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This page shows you the most recent publications within this specialty of the MedWorm directory. This is page number 18.

Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood
Summary: Genetic correlations are the genome-wide aggregate effects of causal variants affecting multiple traits. Traditionally, genetic correlations between complex traits are estimated from pedigree studies, but such estimates can be confounded by shared environmental factors. Moreover, for diseases, low prevalence rates imply that even if the true genetic correlation between disorders was high, co-aggregation of disorders in families might not occur or could not be distinguished from chance. We have developed and implemented statistical methods based on linear mixed models to obtain unbiased estimates of the genetic cor...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Lee, S. H., Yang, J., Goddard, M. E., Visscher, P. M., Wray, N. R. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update
Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G'ST, G''ST, Jost’s Dest and F'ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis ...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Peakall, R., Smouse, P. E. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection
Summary: With the rapid advances and prevalence of high-throughput genomic technologies, integrating information of multiple relevant genomic studies has brought new challenges. Microarray meta-analysis has become a frequently used tool in biomedical research. Little effort, however, has been made to develop a systematic pipeline and user-friendly software. In this article, we present MetaOmics, a suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expressed gene identification and enriched pathway detection for microarray meta-analysis. MetaQC provides a quantitative and objective to...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Wang, X., Kang, D. D., Shen, K., Song, C., Lu, S., Chang, L.-C., Liao, S. G., Huo, Z., Tang, S., Ding, Y., Kaminski, N., Sibille, E., Lin, Y., Li, J., Tseng, G. C. Tags: GENE EXPRESSION Source Type: research

easyRNASeq: a bioconductor package for processing RNA-Seq data
Motivation: RNA sequencing is becoming a standard for expression profiling experiments and many tools have been developed in the past few years to analyze RNA-Seq data. Numerous ‘Bioconductor’ packages are available for next-generation sequencing data loading in R, e.g. ShortRead and Rsamtools as well as to perform differential gene expression analyses, e.g. DESeq and edgeR. However, the processing tasks lying in between these require the precise interplay of many Bioconductor packages, e.g. Biostrings, IRanges or external solutions are to be sought. Results: We developed ‘easyRNASeq’, an R package ...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Delhomme, N., Padioleau, I., Furlong, E. E., Steinmetz, L. M. Tags: GENE EXPRESSION Source Type: research

Folding RNA/DNA hybrid duplexes
We present here an extension to the widely used ViennaRNA Package (Lorenz et al., 2011) for the prediction of the structure of RNA/DNA hetero-dimers. Availability: http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html Contact: ronny@tbi.univie.ac.at, berni@bioinf.uni-leipzig.de Supplementary Information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Lorenz, R., Hofacker, I. L., Bernhart, S. H. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

DELIMINATE--a fast and efficient method for loss-less compression of genomic sequences: Sequence analysis
We present a novel compression algorithm (DELIMINATE) that can rapidly compress genomic sequence data in a loss-less fashion. Validation results indicate relatively higher compression efficiency of DELIMINATE when compared with popular general purpose compression algorithms, namely, gzip, bzip2 and lzma. Availability and implementation: Linux, Windows and Mac implementations (both 32 and 64-bit) of DELIMINATE are freely available for download at: http://metagenomics.atc.tcs.com/compression/DELIMINATE. Contact: sharmila@atc.tcs.com Supplementary Information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Mohammed, M. H., Dutta, A., Bose, T., Chadaram, S., Mande, S. S. Tags: SEQUENCE ANALYSIS Source Type: research

RILogo: visualizing RNA-RNA interactions
Summary: With the increasing amount of newly discovered non-coding RNAs, the interactions between RNA molecules become an increasingly important aspect for characterizing their functionality. Many computational tools have been developed to predict the formation of duplexes between two RNAs, either based on single sequences or alignments of homologous sequences. Here, we present RILogo, a program to visualize inter- and intramolecular base pairing between two RNA molecules. The input for RILogo is a pair of structure-annotated sequences or alignments. In the latter case, RILogo displays the alignments in the form of sequenc...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Menzel, P., Seemann, S. E., Gorodkin, J. Tags: SEQUENCE ANALYSIS Source Type: research

Snakemake--a scalable bioinformatics workflow engine
Summary: Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. Availability: http://snakemake.googlecode.com. Contact: johannes.koester@uni-due.de
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Koster, J., Rahmann, S. Tags: GENOME ANALYSIS Source Type: research

Nebula--a web-server for advanced ChIP-seq data analysis
We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data. Results: Nebula was designed for both bioinformaticians and biologists. It is based on the Galaxy open source framework. Galaxy already includes a large number of functionalities for mapping reads and peak calling. We added the following to Galaxy: (i) peak calling with FindPeaks and a module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start ...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Boeva, V., Lermine, A., Barette, C., Guillouf, C., Barillot, E. Tags: GENOME ANALYSIS Source Type: research

GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes
Summary: Next-generation sequencing has become a powerful tool in personalized medicine. Exomes or even whole genomes of patients suffering from rare diseases are screened for sequence variants. After filtering out common polymorphisms, the assessment and interpretation of detected personal variants in the clinical context is an often time-consuming effort. We have developed GeneTalk, a web-based platform that serves as an expert exchange network for the assessment of personal and potentially disease-relevant sequence variants. GeneTalk assists a clinical geneticist who is searching for information about specific sequence ...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Kamphans, T., Krawitz, P. M. Tags: GENOME ANALYSIS Source Type: research

VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets
Summary: Identification of genetic alterations of tumor cells has become a common method to detect the genes involved in development and progression of cancer. In order to detect driver genes, several samples need to be simultaneously analyzed. The Cancer Genome Atlas (TCGA) project provides access to a large amount of data for several cancer types. TGCA is an invaluable source of information, but analysis of this huge dataset possess important computational problems in terms of memory and execution times. Here, we present a R/package, called VegaMC (Vega multi-channel), that enables fast and efficient detection of signifi...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Morganella, S., Ceccarelli, M. Tags: GENOME ANALYSIS Source Type: research

UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ
Summary: UniMoG is a software combining five genome rearrangement models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion and translocation. It can compute the pairwise genomic distances and a corresponding optimal sorting scenario for an arbitrary number of genomes. All five models can be unified through the DCJ model, thus the implementation is based on DCJ and, where reasonable, uses the most efficient existing algorithms for each distance and sorting problem. Both textual and graphical output is possible for visualizing the operations. Availability and implementation: The software is ...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Hilker, R., Sickinger, C., Pedersen, C. N. S., Stoye, J. Tags: GENOME ANALYSIS Source Type: research

Bayesian ontology querying for accurate and noise-tolerant semantic searches
We present a method for combining ontological analysis with Bayesian networks to deal with noise, imprecision and attribute frequencies and demonstrate an application of our method as a differential diagnostic support system for human genetics. Availability: We provide an implementation for the algorithm and the benchmark at http://compbio.charite.de/boqa/. Contact: Sebastian.Bauer@charite.de or Peter.Robinson@charite.de Supplementary Information: Supplementary Material for this article is available at Bioinformatics online.
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Bauer, S., Kohler, S., Schulz, M. H., Robinson, P. N. Tags: DATABASES AND ONTOLOGIES Source Type: research

Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data
Conclusion: Meta-Storms method would serve as a suitable database management and search system to quickly identify similar metagenomic samples from a large pool of samples. Contact: ningkang@qibebt.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Su, X., Xu, J., Ning, K. Tags: SYSTEMS BIOLOGY Source Type: research

iBBiG: iterative binary bi-clustering of gene sets
Motivation: Meta-analysis of genomics data seeks to identify genes associated with a biological phenotype across multiple datasets; however, merging data from different platforms by their features (genes) is challenging. Meta-analysis using functionally or biologically characterized gene sets simplifies data integration is biologically intuitive and is seen as having great potential, but is an emerging field with few established statistical methods. Results: We transform gene expression profiles into binary gene set profiles by discretizing results of gene set enrichment analyses and apply a new iterative bi-clustering alg...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Gusenleitner, D., Howe, E. A., Bentink, S., Quackenbush, J., Culhane, A. C. Tags: SYSTEMS BIOLOGY Source Type: research

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks
Motivation: In the context of studying whole metabolic networks and their interaction with the environment, the following question arises: given a set of target metabolites T and a set of possible external source metabolites , which are the minimal subsets of that are able to produce all the metabolites in T. Such subsets are called the minimal precursor sets of T. The problem is then whether we can enumerate all of them efficiently. Results: We propose a new characterization of precursor sets as the inputs of reaction sets called factories and an efficient algorithm to decide if a set of sources is precursor set of T. ...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Acuna, V., Milreu, P. V., Cottret, L., Marchetti-Spaccamela, A., Stougie, L., Sagot, M.-F. Tags: SYSTEMS BIOLOGY Source Type: research

Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification
Motivation: In many situations, genome-wide association studies are performed in populations presenting stratification. Mixed models including a kinship matrix accounting for genetic relatedness among individuals have been shown to correct for population and/or family structure. Here we extend this methodology to generalized linear mixed models which properly model data under various distributions. In addition we perform association with ancestral haplotypes inferred using a hidden Markov model. Results: The method was shown to properly account for stratification under various simulated scenari presenting population and/or...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Zhang, Z., Guillaume, F., Sartelet, A., Charlier, C., Georges, M., Farnir, F., Druet, T. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data
Motivation: Eukaryotic gene expression (GE) is subjected to precisely coordinated multi-layer controls, across the levels of epigenetic, transcriptional and post-transcriptional regulations. Recently, the emerging multi-dimensional genomic dataset has provided unprecedented opportunities to study the cross-layer regulatory interplay. In these datasets, the same set of samples is profiled on several layers of genomic activities, e.g. copy number variation (CNV), DNA methylation (DM), GE and microRNA expression (ME). However, suitable analysis methods for such data are currently sparse. Results: In this article, we introduce...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Li, W., Zhang, S., Liu, C.-C., Zhou, X. J. Tags: GENE EXPRESSION Source Type: research

Deep architectures for protein contact map prediction
Motivation: Residue–residue contact prediction is important for protein structure prediction and other applications. However, the accuracy of current contact predictors often barely exceeds 20% on long-range contacts, falling short of the level required for ab initio structure prediction. Results: Here, we develop a novel machine learning approach for contact map prediction using three steps of increasing resolution. First, we use 2D recursive neural networks to predict coarse contacts and orientations between secondary structure elements. Second, we use an energy-based method to align secondary structure elements an...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Di Lena, P., Nagata, K., Baldi, P. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features
Motivation: The prediction of a protein’s contact map has become in recent years, a crucial stepping stone for the prediction of the complete 3D structure of a protein. In this article, we describe a methodology for this problem that was shown to be successful in CASP8 and CASP9. The methodology is based on (i) the fusion of the prediction of a variety of structural aspects of protein residues, (ii) an ensemble strategy used to facilitate the training process and (iii) a rule-based machine learning system from which we can extract human-readable explanations of the predictor and derive useful information about the co...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Bacardit, J., Widera, P., Marquez-Chamorro, A., Divina, F., Aguilar-Ruiz, J. S., Krasnogor, N. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

Measuring and comparing structural fluctuation patterns in large protein datasets
Motivation: The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of experimental and theoretical work on protein dynamics. Further insight into the dynamics–function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native structure. ...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Fuglebakk, E., Echave, J., Reuter, N. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

TMBB-DB: a transmembrane {beta}-barrel proteome database
Motivation: We previously reported the development of a highly accurate statistical algorithm for identifying β-barrel outer membrane proteins or transmembrane β-barrels (TMBBs), from genomic sequence data of Gram-negative bacteria (Freeman,T.C. and Wimley,W.C. (2010) Bioinformatics, 26, 1965–1974). We have now applied this identification algorithm to all available Gram-negative bacterial genomes (over 600 chromosomes) and have constructed a publicly available, searchable, up-to-date, database of all proteins in these genomes. Results: For each protein in the database, there is information on (i) β-bar...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Freeman, T. C., Wimley, W. C. Tags: SEQUENCE ANALYSIS Source Type: research

YAHA: fast and flexible long-read alignment with optimal breakpoint detection
We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoi...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Faust, G. G., Hall, I. M. Tags: SEQUENCE ANALYSIS Source Type: research

MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks
Summary: We developed MolBioLib to address the need for adaptable next-generation sequencing analysis tools. The result is a compact, portable and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. MolBioLib is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Ohsumi, T. K., Borowsky, M. L. Tags: GENOME ANALYSIS Source Type: research

Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms
Summary: Gibberellic acids (GAs) are key plant hormones, regulating various aspects of growth and development, which have been at the center of the ‘green revolution’. GRAS family proteins, the primary players in GA signaling pathways, remain poorly understood. Using sequence-profile searches, structural comparisons and phylogenetic analysis, we establish that the GRAS family first emerged in bacteria and belongs to the Rossmann fold methyltransferase superfamily. All bacterial and a subset of plant GRAS proteins are likely to function as small-molecule methylases. The remaining plant versions have lost one or ...
Source: Bioinformatics - September 28, 2012 Category: Bioinformatics Authors: Zhang, D., Iyer, L. M., Aravind, L. Tags: SEQUENCE ANALYSIS Source Type: research

Comparative analysis of hemolymph proteome maps in diapausing and non-diapausing larvae of sesamia nonagrioides
Conclusions: The 2-DE proteomic map of S. nonagrioides hemolymph shows differential protein expression in diapausing and non-diapausing larvae. Some proteins that showed higher expression in the diapausing larvae at the end of the sixth instar could be involved in JH level maintenance thus in the diapause status maintenance. On the contrary, other proteins that showed the highest expression or that were expressed only in the non-diapausing larvae could be involved in larval-pupal metamorphosis.
Source: Proteome Science - September 28, 2012 Category: Bioinformatics Authors: Meritxell Perez-HedoIsabel Sanchez-LopezMatilde Eizaguirre Source Type: research

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail
Conclusions: The PIM concept provides a common basis for two modeling formalisms tailored to the study of signaling systems: a quantitative (rule-based) and a qualitative (logical) modeling formalism. Every PIM is a compact specification of a rule-based model and facilitates the systematic set-up of a rule-based model, while at the same time facilitating the automatic generation of a site-specific logical model. Consequently, modifications can be made on the underlying basis and then be propagated into the different model specifications - ensuring consistency of all models, regardless of the modeling formalism. This facili...
Source: BMC Bioinformatics - Latest articles - September 28, 2012 Category: Bioinformatics Authors: Katrin KolczykRegina SamagaHolger ConzelmannSebastian MirschelCarsten Conradi Source Type: research

QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data
Conclusion: We present a pipeline constructed from two new R packages for importing manually gated flow cytometry data and performing flexible and robust quality assessment checks. The pipeline addresses the increasing demand for tools capable of performing quality checks on large flow data sets generated in typical clinical trials.The QUAliFiER tool objectively, efficiently, and reproducibly identifies outlier samples in an automated manner by monitoring cell population statistics from gated or ungated flow data conditioned on experiment-level metadata.
Source: BMC Bioinformatics - Latest articles - September 28, 2012 Category: Bioinformatics Authors: Greg FinakWenxin JiangJorge PardoAdam AsareRaphael Gottardo Source Type: research

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
Conclusions: Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The software is available at http://docpollard.org/software.html
Source: BMC Bioinformatics - Latest articles - September 28, 2012 Category: Bioinformatics Authors: Danielle LemayWilliam MartinAngie HinrichsMonique RijnkelsJ GermanIan KorfKatherine Pollard Source Type: research

HIDEN: Hierarchical decomposition of regulatory networks
Conclusions: Our experiments demonstratethat: (i) Our method gives statistically betterresults than three existing state of the art methods; (ii) Our method is robustagainst errors in the data and (iii) Our method's performance isnot affected by the different topologies in the data
Source: BMC Bioinformatics - Latest articles - September 28, 2012 Category: Bioinformatics Authors: Gunhan GulsoyNirmalya BandhyopadhyayTamer Kahveci Source Type: research

Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs)
Conclusions: MeSHOPs allows quantitative measurement of the degree of association between any entity and the annotated medical concepts, based directly on relevant primary literature. Comparison of MeSHOPs allows entities to be related based on shared medical themes in their literature. A web interface is provided for generating and visualizing MeSHOPs.
Source: BMC Bioinformatics - Latest articles - September 27, 2012 Category: Bioinformatics Authors: Warren CheungBF Francis OuelletteWyeth Wasserman Source Type: research

PrePrint: KungFQ: A Simple and Powerful Approach to Compress Fastq Files
Nowadays storing data derived from deep sequencing experiments has become pivotal and standard compression algorithms do not exploit in a satisfying manner their structure. A number of reference based compression algorithms have been developed but they are less adequate when approaching new species without fully sequenced genomes or non genomic data. We developed a tool that takes advantages of fastq characteristics and encodes them in a binary format optimized in order to be further compressed with standard tools (such as gzip or lzma). The algorithm is straightforward and does not need any external reference file, it sca...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - September 26, 2012 Category: Bioinformatics Source Type: research

Non invasive classification system of scoliosis curve types using least-squares support vector machines
Conclusion: This study shows that it is possible to find a relationship between the internal deformity and the back surface deformity in scoliosis with machine learning methods. The proposed system uses non invasive surface acquisition, which is safe for the patient as it involves no radiation. Also, the design of a specific kernel improved classification performance.
Source: Artificial Intelligence in Medicine - September 26, 2012 Category: Bioinformatics Authors: Mathias M. Adankon, Jean Dansereau, Hubert Labelle, Farida Cheriet Tags: Research Articles Source Type: research

Predicting the difficulty of pure, strict, epistatic models: metrics for simulated model selection
Conclusions: This study formally identifies and evaluates metrics which quantify model detection difficulty. We utilize these metrics to intelligently select models from a population of potential architectures. This allows for an improved simulation study design which accounts for differences in detection difficulty attributed to model architecture. We implement the calculation and utilization of EDM and COR into GAMETES, an algorithm which rapidly and precisely generates pure, strict, n-locus epistatic models.
Source: BioData Mining - September 26, 2012 Category: Bioinformatics Authors: Ryan UrbanowiczJeff KiralisJonathan FisherJason Moore Source Type: research

ESTclean: A Cleaning Tool for Next-Gen Transcriptome Shotgun Sequencing
Conclusions: ESTclean is a software package not only for cleaning cDNA sequences, but also for helping to develop sequencing protocols by providing summary tables and figures for sequencing quality control in a graphical user interface. It outperforms in cleaning read sequences from complicated sequencing protocols which use barcodes and multiple amplification primers.
Source: BMC Bioinformatics - Latest articles - September 26, 2012 Category: Bioinformatics Authors: Hongseok TaeDongsung RyuSuhas SureshchandraJeong-Hyeon Choi Source Type: research

The simulation of meiosis in diploid and tetraploid organisms using various genetic models
Conclusions: This is the first simulation software that implements all features of meiosis in tetraploids. It allows to generate data for tetraploid and diploid populations, and to investigate different models of tetraploid meiosis. The software and manual are available from http://www.plantbreeding.wur.nl/UK/software_pedigreeSim.html and as Additional files 1, 2, 3 and 4 with this publication.
Source: BMC Bioinformatics - Latest articles - September 26, 2012 Category: Bioinformatics Authors: Roeland VoorripsChris Maliepaard Source Type: research

Texture feature ranking with relevance learning to classify interstitial lung disease patterns
Abstract: Objective: The generalized matrix learning vector quantization (GMLVQ) is used to estimate the relevance of texture features in their ability to classify interstitial lung disease patterns in high-resolution computed tomography images.Methodology: After a stochastic gradient descent, the GMLVQ algorithm provides a discriminative distance measure of relevance factors, which can account for pairwise correlations between different texture features and their importance for the classification of healthy and diseased patterns. 65 texture features were extracted from gray-level co-occurrence matrices (GLCMs). These feat...
Source: Artificial Intelligence in Medicine - September 25, 2012 Category: Bioinformatics Authors: Markus B. Huber, Kerstin Bunte, Mahesh B. Nagarajan, Michael Biehl, Lawrence A. Ray, Axel Wismüller Tags: Research Articles Source Type: research

Proteomic identification of MYC2-dependent jasmonate-regulated proteins in Arabidopsis thaliana
Conclusions: We have identified MYC2-dependent jasmonate-regulated proteins in Arabidopsis thaliana by performing two-dimensional gel electrophoresis and MALDI-TOF/TOF MS analysis. The observed pattern of protein expression suggests that MYC2 has opposite effects on the biosynthetic enzymes of indolic and aliphatic glucosinolate pathways and positively regulates JA-mediated carbohydrate metabolism and oxidative stress tolerance-related proteins. Furthermore, it is very interesting to note that MYC2 plays opposite roles in the modulation of a subset of JA-regulated photosynthetic proteins during short-term and long-term JA ...
Source: Proteome Science - September 25, 2012 Category: Bioinformatics Authors: Jing GuoQiuying PangLihua WangPing YuNan LiXiufeng Yan Source Type: research

An algorithm for chemical genomic profiling that minimizes batch effects: Bucket evaluations
Conclusions: BE, along with various correlation methods on a collection of datasets proved to be highly accurate for locating similarity between experiments. BE is a non-parametric correlation approach, which is suitable for locating correlations in somewhat perturbed datasets such as chemical genomic profiles. We created software and a user interface for using BE, which is publically available.
Source: BMC Bioinformatics - Latest articles - September 25, 2012 Category: Bioinformatics Authors: Daniel ShabtaiGuri GiaeverCorey Nislow Source Type: research

ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins
Conclusions: We provide a tool enabling the identification of repetitive elements in precursor ncRNA sequences. ncRNAclassifier is available at http://EvryRNA.ibisc.univ-evry.fr
Source: BMC Bioinformatics - Latest articles - September 25, 2012 Category: Bioinformatics Authors: Sebastien TempelNicolas PolletFariza Tahi Source Type: research

An efficient procedure for protein extraction from formalin-fixed, paraffin-embedded tissues for reverse phase protein arrays
Conclusions: With optimized protein extraction methods, FFPE tissues can be a valuable source in generating reproducible and biologically relevant proteomic profiles using RPPA, with specific marker performance varying according to tissue type.
Source: Proteome Science - September 24, 2012 Category: Bioinformatics Authors: Huifang GuoWenbin LiuZhenlin JuPheroze TamboliEric JonaschGordon MillsYiling LuBryan HennessyDimitra Tsavachidou Source Type: research

Regulatory Network Operations in the Pathway Tools Software
We present algorithms for ranking the degree of regulatory influence of genes , and for computing the net positive and negative regulatory influences on a gene.
Source: BMC Bioinformatics - Latest articles - September 24, 2012 Category: Bioinformatics Authors: Suzanne PaleyMario LatendressePeter Karp Source Type: research

The LO-BaFL method and ALS microarray expression analysis
Conclusion: LO-BaFL predicts DE results that are broadly similar to those of other methods. The small healthy control cohort in the sALS study is a reasonable foundation for predicting DE genes. Modifying the BaFL pipeline allowed us to remove noise and systematic errors, improving the power of this study, which had a small sample size. Each bioinformatics approach revealed DE genes not predicted by the other; subsequent PCR assays confirmed seven of twelve candidates, a relatively high success rate.
Source: BMC Bioinformatics - Latest articles - September 24, 2012 Category: Bioinformatics Authors: Cristina BaciuKevin ThompsonJean-Luc MougeotBenjamin BrooksJennifer Weller Source Type: research

Predicting biological activity: Computational approach using novel distance based molecular descriptors
Abstract: Four novel distance based molecular descriptors termed as superpendentic eccentric distance sum indices 1–4 (denoted by:, , and ) as well as their topochemical counterparts (denoted by:, , and ) have been conceptualized and developed in the present study. The sensitivity towards branching, discriminating power, and degeneracy of the proposed novel descriptors were investigated. Utility of these indices was investigated for development of models through decision tree and moving average analysis for the prediction of human corticotropin releasing factor-1 receptor binding affinity of substituted pyrazines. A wide...
Source: Computers in Biology and Medicine - September 22, 2012 Category: Bioinformatics Authors: R. Dutt, A.K. Madan Source Type: research

Computer-aided techniques for chromogenic immunohistochemistry: Status and directions
Abstract: Although immunohistochemistry (IHC) is a popular imaging technique, the quantitative analysis of IHC images via computer-aided methods is an emerging field that is gaining more and more importance thanks to the new developments in digital high-throughput scanners. In this paper, we discuss the main steps of IHC and review the techniques for computer-aided chromogenic IHC analysis, including methods to determine the location of interest of the antigens and quantify their activations. Moreover, we discuss the issues arising from the standardization of the immunostaining process, that are generally overlooked by the...
Source: Computers in Biology and Medicine - September 22, 2012 Category: Bioinformatics Authors: Santa Di Cataldo, Elisa Ficarra, Enrico Macii Source Type: research

Pattern discovery from patient controlled analgesia demand behavior
Abstract: Unlike previous research on patient controlled analgesia, this study explores patient demand behavior over time. We apply clustering methods to disclose demand patterns among patients over the first 24h of analgesic medication after surgery. We consider demographic, biomedical, and surgery-related data in statistical analyses to determine predictors for patient demand behavior, and use stepwise regression and Bayes risk analysis to evaluate the influence of demand pattern on analgesic requirements. We identify three demand patterns from 1655 patient controlled analgesia request log files. Statistical tests show c...
Source: Computers in Biology and Medicine - September 22, 2012 Category: Bioinformatics Authors: Yuh-Jyh Hu, Tien-Hsiung Ku Source Type: research

HeMoLab – Hemodynamics Modelling Laboratory: An application for modelling the human cardiovascular system
Abstract: In this work we present HeMoLab (Hemodynamics Modeling Laboratory), a computational environment for modeling the Human Cardiovascular System. Its integrates novel computational tools, running from medical image processing to numerical simulation and visualization. As a simulation tool, it allows to accommodate complex physiological and/or pathophysiological (virtual) scenarios aimed to retrieve detailed information from the numerical computations. Such application makes possible to speed up research in the study and analysis of the cardiovascular system and, to provide a virtual laboratory for medical training an...
Source: Computers in Biology and Medicine - September 22, 2012 Category: Bioinformatics Authors: I. Larrabide, P.J. Blanco, S.A. Urquiza, E.A. Dari, M.J. Vénere, N.A. de Souza e Silva, R.A. Feijóo Source Type: research

A multi-physics and multi-scale lumped parameter model of cardiac contraction of the left ventricle: A conceptual model from the protein to the organ scale
Abstract: In cardiovascular computational physiology the importance of understanding cardiac contraction as a multi-scale process is of paramount importance to understand causality across different scales. Within this study, a multi-scale and multi-physics model of the left ventricle that connects the process of cardiac excitation and contraction from the protein to the organ level is presented in a novel way. The model presented here includes the functional description of a cardiomyocyte (cellular scale), which explains the dynamic behaviour of the calcium concentration within the cell whilst an action potential develops....
Source: Computers in Biology and Medicine - September 22, 2012 Category: Bioinformatics Authors: Benjamin Bhattacharya-Ghosh, Silvia Schievano, Vanessa Díaz-Zuccarini Source Type: research

Gene comparison based on the repetition of single-nucleotide structure patterns
Abstract: According to the repetition structure patterns of single-nucleotides, we propose a novel digital representation method to characterize primary DNA sequences. Based on this representation we give a new RP-SP (repeat and space) vector to compute the distance of different sequences. The examination of similarities/dissimilarities among different sequences illustrates the utility of the proposed RP-SP vector distance. Then, we use the proposed RP-SP vector method to analyze two groups of genomes, 15 E. coli genomes and 31 mitochondrial genomes. For comparison, we also apply other alignment-free methods to the two gro...
Source: Computers in Biology and Medicine - September 22, 2012 Category: Bioinformatics Authors: Zhao-Hui Qi, Ming-Hui Du, Xiao-Qin Qi, Li-Juan Zheng Source Type: research

Automation of Food Questionnaires in Medical Studies: A state-of-the-art review and future prospects
Abstract: Applications for automating the most commonly used dietary surveys in nutritional research, Food Frequency Questionnaires (FFQs) and 24h Dietary Recalls (24HDRs), are reviewed in this paper. A comprehensive search of electronic databases was carried out and findings were classified by a group of experts in nutrition and computer science into: (i) Computerized Questionnaires and Web-based Questionnaires; (ii) FFQs and 24HDRs and combinations of both; and (iii) interviewer-administered or self-administered questionnaires. A discussion on the classification made and the works reported is included. Finally, works tha...
Source: Computers in Biology and Medicine - September 22, 2012 Category: Bioinformatics Authors: Zoe Falomir, María Arregui, Francisco Madueño, Dolores Corella, Óscar Coltell Source Type: research