1,721,026 research outputs found
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MicrobesOnline: an integrated portal for comparative and functional genomics
Full text linkSince 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html
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ESPP Computational Core Overview
Full text linkBackground: The VIMSS Computational Core group is responsible for data management, data integration, data analysis, and comparative and evolutionary genomic analysis of the data for the VIMSS project. We have expanded and extended our existing tools sets for comparative and evolutionary genomics and microarray analysis as well as creating new tools for our proteomic and metabolomic data sets. Our analysis has been incorporated into our comparative genomics website MicrobesOnline (http://www.microbesonline.org) and made available to the wider research community. By taking advantage of the diverse functional and comparative datasets, we have been able to pursue large evolutionary studies. Data Analysis: During the course of analysis of various stress responses of DvH, the computational core has continued to develop new statistical analyses of data that take advantage of the predicted regulatory structures (operons, regulons, etc.) from our comparative analyses. This year we have used these analyses to investigate the response of DvH to oxygen stress and pH stress. Our analysis has focused on the combined results from both transcriptomic and proteomic datasets to interpret oxygen stress. Additionally, we have worked with metabolomic datasets within the framework of predicted metabolic activities to find missing pathway members. Data Management: All data generated by ESPP continues to be stored in our Experimental Information and Data Repository (http://vimss.lbl.gov/EIDR/). Researches have access to datasets from biomass production, growth curves, image data, mass spec data, phenotype microarray data and transcriptomic, proteomic and metabolomic data. New functionality has been added for storage of information relating to mutants and protein complex data, in addition to new visualization for assessing existing data sets such as the phenotype microarrays. The MicrobesOnline Database: The MicrobesOnline database (http://www.microbesonline.org) currently holds over 700 microbial genomes and will be updated quarterly, providing an important comparative genomics resource to the community. New functionality added this year includes the addition of a thousands of phage genomes and plasmids, an updated user interface for the phylogenetic tree based genome browser that allows users to view their genes and genomes of interest within an evolutionary framework, tools to compare multiple microarray expression data across genes and genomes, addition of external microarray data from the Many Microbial Microarrays Database, integration with the RegTransBase of experimentally verified regulatory binding sites and links to three dimensional protein structures of proteins and their close relatives. MicrobesOnline continues to provide an interface for genome annotation, which like all the tools reported here, is freely available to the scientific community. To keep up with the rapidly expanding set of sequenced genomes, we have begun to investigate methods for accelerating our annotation pipeline. In particular we have completed work on methods to speed up the most time consuming process, homology searching through HMM alignments and all against all BLAST. These methods now enable us to deal with the many millions of gene sequences generated from metagenomics. Over the next year, several new features will be added to the MicrobesOnline resource. Microarray expression data will be added from the NCBI GEO database, in addition to datasets generated from the VIMSS team. To supplement the analysis tools we already have, enrichment of functional genes and operon-wise analysis, we will provide tools for comparing multiple experiments across multiple genomes. We will also expand our regulatory binding motif search to incorporate co-expression data to support predictions. Evolutionary Analysis: The computational core continues work on understanding the evolution of regulatory networks. Transcription factors form large par
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Comparative Sequencing and Analysis of Multiple Desulfovibrio and Other Sulfate Reducing Species
Full text linkAs part of the work being done for the DOE GTL:Genomics program, the Virtual Institute for Microbial Stress and Survival (VIMSS) is sequencing multiple relatives of the environmental microbe Desulfovibrio vulgaris Hildenborough at several phylogenetic levels to aide in the analysis and annotation, as well as understanding larger questions of sulfate reduction and environmental stress response. We have sought to balance the selection of species based on the resources available for each species and the phylogenetic position the species occupies. By sequencing multiple Desulfovibrio species, we will be able to improve our predictions for genes, regulons, operons, regulatory elements, core genes, and environmental stress response genes. Sequenced genomes so far include: Desulfovibrio aespoeensis, Desulfovibrio vulgaris Miyazaki F, Desulfovibrio hanfordensis, Desulfovibrio sp. FW1012B, Desulfovibrio vulgaris DP4, Desulfovibrio vulgaris RCH1, Desulfovibrio salexigens DSM 2638, Desulfovibrio fructosovorans, Desulfovibrio desulfuricans 27774 and Desulforudis audaxviator. Environmental isolates, such as D. FW1012B, D. hanfordensis, DvDP4, DvRCH1 are critical for understanding the DOE field research sites. Other species such as D. aespoeensis play a role in geochemical radionuclei migration in the deep sub-surface. Here we describe our initial analysis of Desulfovibrio species
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate Genome
Full text linkThe hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish-tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of 4-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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