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  • Computational Methods, Genomics  (140)
  • 04. Solid Earth::04.04. Geology::04.04.09. Structural geology
  • JSTOR Archive Collection Business II
  • Oxford University Press  (145)
  • Wiley  (6)
  • 1
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    Reply to: Comment on ‘Insights from the Mw 6.3, 2009 L’Aquila earthquake (central Apennines) - Unveiling new seismogenic sources through their surface signatures: the adjacent San Pio Fault’ (2011)
    Wiley
    Details
    Publikationsdatum: 2017-04-04
    Beschreibung: We reply to a comment by Messina et al., who strongly criticized our paper on the San Pio Fault, by showing that in areas of complex geology such as the central Apennines, where the current tectonic setting results from the superposition of different tectonic regimes, the equation: “most visible active fault = major seismogenic fault” can be misleading.
    Beschreibung: Published
    Beschreibung: 421-423
    Beschreibung: 3.2. Tettonica attiva
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): Seismotectonics ; morphotectonics ; active fault ; San Pio basin ; 04. Solid Earth::04.04. Geology::04.04.01. Earthquake geology and paleoseismology ; 04. Solid Earth::04.04. Geology::04.04.03. Geomorphology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 2
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    UPb and 40Ar39Ar geochronology of Palaeozoic units in the northern Apennines: determining protolith age and alpine evolution using the Calamita Schist and Ortano Porphyroid (2012)
    Wiley
    Details
    Publikationsdatum: 2017-04-04
    Beschreibung: In the northern Apennines, the Palaeozoic basement involved in the Late Oligocene–Middle Miocene nappe stack contains metamorphic units for which hypothetical ages have been assigned on the basis of lithological correlations with the Palaeozoic formations of the Variscan chain in Sardinia. This uncertainty concerning the age poses limitations to reconstructing the Palaeozoic stratigraphy, defining the Alpine and pre-Alpine histories and correlations with other domains of the Variscan chain. We present the UPb age of detrital zircon and the 40Ar39Ar age of metamorphic muscovite for the Calamita Schist and Ortano Porphyroid, two metamorphic units of undetermined Palaeozoic age cropping out in the eastern Elba Island. The radioisotopic data allows us to: (i) define the Early Carboniferous and Middle Ordovician ages for the Calamita Schist and Ortano Porphyroid, respectively, as well as their derivation (flysch deposit and magmatic rocks); (ii) pose some constraints concerning their alpine tectonic and metamorphic histories. These new data generate a more precise reconstruction of the Palaeozoic sequence in the northern Apennines, and they document that the Palaeozoic basement involved in the alpine deformation underwent internal stacking with an inversion of the original sequence. Copyright © 2010 John Wiley & Sons, Ltd.
    Beschreibung: Published
    Beschreibung: 288-310
    Beschreibung: 3.2. Tettonica attiva
    Beschreibung: 3.3. Geodinamica e struttura dell'interno della Terra
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): northern Apennines ; Palaeozoic basement ; U-Pb zircon ; 40Ar-39Ar muscovite ; 04. Solid Earth::04.04. Geology::04.04.02. Geochronology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 3
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    U-Pb and 40Ar-39Ar geochronology of Palaeozoic units in the northern Apennines: determining protolith age and alpine evolution using the Calamita Schist and Ortano Porphyroid (2011)
    Wiley
    Details
    Publikationsdatum: 2017-04-04
    Beschreibung: In the northern Apennines, the Palaeozoic basement involved in the Late Oligocene–Middle Miocene nappe stack contains metamorphic units for which hypothetical ages have been assigned on the basis of lithological correlations with the Palaeozoic formations of the Variscan chain in Sardinia. This uncertainty concerning the age poses limitations to reconstructing the Palaeozoic stratigraphy, defining the Alpine and pre-Alpine histories and correlations with other domains of the Variscan chain. We present the U-Pb age of detrital zircon and the 40Ar-39Ar age of metamorphic muscovite for the Calamita Schist and Ortano Porphyroid, two metamorphic units of undetermined Palaeozoic age cropping out in the eastern Elba Island. The radioisotopic data allows us to: (i) define the Early Carboniferous and Middle Ordovician ages for the Calamita Schist and Ortano Porphyroid, respectively, as well as their derivation (flysch deposit and magmatic rocks); (ii) pose some constraints concerning their alpine tectonic and metamorphic histories. These new data generate a more precise reconstruction of the Palaeozoic sequence in the northern Apennines, and they document that the Palaeozoic basement involved in the alpine deformation underwent internal stacking with an inversion of the original sequence.
    Beschreibung: In press
    Beschreibung: 3.2. Tettonica attiva
    Beschreibung: 3.3. Geodinamica e struttura dell'interno della Terra
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): northern Apennines ; Palaeozoic basement ; U-Pb zircon ; 40Ar-39Ar muscovite ; 04. Solid Earth::04.04. Geology::04.04.02. Geochronology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 4
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    Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform (2017)
    Oxford University Press
    Details
    Publikationsdatum: 2017-01-10
    Beschreibung: Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 5
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    Methods to increase reproducibility in differential gene expression via meta-analysis (2017)
    Oxford University Press
    Details
    Publikationsdatum: 2017-01-10
    Beschreibung: Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size.
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 6
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    RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data (2016)
    Oxford University Press
    Details
    Publikationsdatum: 2016-12-17
    Beschreibung: We introduce RNA2DNAlign, a computational framework for quantitative assessment of allele counts across paired RNA and DNA sequencing datasets. RNA2DNAlign is based on quantitation of the relative abundance of variant and reference read counts, followed by binomial tests for genotype and allelic status at SNV positions between compatible sequences. RNA2DNAlign detects positions with differential allele distribution, suggesting asymmetries due to regulatory/structural events. Based on the type of asymmetry, RNA2DNAlign outlines positions likely to be implicated in RNA editing, allele-specific expression or loss, somatic mutagenesis or loss-of-heterozygosity (the first three also in a tumor-specific setting). We applied RNA2DNAlign on 360 matching normal and tumor exomes and transcriptomes from 90 breast cancer patients from TCGA. Under high-confidence settings, RNA2DNAlign identified 2038 distinct SNV sites associated with one of the aforementioned asymetries, the majority of which have not been linked to functionality before. The performance assessment shows very high specificity and sensitivity, due to the corroboration of signals across multiple matching datasets. RNA2DNAlign is freely available from http://github.com/HorvathLab/NGS as a self-contained binary package for 64-bit Linux systems.
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 7
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    Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks (2016)
    Oxford University Press
    Details
    Publikationsdatum: 2016-12-01
    Beschreibung: Module identification is a frequently used approach for mining local structures with more significance in global networks. Recently, a wide variety of bilayer networks are emerging to characterize the more complex biological processes. In the light of special topological properties of bilayer networks and the accompanying challenges, there is yet no effective method aiming at bilayer module identification to probe the modular organizations from the more inspiring bilayer networks. To this end, we proposed the pseudo-3D clustering algorithm, which starts from extracting initial non-hierarchically organized modules and then iteratively deciphers the hierarchical organization of modules according to a bottom-up strategy. Specifically, a modularity function for bilayer modules was proposed to facilitate the algorithm reporting the optimal partition that gives the most accurate characterization of the bilayer network. Simulation studies demonstrated its robustness and outperformance against alternative competing methods. Specific applications to both the soybean and human miRNA-gene bilayer networks demonstrated that the pseudo-3D clustering algorithm successfully identified the overlapping, hierarchically organized and highly cohesive bilayer modules. The analyses on topology, functional and human disease enrichment and the bilayer subnetwork involved in soybean fat biosynthesis provided both the theoretical and biological evidence supporting the effectiveness and robustness of pseudo-3D clustering algorithm.
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 8
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    Finding approximate gene clusters with GECKO 3 (2016)
    Oxford University Press
    Details
    Publikationsdatum: 2016-12-01
    Beschreibung: Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in 〈40 min.
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 9
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    NanoStringDiff: a novel statistical method for differential expression analysis based on NanoString nCounter data (2016)
    Oxford University Press
    Details
    Publikationsdatum: 2016-12-01
    Beschreibung: The advanced medium-throughput NanoString nCounter technology has been increasingly used for mRNA or miRNA differential expression (DE) studies due to its advantages including direct measurement of molecule expression levels without amplification, digital readout and superior applicability to formalin fixed paraffin embedded samples. However, the analysis of nCounter data is hampered because most methods developed are based on t-tests, which do not fit the count data generated by the NanoString nCounter system. Furthermore, data normalization procedures of current methods are either not suitable for counts or not specific for NanoString nCounter data. We develop a novel DE detection method based on NanoString nCounter data. The method, named NanoStringDiff, considers a generalized linear model of the negative binomial family to characterize count data and allows for multifactor design. Data normalization is incorporated in the model framework through data normalization parameters, which are estimated from positive controls, negative controls and housekeeping genes embedded in the nCounter system. We propose an empirical Bayes shrinkage approach to estimate the dispersion parameter in the model and a likelihood ratio test to identify differentially expressed genes. Simulations and real data analysis demonstrate that the proposed method performs better than existing methods.
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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  • 10
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    Global transcript structure resolution of high gene density genomes through multi-platform data integration (2016)
    Oxford University Press
    Details
    Publikationsdatum: 2016-10-14
    Beschreibung: Annotation of herpesvirus genomes has traditionally been undertaken through the detection of open reading frames and other genomic motifs, supplemented with sequencing of individual cDNAs. Second generation sequencing and high-density microarray studies have revealed vastly greater herpesvirus transcriptome complexity than is captured by existing annotation. The pervasive nature of overlapping transcription throughout herpesvirus genomes, however, poses substantial problems in resolving transcript structures using these methods alone. We present an approach that combines the unique attributes of Pacific Biosciences Iso-Seq long-read, Illumina short-read and deepCAGE (Cap Analysis of Gene Expression) sequencing to globally resolve polyadenylated isoform structures in replicating Epstein-Barr virus (EBV). Our method, Transcriptome Resolution through Integration of Multi-platform Data (TRIMD), identifies nearly 300 novel EBV transcripts, quadrupling the size of the annotated viral transcriptome. These findings illustrate an array of mechanisms through which EBV achieves functional diversity in its relatively small, compact genome including programmed alternative splicing (e.g. across the IR1 repeats), alternative promoter usage by LMP2 and other latency-associated transcripts, intergenic splicing at the BZLF2 locus, and antisense transcription and pervasive readthrough transcription throughout the genome.
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
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