled, Llewellyn Jalbert, Radhika Srinivasan, Soonmee Cha, Susan M. Chang, Ruzena Bajcsy, Sarah J. Nelson Tags: Research Articles Source Type: research
Identifying a small set of marker genes using minimum expected cost of misclassificationEmail this article to a colleague.
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Conclusion: The MECM-based feature selection approach is capable of identifying a smaller subset of market genes with comparable or even better performance than that obtained using conventional filter methods.
Source: Artificial Intelligence in Medicine - March 5, 2012 Category: Bioinformatics Authors: Samuel H. Huang, Dengyao Mo, Jarek Meller, Michael Wagner Tags: Research Articles Source Type: research
Characterisation of the vitreous proteome in proliferative diabetic retinopathyEmail this article to a colleague.
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Conclusions:
These data provide an in-depth analysis of the human vitreous proteome and reveal protein alterations that are possibly involved in the pathogenesis of PDR. Further investigation of these special proteins may provide potential new targets for the treatment or the prevention of PDR.
Source: Proteome Science - March 5, 2012 Category: Bioinformatics Authors: Hao WangLe FengJian HuChun XieFang Wang Source Type: research
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversityEmail this article to a colleague.
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Conclusions:
PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution.
Source: BMC Bioinformatics - Latest articles - March 4, 2012 Category: Bioinformatics Authors: Bhakti DwivediRob SchmiederDawn GoldsmithRobert EdwardsMya Breitbart Source Type: research
Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs.Email this article to a colleague.
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Abstract
During a meeting of the SYSGENET working group 'Bioinformatics', currently available software tools and databases for systems genetics in mice were reviewed and the needs for future developments discussed. The group evaluated interoperability and performed initial feasibility studies. To aid future compatibility of software and exchange of already developed software modules, a strong recommendation was made by the group to integrate HAPPY and R/qtl analysis toolboxes, GeneNetwork and XGAP database platforms, and TIQS and xQTL processing platforms. R should be used as the principal computer language for QTL...
Source: Briefings in Bioinformatics - March 1, 2012 Category: Bioinformatics Authors: Durrant C, Swertz MA, Alberts R, Arends D, Möller S, Mott R, Prins P, van der Velde KJ, Jansen RC, Schughart K Tags: Brief Bioinform Source Type: research
LEPSCAN--a web server for searching latent periodicity in DNA sequences.Email this article to a colleague.
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Abstract
A web server for searching latent periodicity based on the method of modified profile analysis has been developed. This method allows searching latent periodicity in presence of insertions and deletions. During searching process, the periodicity classes are used which were found by us earlier for various groups of organisms. Period length belongs to the range 2-20 nt, not including the triplet periodicity. The results obtained are subjected to various filtration steps to ensure their statistical significance. Availability: The use of web server is free for non-commercial users. No registration is require...
Source: Briefings in Bioinformatics - March 1, 2012 Category: Bioinformatics Authors: Shelenkov A, Korotkov E Tags: Brief Bioinform Source Type: research
Biological network motif detection: principles and practice.Email this article to a colleague.
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This article discusses the biological significance of network motifs, the motivation behind solving the motif-finding problem, and strategies to solve the various aspects of this problem. A simple classification scheme is designed to analyze the strengths and weaknesses of several existing algorithms. Experimental results derived from a few comparative studies in the literature are discussed, with conclusions that lead to future research directions.
PMID: 22396487 [PubMed - in process]
Source: Briefings in Bioinformatics - March 1, 2012 Category: Bioinformatics Authors: Wong E, Baur B, Quader S, Huang CH Tags: Brief Bioinform Source Type: research
Subject IndexEmail this article to a colleague.
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Source: Artificial Intelligence in Medicine - March 1, 2012 Category: Bioinformatics Source Type: research
Author IndexEmail this article to a colleague.
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Source: Artificial Intelligence in Medicine - March 1, 2012 Category: Bioinformatics Source Type: research
Editorial BoardEmail this article to a colleague.
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Source: Artificial Intelligence in Medicine - March 1, 2012 Category: Bioinformatics Source Type: research
Modeling Seasonal Rabies Epidemics in China.Email this article to a colleague.
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Abstract
Human rabies, an infection of the nervous system, is a major public-health problem in China. In the last 60 years (1950-2010) there had been 124,255 reported human rabies cases, an average of 2,037 cases per year. However, the factors and mechanisms behind the persistence and prevalence of human rabies have not become well understood. The monthly data of human rabies cases reported by the Chinese Ministry of Health exhibits a periodic pattern on an annual base. The cases in the summer and autumn are significantly higher than in the spring and winter. Based on this observation, we propose a susceptible, exp...
Source: Bulletin of Mathematical Biology - March 1, 2012 Category: Bioinformatics Authors: Zhang J, Jin Z, Sun GQ, Sun XD, Ruan S Tags: Bull Math Biol Source Type: research
Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolatesEmail this article to a colleague.
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Conclusions:
Mass spectrometry and bioinformatic analysis of both MDR and sensitive isolates of M. tuberculosis during intraphagosomal growth showed that majority of commonly upregulated/expressed proteins belonged to the cellular metabolism and respiration category. Inhibitors of the metabolic enzymes/intermediate can therefore serve as suitable drug targets against drug-resistant and sensitive subpopulations of M. tuberculosis.
Source: Proteome Science - March 1, 2012 Category: Bioinformatics Authors: Neelja SinghalPrashant SharmaManish KumarBeenu JoshiDeepa Bisht Source Type: research
GROMACS molecule & liquid databaseEmail this article to a colleague.
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Motivation: The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible with many molecular dynamics force fields; coarse-grained, unified atom, all atom as well as polarizable models based on the charge on a spring concept. To validate simulations, it is necessary to compare results from the simulations to experimental data. To ease the process of setting up topologies and structures for simulations, as...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: van der Spoel, D., van Maaren, P. J., Caleman, C. Tags: DATABASES AND ONTOLOGIES Source Type: research
BESC knowledgebase public portalEmail this article to a colleague.
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The BioEnergy Science Center (BESC) is undertaking large experimental campaigns to understand the biosynthesis and biodegradation of biomass and to develop biofuel solutions. BESC is generating large volumes of diverse data, including genome sequences, omics data and assay results. The purpose of the BESC Knowledgebase is to serve as a centralized repository for experimentally generated data and to provide an integrated, interactive and user-friendly analysis framework. The Portal makes available tools for visualization, integration and analysis of data either produced by BESC or obtained from external resources.
Availabil...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Syed, M. H., Karpinets, T. V., Parang, M., Leuze, M. R., Park, B. H., Hyatt, D., Brown, S. D., Moulton, S., Galloway, M. D., Uberbacher, E. C. Tags: DATABASES AND ONTOLOGIES Source Type: research
IMID: integrated molecular interaction databaseEmail this article to a colleague.
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In this study, we integrate molecular interaction information from literature by automatic information extraction and from manually annotated databases. We further integrate the relationships between protein/gene and other bio-entity terms including gene ontology terms, pathways, species and diseases to build an integrated molecular interaction database (IMID). Interactions can be selected by their associated probabilities. IMID allows complex and versatile queries for context-specific molecular interactions, which are not available currently in other molecular interaction databases.
Availability: The database is located a...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Balaji, S., Mcclendon, C., Chowdhary, R., Liu, J. S., Zhang, J. Tags: DATABASES AND ONTOLOGIES Source Type: research
COPICAT: a software system for predicting interactions between proteins and chemical compoundsEmail this article to a colleague.
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Summary: Since tens of millions of chemical compounds have been accumulated in public chemical databases, fast comprehensive computational methods to predict interactions between chemical compounds and proteins are needed for virtual screening of lead compounds. Previously, we proposed a novel method for predicting protein–chemical interactions using two-layer Support Vector Machine classifiers that require only readily available biochemical data, i.e. amino acid sequences of proteins and structure formulas of chemical compounds.
In this article, the method has been implemented as the COPICAT web service, with an eas...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Sakakibara, Y., Hachiya, T., Uchida, M., Nagamine, N., Sugawara, Y., Yokota, M., Nakamura, M., Popendorf, K., Komori, T., Sato, K. Tags: DATA AND TEXT MINING Source Type: research
medpie: an information extraction package for medical message board postsEmail this article to a colleague.
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Summary: We have developed medpie, a software package for preparing medical message board corpora and extracting patient mentions and statistics for drugs, herbs and adverse effects experienced from them. The package is divided into web-crawling, HTML-cleaning, de-identification and information extraction modules. It also includes a sample controlled vocabulary of drugs, herbs and adverse effect terms.
Availability: http://www.cis.upenn.edu/~ungar/medpie.zip
Dependencies: Python 2.6 or 2.7
Contact: ungar@cis.upenn.edu; adrianb@mail.med.upenn.edu
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Benton, A., Holmes, J. H., Hill, S., Chung, A., Ungar, L. Tags: DATA AND TEXT MINING Source Type: research
Mining and integration of pathway diagrams from imaging dataEmail this article to a colleague.
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Motivation: Pathway diagrams from PubMed and World Wide Web (WWW) contain valuable highly curated information difficult to reach without tools specifically designed and customized for the biological semantics and high-content density of the images. There is currently no search engine or tool that can analyze pathway images, extract their pathway components (molecules, genes, proteins, organelles, cells, organs, etc.) and indicate their relationships.
Results: Here, we describe a resource of pathway diagrams retrieved from article and web-page images through optical character recognition, in conjunction with data mining and...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Kozhenkov, S., Baitaluk, M. Tags: DATA AND TEXT MINING Source Type: research
MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics researchEmail this article to a colleague.
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Motivation: Liquid chromatography–mass spectrometry (LC/MS) is a key technique in metabolomics. Since the efficient assignment of MS signals to true biological metabolites becomes feasible in combination with in vivo stable isotopic labelling, our aim was to provide a new software tool for this purpose.
Results: An algorithm and a program (MetExtract) have been developed to search for metabolites in in vivo labelled biological samples. The algorithm makes use of the chromatographic characteristics of the LC/MS data and detects MS peaks fulfilling the criteria of stable isotopic labelling. As a result of all calculati...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Bueschl, C., Kluger, B., Berthiller, F., Lirk, G., Winkler, S., Krska, R., Schuhmacher, R. Tags: SYSTEMS BIOLOGY Source Type: research
NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environmentEmail this article to a colleague.
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Summary: NetSeed is a web tool and Perl module for analyzing the topology of metabolic networks and calculating the set of exogenously acquired compounds. NetSeed is based on the seed detection algorithm, developed and validated in previous studies.
Availability: The NetSeed web-based tool, open-source Perl module, examples and documentation are freely available online at: http://depts.washington.edu/elbogs/NetSeed.
Contact: elbo@uw.edu
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Carr, R., Borenstein, E. Tags: SYSTEMS BIOLOGY Source Type: research
StochSens--matlab package for sensitivity analysis of stochastic chemical systemsEmail this article to a colleague.
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Motivation: The growing interest in the role of stochasticity in biochemical systems drives the demand for tools to analyse stochastic dynamical models of chemical reactions. One powerful tool to elucidate performance of dynamical systems is sensitivity analysis. Traditionally, however, the concept of sensitivity has mainly been applied to deterministic systems, and the difficulty to generalize these concepts for stochastic systems results from necessity of extensive Monte Carlo simulations.
Results: Here we present a Matlab package, StochSens, that implements sensitivity analysis for stochastic chemical systems using the ...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Komorowski, M., Zurauskiene, J., Stumpf, M. P. H. Tags: SYSTEMS BIOLOGY Source Type: research
IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation dataEmail this article to a colleague.
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Summary: The Illumina Infinium HumanMethylation450 BeadChip is a newly designed high-density microarray for quantifying the methylation level of over 450 000 CpG sites within human genome. Illumina Methylation Analyzer (IMA) is a computational package designed to automate the pipeline for exploratory analysis and summarization of site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray. The pipeline loads the data from Illumina platform and provides user-customized functions commonly required to perform exploratory methylation analysis for individual sites as well ...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Wang, D., Yan, L., Hu, Q., Sucheston, L. E., Higgins, M. J., Ambrosone, C. B., Johnson, C. S., Smiraglia, D. J., Liu, S. Tags: GENE EXPRESSION Source Type: research
nEASE: a method for gene ontology subclassification of high-throughput gene expression dataEmail this article to a colleague.
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Summary: High-throughput technologies can identify genes whose expression profiles correlate with specific phenotypes; however, placing these genes into a biological context remains challenging. To help address this issue, we developed nested Expression Analysis Systematic Explorer (nEASE). nEASE complements traditional gene ontology enrichment approaches by determining statistically enriched gene ontology subterms within a list of genes based on co-annotation. Here, we overview an open-source software version of the nEASE algorithm. nEASE can be used either stand-alone or as part of a pathway discovery pipeline.
Availabil...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Chittenden, T. W., Howe, E. A., Taylor, J. M., Mar, J. C., Aryee, M. J., Gomez, H., Sultana, R., Braisted, J., Nair, S. J., Quackenbush, J., Holmes, C. Tags: GENE EXPRESSION Source Type: research
AnnTools: a comprehensive and versatile annotation toolkit for genomic variantsEmail this article to a colleague.
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Summary: AnnTools is a versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions/deletions (INDEL) and structural variants/copy number variation (SV/CNV). The variants are interpreted by interrogating data compiled from 15 constantly updated sources. In addition to detailed functional characterization of the coding variants, AnnTools searches for overlaps with regulatory elements, disease/trait associated loci, known segmental duplications and artifact prone regions, thereby offering an...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Makarov, V., O'Grady, T., Cai, G., Lihm, J., Buxbaum, J. D., Yoon, S. Tags: GENOME ANALYSIS Source Type: research
FX: an RNA-Seq analysis tool on the cloudEmail this article to a colleague.
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Summary: FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ~160 000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of reads originating from splicing junctions. Unmapped reads not aligned on known transcripts are then mapped on the human genome reference. FX allows analysis of RNA-Seq data on cloud computing infrastructures, supporting access through a user-fri...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Hong, D., Rhie, A., Park, S.-S., Lee, J., Ju, Y. S., Kim, S., Yu, S.-B., Bleazard, T., Park, H.-S., Rhee, H., Chong, H., Yang, K.-S., Lee, Y.-S., Kim, I.-H., Lee, J. S., Kim, J.-I., Seo, J.-S. Tags: GENOME ANALYSIS Source Type: research
A scalable and portable framework for massively parallel variable selection in genetic association studiesEmail this article to a colleague.
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Summary: The deluge of data emerging from high-throughput sequencing technologies poses large analytical challenges when testing for association to disease. We introduce a scalable framework for variable selection, implemented in C++ and OpenCL, that fits regularized regression across multiple Graphics Processing Units. Open source code and documentation can be found at a Google Code repository under the URL http://bioinformatics.oxfordjournals.org/content/early/2012/01/10/bioinformatics.bts015.abstract.
Contact: gary.k.chen@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Chen, G. K. Tags: GENOME ANALYSIS Source Type: research
CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signaturesEmail this article to a colleague.
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Summary: CHROMATRA (CHROmatin Mapping Across TRAnscripts) is a visualization tool available as plug-in for the Galaxy platform. It allows detailed yet concise presentations of data derived from ChIP-chip or ChIP-seq experiments by visualizing enrichment scores across genes or other genomic features while accounting for their length and additional characteristics such as gene expression. It integrates into typical analysis workflows and enables rapid graphical assessment and comparison of genome-wide data at a glance.
Availability: https://github.com/cmmt/chromatra
Contact: msk@cmmt.ubc.ca; eemberly@sfu.ca
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Hentrich, T., Schulze, J. M., Emberly, E., Kobor, M. S. Tags: GENOME ANALYSIS Source Type: research
Roundup 2.0: enabling comparative genomics for over 1800 genomesEmail this article to a colleague.
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Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: DeLuca, T. F., Cui, J., Jung, J.-Y., St. Gabriel, K. C., Wall, D. P. Tags: GENOME ANALYSIS Source Type: research
Mining and evaluation of molecular relationships in literatureEmail this article to a colleague.
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Motivation: Specific information on newly discovered proteins is often difficult to find in literature. Particularly if only sequences and no common names of proteins or genes are available, preceding sequence similarity searches can be crucial for the process of information collection. In drug research, it is important to know whether a small molecule targets only one specific protein or whether similar or homologous proteins are also influenced that may account for possible side effects.
Results: prolific (protein-literature investigation for interacting compounds) provides a one-step solution to investigate available in...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Senger, C., Gruning, B. A., Erxleben, A., Doring, K., Patel, H., Flemming, S., Merfort, I., Gunther, S. Tags: DATA AND TEXT MINING Source Type: research
De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiaeEmail this article to a colleague.
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This article aims at improving the accuracy of inferring TF–TF interactions by incorporating motif discovery as a fundamental step when detecting overlapping targets of TFs based on ChIP-chip data.
Results: The proposed method, simTFBS, outperforms three naïve methods that adopt fixed thresholds when inferring TF–TF interactions based on ChIP-chip data. In addition, simTFBS is compared with two advanced methods and demonstrates its advantages in predicting TF–TF interactions. By comparing simTFBS with predictions based on the set of available annotated yeast TF binding motifs, we demonstrate that the...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Chen, M.-J. M., Chou, L.-C., Hsieh, T.-T., Lee, D.-D., Liu, K.-W., Yu, C.-Y., Oyang, Y.-J., Tsai, H.-K., Chen, C.-Y. Tags: SYSTEMS BIOLOGY Source Type: research
Modeling community-wide molecular networks of multicellular systemsEmail this article to a colleague.
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Motivation: Multicellular systems, such as tissues, are composed of different cell types that form a heterogeneous community. Behavior of these systems is determined by complex regulatory networks within (intracellular networks) and between (intercellular networks) cells. Increasingly more studies are applying genome-wide experimental approaches to delineate the contributions of individual cell types (e.g. stromal, epithelial, vascular cells) to collective behavior of heterogeneous cell communities (e.g. tumors). Although many computational methods have been developed for analyses of intracellular networks based on genome-...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Komurov, K. Tags: SYSTEMS BIOLOGY Source Type: research
influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experimentsEmail this article to a colleague.
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Motivation: The problem of stationary metabolic flux analysis based on isotope labelling experiments first appeared in the early 1950s and was basically solved in early 2000s. Several algorithms and software packages are available for this problem. However, the generic stochastic algorithms (simulated annealing or evolution algorithms) currently used in these software require a lot of time to achieve acceptable precision. For deterministic algorithms, a common drawback is the lack of convergence stability for ill-conditioned systems or when started from a random point.
Results: In this article, we present a new determinist...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Sokol, S., Millard, P., Portais, J.-C. Tags: SYSTEMS BIOLOGY Source Type: research
SSuMMo: rapid analysis, comparison and visualization of microbial communitiesEmail this article to a colleague.
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Motivation: Next-generation sequencing methods are generating increasingly massive datasets, yet still do not fully capture genetic diversity in the richest environments. To understand such complicated and elusive systems, effective tools are needed to assist with delineating the differences found in and between community datasets.
Results: The Small Subunit Markov Modeler (SSuMMo) was developed to probabilistically assign SSU rRNA gene fragments from any sequence dataset to recognized taxonomic clades, producing consistent, comparable cladograms. Accuracy tests predicted >90% of genera correctly for sequences downloade...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Leach, A. L. B., Chong, J. P. J., Redeker, K. R. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research
Interactome-transcriptome integration for predicting distant metastasis in breast cancerEmail this article to a colleague.
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Motivation: High-throughput gene expression profiling yields genomic signatures that allow the prediction of clinical conditions including patient outcome. However, these signatures have limitations, such as dependency on the training set, and worse, lack of generalization.
Results: We propose a novel algorithm called ITI (interactome–transcriptome integration), to extract a genomic signature predicting distant metastasis in breast cancer by superimposition of large-scale protein–protein interaction data over a compendium of several gene expression datasets. Training on two different compendia showed that the e...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Garcia, M., Millat-Carus, R., Bertucci, F., Finetti, P., Birnbaum, D., Bidaut, G. Tags: GENE EXPRESSION Source Type: research
Predicting folding free energy changes upon single point mutationsEmail this article to a colleague.
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We report an approach that predicts the free energy change upon single point mutation by utilizing the 3D structure of the wild-type protein. It is based on variation of the molecular mechanics Generalized Born (MMGB) method, scaled with optimized parameters (sMMGB) and utilizing specific model of unfolded state. The corresponding mutations are built in silico and the predictions are tested against large dataset of 1109 mutations with experimentally measured changes of the folding free energy. Benchmarking resulted in root mean square deviation = 1.78 kcal/mol and slope of the linear regression fit between the experimental...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Zhang, Z., Wang, L., Gao, Y., Zhang, J., Zhenirovskyy, M., Alexov, E. Tags: STRUCTURAL BIOINFORMATICS Source Type: research
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood countsEmail this article to a colleague.
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Conclusion: N2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences.
Availability: The software is part of the open-source C++ library SeqAn (www.seqan.de) and a compiled version can be downloaded at http://www.seqan.de/projects/alf.html
Contact: goeke@molgen.mpg.de; vingron@molgen.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Goke, J., Schulz, M. H., Lasserre, J., Vingron, M. Tags: SEQUENCE ANALYSIS Source Type: research
Application of canonical correlation analysis for identifying viral integration preferencesEmail this article to a colleague.
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Motivation: Gene therapy aims at using viral vectors for attaching helpful genetic code to target genes. Therefore, it is of great importance to develop methods that can discover significant patterns around viral integration sites. Canonical correlation analysis is an unsupervised statistical tool that is used to describe the relations between two related views of the same semantic object, which fits well for identifying such salient patterns.
Results: Proposed method is demonstrated on a sequence dataset obtained from a study on HIV-1 preferred integration regions. The subsequences on the left and right sides of the integ...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Gumus, E., Kursun, O., Sertbas, A., Ustek, D. Tags: SEQUENCE ANALYSIS Source Type: research
SNP calling using genotype model selection on high-throughput sequencing dataEmail this article to a colleague.
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Motivation: A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for.
Results: A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the ...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: You, N., Murillo, G., Su, X., Zeng, X., Xu, J., Ning, K., Zhang, S., Zhu, J., Cui, X. Tags: SEQUENCE ANALYSIS Source Type: research
Evaluating bacterial gene-finding HMM structures as probabilistic logic programsEmail this article to a colleague.
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Motivation: Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog.
Results: We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length modeling and three...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Mork, S., Holmes, I. Tags: SEQUENCE ANALYSIS Source Type: research
Transformations for the compression of FASTQ quality scores of next-generation sequencing dataEmail this article to a colleague.
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This article examines methods for compressing the quality score component of the data to partly address this problem.
Results: We compare several compression policies for quality scores, in terms of both compression effectiveness and overall efficiency. The policies employ lossy and lossless transformations with one of several coding schemes. Experiments show that both lossy and lossless transformations are useful, and that simple coding methods, which consume less computing resources, are highly competitive, especially when random access to reads is needed.
Availability and implementation: Our C++ implementation, released...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Wan, R., Anh, V. N., Asai, K. Tags: SEQUENCE ANALYSIS Source Type: research
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerSEmail this article to a colleague.
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Motivation: The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map.
Results: Here we present a method for ‘split’ read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alt...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: Emde, A.-K., Schulz, M. H., Weese, D., Sun, R., Vingron, M., Kalscheuer, V. M., Haas, S. A., Reinert, K. Tags: GENOME ANALYSIS Source Type: research
PHACTS, a computational approach to classifying the lifestyle of phagesEmail this article to a colleague.
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Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed.
Results: Phage Classification Tool Set (PHACTS) utilizes a novel similarity algorithm and a supe...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: McNair, K., Bailey, B. A., Edwards, R. A. Tags: GENOME ANALYSIS Source Type: research
An effective statistical evaluation of ChIPseq dataset similarityEmail this article to a colleague.
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Motivation: ChIPseq is rapidly becoming a common technique for investigating protein–DNA interactions. However, results from individual experiments provide a limited understanding of chromatin structure, as various chromatin factors cooperate in complex ways to orchestrate transcription. In order to quantify chromtain interactions, it is thus necessary to devise a robust similarity metric applicable to ChIPseq data. Unfortunately, moving past simple overlap calculations to give statistically rigorous comparisons of ChIPseq datasets often involves arbitrary choices of distance metrics, with significance being estimate...
Source: Bioinformatics - February 29, 2012 Category: Bioinformatics Authors: D. Chikina, M., G. Troyanskaya, O. Tags: GENOME ANALYSIS Source Type: research
