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 26.
RFMapp: ribosome flow model application
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Summary: The RFMapp is a graphical user interface application based on the RFM (ribosome flow model), enabling the estimation of the translation elongation rates of messenger ribonucleic acids (mRNAs) and the profile of ribosomal densities along the mRNAs, in a computationally efficient way. The RFMapp is based on the approach previously described by Reuveni et al., and unlike other traditional approaches in the field, which are mainly related to the genes' mean codon translation efficiency, the RFM additionally considers the codon order, the ribosomes' size and their order. Thus, it has been shown that RFM outperforms tra...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Zur, H., Tuller, T. Tags: GENE EXPRESSION Source Type: research
DecoyFinder: an easy-to-use python GUI application for building target-specific decoy setsEmail this article to a colleague.
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Summary: Decoys are molecules that are presumed to be inactive against a target (i.e. will not likely bind to the target) and are used to validate the performance of molecular docking or a virtual screening workflow. The Directory of Useful Decoys database (http://dud.docking.org/) provides a free directory of decoys for use in virtual screening, though it only contains a limited set of decoys for 40 targets.To overcome this limitation, we have developed an application called DecoyFinder that selects, for a given collection of active ligands of a target, a set of decoys from a database of compounds. Decoys are selected if ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Cereto-Massague, A., Guasch, L., Valls, C., Mulero, M., Pujadas, G., Garcia-Vallve, S. Tags: STRUCTURAL BIOINFORMATICS Source Type: research
FindGeo: a tool for determining metal coordination geometryEmail this article to a colleague.
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Summary: Metals are essential for the structure and function of many proteins and nucleic acids. The geometrical arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. At present, however, this information can be retrieved only from the literature, which sometimes contains an improper or incorrect description of the geometry, and often lacks it altogether. Thus, we developed FindGeo to quickly and easily determine the coordination geometry of selected, or all, metals in a given structure. FindGeo works by superimposing the metal-...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Andreini, C., Cavallaro, G., Lorenzini, S. Tags: STRUCTURAL BIOINFORMATICS Source Type: research
DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocolEmail this article to a colleague.
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Summary: A new edition of the DelPhi web server, DelPhi web server v2, is released to include atomic presentation of geometrical figures. These geometrical objects can be used to model nano-size objects together with real biological macromolecules. The position and size of the object can be manipulated by the user in real time until desired results are achieved. The server fixes structural defects, adds hydrogen atoms and calculates electrostatic energies and the corresponding electrostatic potential and ionic distributions.
Availability and implementation: The web server follows a client–server architecture built on...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Smith, N., Witham, S., Sarkar, S., Zhang, J., Li, L., Li, C., Alexov, E. Tags: STRUCTURAL BIOINFORMATICS Source Type: research
Improving the TFold test for differential shotgun proteomicsEmail this article to a colleague.
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We present an updated version of the TFold software for pinpointing differentially expressed proteins in shotgun proteomics experiments. Given an FDR bound, the updated approach uses a theoretical FDR estimator to maximize the number of identifications that satisfy both a fold-change cutoff that varies with the t-test P-value as a power law and a stringency criterion that aims to detect lowly abundant proteins. The new version has yielded significant improvements in sensitivity over the previous one.
Availability: Freely available for academic use at http://pcarvalho.com/patternlab.
Contact: paulo@pcarvalho.com
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Carvalho, P. C., Yates, J. R., Barbosa, V. C. Tags: SEQUENCE ANALYSIS Source Type: research
PSI-Search: iterative HOE-reduced profile SSEARCH searchingEmail this article to a colleague.
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Summary: Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignments are extended into unrelated protein domains—homologous over-extension (HOE). PSI-Search combines an optimal Smith–Waterman local alignment sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy. An optional sequence boundary-masking procedure, which prevents alignments from being extended after they are initially included, can reduce HOE errors in the PSSM profile. Preventing HOE improves se...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Li, W., McWilliam, H., Goujon, M., Cowley, A., Lopez, R., Pearson, W. R. Tags: SEQUENCE ANALYSIS Source Type: research
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence dataEmail this article to a colleague.
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Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ab...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., Drummond, A. Tags: SEQUENCE ANALYSIS Source Type: research
Tachyon search speeds up retrieval of similar sequences by several orders of magnitudeEmail this article to a colleague.
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Summary: The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic.
Availability and implementation: The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP.
Contact: sebastianms@bii.a-star.edu.sg
Supplementary information: Supplementary data are available at the Bioinformatics online.
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Tan, J., Kuchibhatla, D., Sirota, F. L., Sherman, W. A., Gattermayer, T., Kwoh, C. Y., Eisenhaber, F., Schneider, G., Maurer-Stroh, S. Tags: SEQUENCE ANALYSIS Source Type: research
NuST: analysis of the interplay between nucleoid organization and gene expressionEmail this article to a colleague.
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Summary: Different experimental results suggest the presence of an interplay between global transcriptional regulation and chromosome spatial organization in bacteria. The identification and clear visualization of spatial clusters of contiguous genes targeted by specific DNA-binding proteins or sensitive to nucleoid perturbations can elucidate links between nucleoid structure and gene expression patterns. Similarly, statistical analysis to assess correlations between results from independent experiments can provide the integrated analysis needed in this line of research. NuST (Nucleoid Survey tools), based on the Escherich...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Scolari, V. F., Zarei, M., Osella, M., Cosentino Lagomarsino, M. Tags: GENOME ANALYSIS Source Type: research
TSSi--an R package for transcription start site identification from 5' mRNA tag dataEmail this article to a colleague.
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Summary: High-throughput sequencing has become an essential experimental approach for the investigation of transcriptional mechanisms. For some applications like ChIP-seq, several approaches for the prediction of peak locations exist. However, these methods are not designed for the identification of transcription start sites (TSSs) because such datasets contain qualitatively different noise.
In this application note, the R package TSSi is presented which provides a heuristic framework for the identification of TSSs based on 5' mRNA tag data. Probabilistic assumptions for the distribution of the data, i.e. for the observed ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Kreutz, C., Gehring, J. S., Lang, D., Reski, R., Timmer, J., Rensing, S. A. Tags: GENOME ANALYSIS Source Type: research
ChemSpot: a hybrid system for chemical named entity recognitionEmail this article to a colleague.
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We present ChemSpot, a named entity recognition (NER) tool for identifying mentions of chemicals in natural language texts, including trivial names, drugs, abbreviations, molecular formulas and International Union of Pure and Applied Chemistry entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a hybrid approach combining a Conditional Random Field with a dictionary. It achieves an F1 measure of 68.1% on the SCAI corpus, outperforming the only other freely available chemical NER tool, OSCAR4, by 10.8 percentage points.
Availability: ChemSpot is freely avail...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Rocktaschel, T., Weidlich, M., Leser, U. Tags: DATA AND TEXT MINING Source Type: research
Ranking viruses: measures of positional importance within networks define core viruses for rational polyvalent vaccine developmentEmail this article to a colleague.
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Conclusion: Our approach relies on the network structure of PRRSV but applies to any diverse RNA virus because it identifies subsets of viral variants that are most important to overall viral diversity. We suggest that this method, through the objective quantification of variant importance, provides criteria for choosing viral variants for further characterization, diagnostics, surveillance and ultimately polyvalent vaccine development.
Contact: tgoldberg@vetmed.wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Anderson, T. K., Laegreid, W. W., Cerutti, F., Osorio, F. A., Nelson, E. A., Christopher-Hennings, J., Goldberg, T. L. Tags: DATA AND TEXT MINING Source Type: research
Truncated branch and bound achieves efficient constraint-based genetic designEmail this article to a colleague.
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Motivation: Computer-aided genetic design is a promising approach to a core problem of metabolic engineering—that of identifying genetic manipulation strategies that result in engineered strains with favorable product accumulation. This approach has proved to be effective for organisms including Escherichia coli and Saccharomyces cerevisiae, allowing for rapid, rational design of engineered strains. Finding optimal genetic manipulation strategies, however, is a complex computational problem in which running time grows exponentially with the number of manipulations (i.e. knockouts, knock-ins or regulation changes) in ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Egen, D., Lun, D. S. Tags: SYSTEMS BIOLOGY Source Type: research
Stability of gene rankings from RNAi screensEmail this article to a colleague.
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Motivation: Genome-wide RNA interference (RNAi) experiments are becoming a widely used approach for identifying intracellular molecular pathways of specific functions. However, detecting all relevant genes involved in a biological process is challenging, because typically only few samples per gene knock-down are available and readouts tend to be very noisy. We investigate the reliability of top scoring hit lists obtained from RNAi screens, compare the performance of different ranking methods, and propose a new ranking method to improve the reproducibility of gene selection.
Results: The performance of different ranking met...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Siebourg, J., Merdes, G., Misselwitz, B., Hardt, W.-D., Beerenwinkel, N. Tags: SYSTEMS BIOLOGY Source Type: research
On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approachEmail this article to a colleague.
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Motivation: The major function of signal transduction pathways in cells is to sense signals from the environment and process the information through signaling molecules in order to regulate the activity of transcription factors. On the molecular level, the information transmitted by a small number of signal molecules is amplified in the internal signaling pathway through enzyme catalysis, molecular modification and via the activation or inhibition of interactions. However, the dynamic system behavior of a signaling pathway can be complex and, despite knowledge of the pathway components and interactions, it is still a chall...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Chen, B.-S., Wu, C.-C. Tags: SYSTEMS BIOLOGY Source Type: research
optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variantsEmail this article to a colleague.
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Motivation: Existing microarray genotype-calling algorithms adopt either SNP-by-SNP (SNP-wise) or sample-by-sample (sample-wise) approaches to calling. We have developed a novel genotype-calling algorithm for the Illumina platform, optiCall, that uses both SNP-wise and sample-wise calling to more accurately ascertain genotypes at rare, low-frequency and common variants.
Results: Using data from 4537 individuals from the 1958 British Birth Cohort genotyped on the Immunochip, we estimate the proportion of SNPs lost to downstream analysis due to false quality control failures, and rare variants misclassified as monomorphic, i...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Shah, T. S., Liu, J. Z., Floyd, J. A. B., Morris, J. A., Wirth, N., Barrett, J. C., Anderson, C. A. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research
Utilizing RNA-Seq data for de novo coexpression network inferenceEmail this article to a colleague.
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Motivation: RNA-Seq experiments have shown great potential for transcriptome profiling. While sequencing increases the level of biological detail, integrative data analysis is also important. One avenue is the construction of coexpression networks. Because the capacity of RNA-Seq data for network construction has not been previously evaluated, we constructed a coexpression network using striatal samples, derived its network properties and compared it with microarray-based networks.
Results: The RNA-Seq coexpression network displayed scale-free, hierarchical network structure. We detected transcripts groups (modules) with c...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Iancu, O. D., Kawane, S., Bottomly, D., Searles, R., Hitzemann, R., McWeeney, S. Tags: GENE EXPRESSION Source Type: research
A hybrid approach to protein differential expression in mass spectrometry-based proteomicsEmail this article to a colleague.
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Motivation: Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks. However, typical MS-based proteomics datasets have substantial proportions of missing observations, due at least in part to censoring of low intensities. This complicates intensity-based differential expression analysis.
Results: We outline a statistical method for protein differential expression, based on a simple Binomial likelihood. By modeling peak intensities as binary, in terms of ‘presence/absence,’ we enable the selection o...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Wang, X., Anderson, G. A., Smith, R. D., Dabney, A. R. Tags: GENE EXPRESSION Source Type: research
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein trianglesEmail this article to a colleague.
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Motivation: Knowledge about the site at which a ligand binds provides an important clue for predicting the function of a protein and is also often a prerequisite for performing docking computations in virtual drug design and screening. We have previously shown that certain ligand-interacting triangles of protein atoms, called protein triangles, tend to occur more frequently at ligand-binding sites than at other parts of the protein.
Results: In this work, we describe a new ligand-binding site prediction method that was developed based on binding site-enriched protein triangles. The new method was tested on 2 benchmark data...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Xie, Z.-R., Hwang, M.-J. Tags: STRUCTURAL BIOINFORMATICS Source Type: research
Automated gene-model curation using global discriminative learningEmail this article to a colleague.
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Motivation: Gene-model curation creates consensus gene models by combining multiple sources of protein-coding evidence that may be incomplete or inconsistent. To date, manual curation still produces the highest quality models. However, manual curation is too slow and costly to be completed even for the most important organisms. In recent years, machine-learned ensemble gene predictors have become a viable alternative to manual curation. Current approaches make use of signal and genomic region consistency among sources and some voting scheme to resolve conflicts in the evidence. As a further step in that direction, we have ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Bernal, A., Crammer, K., Pereira, F. Tags: SEQUENCE ANALYSIS Source Type: research
MMFPh: a maximal motif finder for phosphoproteomics datasetsEmail this article to a colleague.
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Motivation: Protein phosphorylation, driven by specific recognition of substrates by kinases and phosphatases, plays central roles in a variety of important cellular processes such as signaling and enzyme activation. Mass spectrometry enables the determination of phosphorylated peptides (and thereby proteins) in scenarios ranging from targeted in vitro studies to in vivo cell lysates under particular conditions. The characterization of commonalities among identified phosphopeptides provides insights into the specificities of the kinases involved in a study. Several algorithms have been developed to uncover linear motifs re...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Wang, T., Kettenbach, A. N., Gerber, S. A., Bailey-Kellogg, C. Tags: SEQUENCE ANALYSIS Source Type: research
Estimating the order of mutations during tumorigenesis from tumor genome sequencing dataEmail this article to a colleague.
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Motivation: Tumors are thought to develop and evolve through a sequence of genetic and epigenetic somatic alterations to progenitor cells. Early stages of human tumorigenesis are hidden from view. Here, we develop a method for inferring some aspects of the order of mutational events during tumorigenesis based on genome sequencing data for a set of tumors. This method does not assume that the sequence of driver alterations is the same for each tumor, but enables the degree of similarity or difference in the sequence to be evaluated.
Results: To evaluate the new method, we applied it to colon cancer tumor sequencing data and...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Youn, A., Simon, R. Tags: SEQUENCE ANALYSIS Source Type: research
AUTHOR INDEXEmail this article to a colleague.
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Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Tags: AUTHOR INDEX Source Type: research
Extending ontologies by finding siblings using set expansion techniquesEmail this article to a colleague.
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Motivation: Ontologies are an everyday tool in biomedicine to capture and represent knowledge. However, many ontologies lack a high degree of coverage in their domain and need to improve their overall quality and maturity. Automatically extending sets of existing terms will enable ontology engineers to systematically improve text-based ontologies level by level.
Results: We developed an approach to extend ontologies by discovering new terms which are in a sibling relationship to existing terms of an ontology. For this purpose, we combined two approaches which retrieve new terms from the web. The first approach extracts sib...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Fabian, G., Wachter, T., Schroeder, M. Tags: DATABASES AND ONTOLOGIES Source Type: research
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and lossEmail this article to a colleague.
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We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000-fold speed-up over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous e...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Bansal, M. S., Alm, E. J., Kellis, M. Tags: EVOLUTION AND COMPARATIVE GENOMICS Source Type: research
DACTAL: divide-and-conquer trees (almost) without alignmentsEmail this article to a colleague.
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We present DACTAL, a method for phylogeny estimation that produces trees from unaligned sequence datasets without ever needing to estimate an alignment on the entire dataset. DACTAL combines iteration with a novel divide-and-conquer approach, so that each iteration begins with a tree produced in the prior iteration, decomposes the taxon set into overlapping subsets, estimates trees on each subset, and then combines the smaller trees into a tree on the full taxon set using a new supertree method. We prove that DACTAL is guaranteed to produce the true tree under certain conditions. We compare DACTAL to SATé and maximu...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Nelesen, S., Liu, K., Wang, L.-S., Linder, C. R., Warnow, T. Tags: EVOLUTION AND COMPARATIVE GENOMICS Source Type: research
Fast alignment of fragmentation treesEmail this article to a colleague.
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Motivation: Mass spectrometry allows sensitive, automated and high-throughput analysis of small molecules such as metabolites. One major bottleneck in metabolomics is the identification of ‘unknown’ small molecules not in any database. Recently, fragmentation tree alignments have been introduced for the automated comparison of the fragmentation patterns of small molecules. Fragmentation pattern similarities are strongly correlated with the chemical similarity of the molecules, and allow us to cluster compounds based solely on their fragmentation patterns.
Results: Aligning fragmentation trees is computationally...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Hufsky, F., Duhrkop, K., Rasche, F., Chimani, M., Bocker, S. Tags: MASS SPECTROMETRY AND PROTEOMICS Source Type: research
Matching experiments across species using expression values and textual informationEmail this article to a colleague.
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Motivation: With the vast increase in the number of gene expression datasets deposited in public databases, novel techniques are required to analyze and mine this wealth of data. Similar to the way BLAST enables cross-species comparison of sequence data, tools that enable cross-species expression comparison will allow us to better utilize these datasets: cross-species expression comparison enables us to address questions in evolution and development, and further allows the identification of disease-related genes and pathways that play similar roles in humans and model organisms. Unlike sequence, which is static, expression...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Wise, A., Oltvai, Z. N., Bar-Joseph, Z. Tags: GENE REGULATION AND TRANSCRIPTOMICS Source Type: research
Lineage-based identification of cellular states and expression programsEmail this article to a colleague.
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We present a method, LineageProgram, that uses the developmental lineage relationship of observed gene expression measurements to improve the learning of developmentally relevant cellular states and expression programs. We find that incorporating lineage information allows us to significantly improve both the predictive power and interpretability of expression programs that are derived from expression measurements from in vitro differentiation experiments. The lineage tree of a differentiation experiment is a tree graph whose nodes describe all of the unique expression states in the input expression measurements, and edges...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Hashimoto, T., Jaakkola, T., Sherwood, R., Mazzoni, E. O., Wichterle, H., Gifford, D. Tags: GENE REGULATION AND TRANSCRIPTOMICS Source Type: research
NORMAL: accurate nucleosome positioning using a modified Gaussian mixture modelEmail this article to a colleague.
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Motivation: Nucleosomes are the basic elements of chromatin structure. They control the packaging of DNA and play a critical role in gene regulation by allowing physical access to transcription factors. The advent of second-generation sequencing has enabled landmark genome-wide studies of nucleosome positions for several model organisms. Current methods to determine nucleosome positioning first compute an occupancy coverage profile by mapping nucleosome-enriched sequenced reads to a reference genome; then, nucleosomes are placed according to the peaks of the coverage profile. These methods are quite accurate on placing iso...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Polishko, A., Ponts, N., Le Roch, K. G., Lonardi, S. Tags: GENE REGULATION AND TRANSCRIPTOMICS Source Type: research
Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networksEmail this article to a colleague.
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In this study, we outline a hierarchical, non-parametric Bayesian approach for reverse engineering GRNs using multiple time series that can be applied in a number of novel situations including: (i) where different, but overlapping sets of transcription factors are expected to bind in the different experimental conditions; that is, where switching events could potentially arise under the different treatments and (ii) for inference in evolutionary related species in which orthologous GRNs exist. More generally, the method can be used to identify context-specific regulation by leveraging time series gene expression data along...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Penfold, C. A., Buchanan-Wollaston, V., Denby, K. J., Wild, D. L. Tags: GENE REGULATION AND TRANSCRIPTOMICS Source Type: research
GraphClust: alignment-free structural clustering of local RNA secondary structuresEmail this article to a colleague.
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We present a novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure. The approach scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against known ncRNA datasets and is comparable to state-of-the-art sequence–structure methods although achieving speedups of several orders of magnitude. A selection of applications aiming at the detection of novel structural ncRNAs are presented. Exemplarily, we predicted local structural elements specific to lincRNAs likely functionally associating involved transcr...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Heyne, S., Costa, F., Rose, D., Backofen, R. Tags: SEQUENCE ANALYSIS/RNA Source Type: research
Identification of sequence-structure RNA binding motifs for SELEX-derived aptamersEmail this article to a colleague.
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Motivation: Systematic Evolution of Ligands by EXponential Enrichment (SELEX) represents a state-of-the-art technology to isolate single-stranded (ribo)nucleic acid fragments, named aptamers, which bind to a molecule (or molecules) of interest via specific structural regions induced by their sequence-dependent fold. This powerful method has applications in designing protein inhibitors, molecular detection systems, therapeutic drugs and antibody replacement among others. However, full understanding and consequently optimal utilization of the process has lagged behind its wide application due to the lack of dedicated computa...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Hoinka, J., Zotenko, E., Friedman, A., Sauna, Z. E., Przytycka, T. M. Tags: SEQUENCE ANALYSIS/RNA Source Type: research
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structureEmail this article to a colleague.
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Motivation: The prediction of RNA 3D structures from its sequence only is a milestone to RNA function analysis and prediction. In recent years, many methods addressed this challenge, ranging from cycle decomposition and fragment assembly to molecular dynamics simulations. However, their predictions remain fragile and limited to small RNAs. To expand the range and accuracy of these techniques, we need to develop algorithms that will enable to use all the structural information available. In particular, the energetic contribution of secondary structure interactions is now well documented, but the quantification of non-canoni...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Reinharz, V., Major, F., Waldispuhl, J. Tags: SEQUENCE ANALYSIS/RNA Source Type: research
Weighted pooling--practical and cost-effective techniques for pooled high-throughput sequencingEmail this article to a colleague.
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We describe and study a powerful example of such weighted designs, using non-overlapping pools. We demonstrate that this approach is not only easier to implement and analyze but is also competitive in terms of accuracy with combinatorial designs when identifying rare variants, and is superior when sequencing common variants.
We then discuss how weighting can be incorporated into existing combinatorial designs to increase their accuracy and demonstrate the resulting improvement using simulations. Finally, we argue that weighted designs have enough power to facilitate detection of common alleles, so they can be used as a cor...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Golan, D., Erlich, Y., Rosset, S. Tags: SEQUENCE ANALYSIS Source Type: research
SEQuel: improving the accuracy of genome assembliesEmail this article to a colleague.
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Motivation: Assemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the assembly process. We develop SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model.
Results: SEQuel reduced the number of small insertions and deletions in the assemblies of standard multi-cell Escherichia ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Ronen, R., Boucher, C., Chitsaz, H., Pevzner, P. Tags: SEQUENCE ANALYSIS Source Type: research
Dissect: detection and characterization of novel structural alterations in transcribed sequencesEmail this article to a colleague.
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Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention.
In this article, we introduce two novel algorithmic formulations for identifying transcriptomic structural variants through aligning transcripts to the reference genome under the consideration of such variation. The first formulation is ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Yorukoglu, D., Hach, F., Swanson, L., Collins, C. C., Birol, I., Sahinalp, S. C. Tags: SEQUENCE ANALYSIS Source Type: research
Xenome--a tool for classifying reads from xenograft samplesEmail this article to a colleague.
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We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.
Availability: Xenome is available for non-commercial use from http://www.nicta.com.au/bioinformatics
Contact: tom.conway@nicta.com.au
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Conway, T., Wazny, J., Bromage, A., Tymms, M., Sooraj, D., Williams, E. D., Beresford-Smith, B. Tags: SEQUENCE ANALYSIS Source Type: research
Detection of allele-specific methylation through a generalized heterogeneous epigenome modelEmail this article to a colleague.
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Motivations: High-throughput sequencing has made it possible to sequence DNA methylation of a whole genome at the single-base resolution. A sample, however, may contain a number of distinct methylation patterns. For instance, cells of different types and in different developmental stages may have different methylation patterns. Alleles may be differentially methylated, which may partially explain that the large portions of epigenomes from single cell types are partially methylated, and may have major effects on transcriptional output. Approaches relying on DNA sequence polymorphism to identify individual patterns from a mi...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Peng, Q., Ecker, J. R. Tags: SEQUENCE ANALYSIS Source Type: research
DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autismEmail this article to a colleague.
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Motivation: The understanding of the genetic determinants of complex disease is undergoing a paradigm shift. Genetic heterogeneity of rare mutations with deleterious effects is more commonly being viewed as a major component of disease. Autism is an excellent example where research is active in identifying matches between the phenotypic and genomic heterogeneities. A considerable portion of autism appears to be correlated with copy number variation, which is not directly probed by single nucleotide polymorphism (SNP) array or sequencing technologies. Identifying the genetic heterogeneity of small deletions remains a major ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Aguiar, D., Halldorsson, B. V., Morrow, E. M., Istrail, S. Tags: POPULATION GENOMICS Source Type: research
Incorporating prior information into association studiesEmail this article to a colleague.
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Summary: Recent technological developments in measuring genetic variation have ushered in an era of genome-wide association studies which have discovered many genes involved in human disease. Current methods to perform association studies collect genetic information and compare the frequency of variants in individuals with and without the disease. Standard approaches do not take into account any information on whether or not a given variant is likely to have an effect on the disease. We propose a novel method for computing an association statistic which takes into account prior information. Our method improves both power a...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Darnell, G., Duong, D., Han, B., Eskin, E. Tags: POPULATION GENOMICS Source Type: research
Leveraging input and output structures for joint mapping of epistatic and marginal eQTLsEmail this article to a colleague.
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Motivation: As many complex disease and expression phenotypes are the outcome of intricate perturbation of molecular networks underlying gene regulation resulted from interdependent genome variations, association mapping of causal QTLs or expression quantitative trait loci must consider both additive and epistatic effects of multiple candidate genotypes. This problem poses a significant challenge to contemporary genome-wide-association (GWA) mapping technologies because of its computational complexity. Fortunately, a plethora of recent developments in biological network community, especially the availability of genetic int...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Lee, S., Xing, E. P. Tags: POPULATION GENOMICS Source Type: research
Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learningEmail this article to a colleague.
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Motivation: Recent advances in brain imaging and high-throughput genotyping techniques enable new approaches to study the influence of genetic and anatomical variations on brain functions and disorders. Traditional association studies typically perform independent and pairwise analysis among neuroimaging measures, cognitive scores and disease status, and ignore the important underlying interacting relationships between these units.
Results: To overcome this limitation, in this article, we propose a new sparse multimodal multitask learning method to reveal complex relationships from gene to brain to symptom. Our main contri...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Wang, H., Nie, F., Huang, H., Risacher, S. L., Saykin, A. J., Shen, L., For the Alzheimer's Disease Neuroimaging Initiative Tags: DISEASE MODELS AND EPIDEMIOLOGY Source Type: research
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with diseaseEmail this article to a colleague.
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Motivation: Complex diseases, such as Type 2 Diabetes Mellitus (T2D), result from the interplay of both environmental and genetic factors. However, most studies investigate either the genetics or the environment and there are a few that study their possible interaction in context of disease. One key challenge in documenting interactions between genes and environment includes choosing which of each to test jointly. Here, we attempt to address this challenge through a data-driven integration of epidemiological and toxicological studies. Specifically, we derive lists of candidate interacting genetic and environmental factors ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Patel, C. J., Chen, R., Butte, A. J. Tags: DISEASE MODELS AND EPIDEMIOLOGY Source Type: research
Statistical model-based testing to evaluate the recurrence of genomic aberrationsEmail this article to a colleague.
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This article thus proposes a powerful statistical framework for the identification of driver aberrations, which would be applicable to ever-increasing amounts of cancer genomic data seen in the era of next generation sequencing.
Availability: Our implementations of PART and PART-up are available from http://www.hgc.jp/~niiyan/PART/manual.html.
Contact: aniida@ims.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Niida, A., Imoto, S., Shimamura, T., Miyano, S. Tags: DISEASE MODELS AND EPIDEMIOLOGY Source Type: research
Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scoresEmail this article to a colleague.
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Motivation: The recent development of high-throughput drug profiling (high content screening or HCS) provides a large amount of quantitative multidimensional data. Despite its potentials, it poses several challenges for academia and industry analysts alike. This is especially true for ranking the effectiveness of several drugs from many thousands of images directly. This paper introduces, for the first time, a new framework for automatically ordering the performance of drugs, called fractional adjusted bi-partitional score (FABS). This general strategy takes advantage of graph-based formulations and solutions and avoids ma...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Hochbaum, D. S., Hsu, C.-N., Yang, Y. T. Tags: DISEASE MODELS AND EPIDEMIOLOGY Source Type: research
Minimum message length inference of secondary structure from protein coordinate dataEmail this article to a colleague.
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We report a new method to infer secondary structure based on the Bayesian method of minimum message length inference. It treats assignments of secondary structure as hypotheses that explain the given coordinate data. The method seeks to maximize the joint probability of a hypothesis and the data. There is a natural null hypothesis and any assignment that cannot better it is unacceptable. We developed a program SST based on this approach and compared it with popular programs, such as DSSP and STRIDE among others. Our evaluation suggests that SST gives reliable assignments even on low-resolution structures.
Availability: htt...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Konagurthu, A. S., Lesk, A. M., Allison, L. Tags: PROTEIN STRUCTURE AND FUNCTION Source Type: research
Ranking models of transmembrane {beta}-barrel proteins using Z-coordinate predictionsEmail this article to a colleague.
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Motivation: Transmembrane β-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few β-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful.
Results: Here, we present tobmodel; a method for generating 3D models of β-barrel transmembrane proteins. First, alternativ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Hayat, S., Elofsson, A. Tags: PROTEIN STRUCTURE AND FUNCTION Source Type: research
Recognition models to predict DNA-binding specificities of homeodomain proteinsEmail this article to a colleague.
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Motivation: Recognition models for protein-DNA interactions, which allow the prediction of specificity for a DNA-binding domain based only on its sequence or the alteration of specificity through rational design, have long been a goal of computational biology. There has been some progress in constructing useful models, especially for C2H2 zinc finger proteins, but it remains a challenging problem with ample room for improvement. For most families of transcription factors the best available methods utilize k-nearest neighbor (KNN) algorithms to make specificity predictions based on the average of the specificities of the k ...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Christensen, R. G., Enuameh, M. S., Noyes, M. B., Brodsky, M. H., Wolfe, S. A., Stormo, G. D. Tags: PROTEIN STRUCTURE AND FUNCTION Source Type: research
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteinsEmail this article to a colleague.
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Motivation: Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered regions that bind to protein partners via disorder-to-order transitions. MoRFs are implicated in important processes including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains.
Results: We introduce a new MoRF predictor, MoRFpred, which identifies all MoRF types (α, β, coil and complex). We develop a comprehensive dataset of annotated MoRFs to build...
Source: Bioinformatics - June 11, 2012 Category: Bioinformatics Authors: Disfani, F. M., Hsu, W.-L., Mizianty, M. J., Oldfield, C. J., Xue, B., Dunker, A. K., Uversky, V. N., Kurgan, L. Tags: PROTEIN STRUCTURE AND FUNCTION Source Type: research
