ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Computational Methods, Massively Parallel (Deep) Sequencing, Genomics  (16)
  • 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring  (6)
  • Oxford University Press  (16)
  • Springer  (6)
  • Copernicus
  • Periodicals Archive Online (PAO)
  • 2010-2014  (22)
  • 1960-1964
Collection
Keywords
Publisher
Years
Year
  • 1
    facet.materialart.
    Unknown
    RNASEQR--a streamlined and accurate RNA-seq sequence analysis program (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-29
    Description: Next-generation sequencing (NGS) technologies-based transcriptomic profiling method often called RNA-seq has been widely used to study global gene expression, alternative exon usage, new exon discovery, novel transcriptional isoforms and genomic sequence variations. However, this technique also poses many biological and informatics challenges to extracting meaningful biological information. The RNA-seq data analysis is built on the foundation of high quality initial genome localization and alignment information for RNA-seq sequences. Toward this goal, we have developed RNASEQR to accurately and effectively map millions of RNA-seq sequences. We have systematically compared RNASEQR with four of the most widely used tools using a simulated data set created from the Consensus CDS project and two experimental RNA-seq data sets generated from a human glioblastoma patient. Our results showed that RNASEQR yields more accurate estimates for gene expression, complete gene structures and new transcript isoforms, as well as more accurate detection of single nucleotide variants (SNVs). RNASEQR analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers.
    Keywords: Computational Methods, Massively Parallel (Deep) Sequencing, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    BlackOPs: increasing confidence in variant detection through mappability filtering (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-19
    Description: Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.
    Keywords: Computational Methods, Massively Parallel (Deep) Sequencing, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    Geochemical evidence of the renewal of volcanic activity inferred from CO2 soil and SO2 plume fluxes: the 2007 Stromboli eruption (Italy) (2011)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: On 27 February 2007, a new eruption occurred on Stromboli which lasted until 2 April. It was characterized by effusive activity on the Sciara del Fuoco and by a paroxysmal event (15 March). This crisis represented an opportunity for us to refine the model that had been developed previously (2002–2003 eruption) and to improve our understanding of the relationship between the magmatic dynamics of the volcano and the geochemical variations in the fluids. In particular, the evaluation of the dynamic equilibrium between the volatiles (CO2 and SO2) released from the magma and the corresponding fluids discharged from the summit area allowed us to evaluate the level of criticality of the volcanic activity. One of the major accomplishments of this study is a 4-year database of summit soil CO2 flux on the basis of which we define the thresholds (low–medium–high) for this parameter that are empirically based on the natural volcanological evolution of Stromboli. The SO2 fluxes of the degassing plume and the CO2 fluxes emitted from the soil at Pizzo Sopra la Fossa are also presented. It is noteworthy that geochemical signals of volcanic unrest have been clearly identified before, during and after the effusive activity. These signals were found almost simultaneously in the degassing plume (SO2 flux) and in soil degassing (CO2 flux) at the summit, although the two degassing processes are shown to be clearly different. The interpretation of the results will be useful for future volcanic surveillance at Stromboli.
    Description: Published
    Description: 443-456
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli volcano ; CO2 soil flux ; Geochemical monitoring ; 2007 eruption ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 4
    facet.materialart.
    Unknown
    Towards an Automatic Monitoring System of Infrasonic Events at Mt. Etna: Strategies for Source Location and Modeling (2010)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: Active volcanoes characterized by open conduit conditions generate sonic and infrasonic signals, whose investigation provides useful information for both monitoring purposes and studying the dynamics of explosive processes. In this work, we discuss the automatic procedures implemented for a real-time application to the data acquired by a permanent network of five infrasound stations running at Mt. Etna volcano. The infrasound signals at Mt. Etna consist in amplitude transients, called infrasound events. The adopted procedure uses a multi-algorithm approach for event detection, counting, characterization and location. It is designed for an efficient and accurate processing of infrasound records provided by single-site and array stations. Moreover, the source mechanism of these events can be investigated off-line or in near real-time by using three different models: (1) Strombolian bubble; (2) resonating conduit and (3) Helmholtz resonator. The infrasound waveforms allow us to choose the most suitable model, to get quantitative information about the source and to follow the time evolution of the source parameters.
    Description: Published
    Description: 1215–1231
    Description: 1.4. TTC - Sorveglianza sismologica delle aree vulcaniche attive
    Description: JCR Journal
    Description: reserved
    Keywords: Infrasound ; monitoring system ; Mt. Etna volcano ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 5
    facet.materialart.
    Unknown
    CO2 and He degassing at El Chichón volcano, Chiapas, Mexico: gas flux, origin and relationship with local and regional tectonics (2011)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: During 2007–2008, three CO2 flux surveys were performed on El Chichón volcanic lake, Chiapas, Mexico, with an additional survey in April 2008 covering the entire crater floor (including the lake). The mean CO2 flux calculated by sequential Gaussian simulation from the lake was 1,190 (March 2007), 730 (December 2007) and 1,134 g m−2 day−1 (April 2008) with total emission rates of 164±9.5 (March 2007), 59±2.5 (December 2007) and 109±6.6 t day−1 (April 2008). The mean CO2 flux estimated from the entire crater floor area was 1,102 g m−2 day−1 for April 2008 with a total emission rate of 144±5.9 t day−1. Significant change in CO2 flux was not detected during the period of survey, and the mapping of the CO2 flux highlighted lineaments reflecting the main local and regional tectonic patterns. The 3He/4He ratio (as high as 8.1 RA) for gases in the El Chichón crater is generally higher than those observed at the neighbouring Transmexican Volcanic Belt and the Central American Volcanic Arc. The CO2/3He ratios for the high 3He/4He gases tend to have the MORB-like values (1.41×109), and the CO2/3He ratios for the lower 3He/4He gases fall within the range for the arc-type gases. The high 3He/4He ratios, the MORB-like CO2/3He ratios for the high 3He/4He gases and high proportion of MORB-CO2 (M=25 ±15%) at El Chichón indicate a greater depth for the generation of magma when compared to typical arc volcanoes.
    Description: Published
    Description: 423-441
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: reserved
    Keywords: El Chichon ; CO2 soil flux ; Crater Lake ; Gas geochemistry ; He-C isotopes ; Fumarolic and bubbling gases ; Tectonics ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.05. Geomagnetism::04.05.08. Instruments and techniques ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.01. Geochemical data
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 6
    facet.materialart.
    Unknown
    Geochemical evidence of the renewal of volcanic activity 5 inferred from CO2 soil and SO2 plume fluxes: the 2007 6 Stromboli eruption (Italy) (2011)
    Springer
    Details
    Publication Date: 2020-02-24
    Description: On 27 February 2007, a new eruption occurred on Stromboli which lasted until 2 April. It was characterized by effusive activity on the Sciara del Fuoco and by a paroxysmal event (15 March). This crisis represented an opportunity for us to refine the model that had been developed previously (2002-2003 eruption) and to improve our understanding of the relationship between the magmatic dynamics of the volcano and the geochemical variations in the fluids. In particular, the evaluation of the dynamic equilibrium between the volatiles (CO2 and SO2) released from the magma and the corresponding fluids discharged from the summit area allowed us to evaluate the level of criticality of the volcanic activity. One of the major accomplishments of this study is a four-year database of summit soil CO2 flux on the basis of which we define the thresholds (Low-Medium-High) for this parameter that are empirically based on the natural volcanological evolution of Stromboli. The SO2 fluxes of the degassing plume and the CO2 fluxes emitted from the soil at Pizzo Sopra la Fossa are also presented. Noteworthy geochemical signals of volcanic unrest have been clearly identified before, during, and after the effusive activity. These signals were found almost simultaneously in the degassing plume (SO2 flux) and in soil degassing (CO2 flux) at the summit, although the two degassing processes are shown to be clearly different. The interpretation of the results will be useful for future volcanic surveillance at Stromboli.
    Description: In press
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli Volcano ; CO2 soil flux ; Geochemical monitoring ; 2007 eruption ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.06. Seismology::04.06.10. Instruments and techniques ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 7
    facet.materialart.
    Unknown
    Slug Flow: Modeling in a Conduit and Associated Elastic Radiation (2012)
    Springer
    Details
    Publication Date: 2017-04-03
    Description: Among the eruptive styles, the Strombolian activity is one of the more easy to study because of its repetitive behavior. For this reason large amount of data can be comfortably collected. Strombolian volcanoes are like natural laborato- ries repeating the same experiment (individual explosions) many times each day. The development of quantitative models of eruptive dynamics is driven by the comparison of experimental ob- servations and synthetic data obtained through mathemat- ical, numerical or analogue modeling. Since Strombolian activity offers a profuse amount of interesting seismic signals, during the last decades there has been growing attention on seismological techniques aimed at retrieving the conduit geometry and the eruption dynamics from the seismological recordings. One of these techniques, the source function inversion, is able to re- trieve a summary of the forces acting on the volcanic con- duit during the VLP event generation [5]. The comparison of observed source functions with synthetic ones, obtained through numerical modeling, allow us to put constraints on the proposed models. Quantitative models, able to fit seismological observa- tions, are a powerful tool for interpreting seismic record- ings and therefor the seismological monitoring of active volcanoes.
    Description: Published
    Description: 1.4. TTC - Sorveglianza sismologica delle aree vulcaniche attive
    Description: restricted
    Keywords: Strombolian activity ; Slug flow ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.01. Computational geophysics::05.01.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 8
    facet.materialart.
    Unknown
    First 13C/12C isotopic characterisation of volcanic plume CO2 (2011)
    Springer
    Details
    Publication Date: 2017-04-04
    Description: We describe analytical details and uncertainty evaluation of a simple technique for the measurement of the carbon isotopic composition of CO2 in volcanic plumes. Data collected at Solfatara and Vulcano, where plumes are fed by fumaroles which are accessible for direct sampling, were first used to validate the technique. For both volcanoes, the plume-derived carbon isotopic compositions are in good agreement with the fumarolic compositions, thus providing confidence on the method, and allowing its application at volcanoes where the volcanic component is inaccessible to direct sampling. As a notable example, we applied the same method to Mount Etna where we derived a δ13C of volcanic CO2 between −0.9 ± 0.27‰ and −1.41 ± 0.27‰ (Bocca Nuova and Voragine craters). The comparison of our measurements to data reported in previous work highlights a temporal trend of systematic increase of δ13C values of Etna CO2 from ~ −4‰, in the 1970’s and the 1980’s, to ~ −1‰ at the present time (2009). This shift toward more positive δ13C values matches a concurrent change in magma composition and an increase in the eruption frequency and energy. We discuss such variations in terms of two possible processes: magma carbonate assimilation and carbon isotopic fractionation due to magma degassing along the Etna plumbing system. Finally, our results highlight potential of systematic measurements of the carbon isotopic composition of the CO2 emitted by volcanic plumes for a better understanding of volcanic processes and for improved surveillance of volcanic activity.
    Description: In press
    Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: reserved
    Keywords: Volcanic plume ; Carbon isotope ; Etna ; Magmatic degassing ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 9
    facet.materialart.
    Unknown
    SVM2: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-10
    Description: Several bioinformatics methods have been proposed for the detection and characterization of genomic structural variation (SV) from ultra high-throughput genome resequencing data. Recent surveys show that comprehensive detection of SV events of different types between an individual resequenced genome and a reference sequence is best achieved through the combination of methods based on different principles (split mapping, reassembly, read depth, insert size, etc.). The improvement of individual predictors is thus an important objective. In this study, we propose a new method that combines deviations from expected library insert sizes and additional information from local patterns of read mapping and uses supervised learning to predict the position and nature of structural variants. We show that our approach provides greatly increased sensitivity with respect to other tools based on paired end read mapping at no cost in specificity, and it makes reliable predictions of very short insertions and deletions in repetitive and low-complexity genomic contexts that can confound tools based on split mapping of reads.
    Keywords: Computational Methods, Massively Parallel (Deep) Sequencing, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    Grinder: a versatile amplicon and shotgun sequence simulator (2012)
    Oxford University Press
    Details
    Publication Date: 2012-06-28
    Description: We introduce Grinder ( http://sourceforge.net/projects/biogrinder/ ), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists. Grinder can create sequence libraries with a specific community structure, α and β diversities and experimental biases (e.g. chimeras, gene copy number variation) for commonly used sequencing platforms. This versatility allows the creation of simple to complex read datasets necessary for hypothesis testing when developing bioinformatic software, benchmarking existing tools or designing sequence-based experiments. Grinder is particularly useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.
    Keywords: Computational Methods, Massively Parallel (Deep) Sequencing, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...