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  • Computational Methods, Genomics  (24)
  • 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring  (13)
  • Oxford University Press  (24)
  • American Geophysical Union  (13)
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  • 1
    Publikationsdatum: 2020-12-14
    Beschreibung: Explosive volcanic eruptions are defined as the violent ejection of gas and hot fragments from a vent in the Earth's crust. Knowledge of ejection velocity is crucial for understanding and modeling relevant physical processes of an eruption, and yet direct measurements are still a difficult task with largely variable results. Here we apply pioneering high-speed imaging to measure the ejection velocity of pyroclasts from Strombolian explosive eruptions with an unparalleled temporal resolution. Measured supersonic velocities, up to 405 m/s, are twice higher than previously reported for such eruptions. Individual Strombolian explosions include multiple, sub-second-lasting ejection pulses characterized by an exponential decay of velocity. When fitted with an empirical model from shock-tube experiments literature, this decay allows constraining the length of the pressurized gas pockets responsible for the ejection pulses. These results directly impact eruption modeling and related hazard assessment, as well as the interpretation of geophysical signals from monitoring networks.
    Beschreibung: INGV-DPC “V2” and “Paroxysm”, FIRB-MIUR “Research and Development of New Technologies for Protection and Defense of Territory from Natural Risks”, and FP7-PEOPLE-IEF-2008 – 235328 Projects
    Beschreibung: Published
    Beschreibung: L02301
    Beschreibung: 3V. Dinamiche e scenari eruttivi
    Beschreibung: JCR Journal
    Beschreibung: open
    Schlagwort(e): strombolian ; ejection velocity ; explosive eruption ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 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::05.02.03. Volcanic eruptions
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2020-12-15
    Beschreibung: We have analyzed a focal mechanism data set for Mount Vesuvius, consisting of 197 focal mechanisms of events recorded from 1999 to 2012. Using different approaches and a comparison between observations and numerical models, we have determined the spatial variations in the stress field beneath the volcano. The main results highlight the presence of two seismogenic volumes characterized by markedly different stress patterns. The two volumes are separated by a layer where the seismic strain release shows a significant decrease. Previous studies postulated the existence, at about the same depth, of a ductile layer allowing the spreading of the Mount Vesuvius edifice. We interpreted the difference in the stress pattern within the two volumes as the effect of a mechanical decoupling caused by the aforementioned ductile layer. The stress pattern in the top volume is dominated by a reverse faulting style, which agrees with the hypothesis of a seismicity driven by the spreading process. This agrees also with the persistent character of the seismicity located within this volume. Conversely, the stress field determined for the deep volume is consistent with a background regional field locally perturbed by the effects of the topography and of heterogeneities in the volcanic structure. Since the seismicity of the deep volume shows an intermittent behavior and has shown to be linked to geochemical variations in the fumaroles of the volcano, we hypothesize that it results from the effect of fluid injection episodes, possibly of magmatic origin, perturbing the pore pressure within the hydrothermal system.
    Beschreibung: Published
    Beschreibung: 1181–1199
    Beschreibung: 4T. Fisica dei terremoti e scenari cosismici
    Beschreibung: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Beschreibung: 5V. Sorveglianza vulcanica ed emergenze
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): vesuvius ; stress inversion ; focal mechanisms ; 04. Solid Earth::04.06. Seismology::04.06.08. Volcano seismology ; 04. Solid Earth::04.06. Seismology::04.06.10. Instruments and techniques ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2017-04-04
    Beschreibung: A new eruption started at Stromboli on August 6, 2014, which had been preceded by 2 months of increased Strombolian activity and several lava overflows from the craters. The eruption was characterized by a lava effusion in Sciara del Fuoco from a fracture at 650 m a.s.l. that lasted until November 13–17. Here we present the first geochemical observations of this eruption, based on the soil CO2 flux in the summit area, and on 3He/4He ratios in the thermal waters near Stromboli village. We infer that this eruption was triggered by the gradual replenishment of the feeding system by a CO2- and 3He-rich magma at the end of 2013 and after June 2014, suggested by the increase in 3He/4He ratio before eruption, which reached its highest value since 2007. We thus infer that this eruption was unusual and we finally speculate on the evolutionary scenario of post eruption.
    Beschreibung: Published
    Beschreibung: 2235–2243
    Beschreibung: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Beschreibung: 3V. Dinamiche e scenari eruttivi
    Beschreibung: 5V. Sorveglianza vulcanica ed emergenze
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): Stromboli ; eruption ; soil CO2 flux ; 3He/4He ratio ; thermal waters ; 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)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2020-02-24
    Beschreibung: This work arises from the field observations made during the civil protection emergency period connected to the 2007 Stromboli eruption. We observed changes in the shallow feeding system of the volcano to which we give a volcanological interpretation and the relative implications. Here we describe the processes that occurred in the upper feeding system from the end of the 2007 effusive eruption on 3 April to the renewal of the strombolian explosive activity at the summit craters (30 June), interpreted using multidisciplinary data. We used thermal camera data collected both from helicopter and from a fixed station at 400 m to retrieve the evolving summit crater activity. These data, compared with seismic signals and published geochemical records, allowed us to detail the shifting of the degassing activity within the crater terrace from NE to SW, occurred between 15 and 25 April 2007 prior to the resumption of the strombolian activity. In particular, from mid-April, a gradual SW displacement in the maximum apparent temperatures was recorded at the vents within the summit craters, together with a change in the very long period location and confirmed by variations in geochemical indicators (CO2∕SO2 plume ratios and CO2 fluxes) from literature. The shallow feeding system experienced a major readjustment after the end of the effusive activity, determining variations in the pressure leakage of the source, slowly deepening and shifting toward SW. All these data, together with the framework supplied by previous structural surveys, allowed us to propose that the compaction of debris accumulated in the uppermost conduit by inward crater collapses, occurred in early March, produced the observed anomalies. At Stromboli, major morphology changes, taking place in the following years, were anticipated by these small and apparently minor processes occurred in the upper feeding system. Other studies are relating similar changes to modifications of the eruptive activity also at other open-conduit volcanoes, so we believe that it may be important to have a constant monitoring of these phenomena in order to better understand their shallow feeding systems.
    Beschreibung: This paper was partially supported by a grant to S.C. (Project INGV-DPC Paroxysm V2/03, 2008–2010) funded by the Istituto Nazionale di Geofisica e Vulcanologia and by the Italian Civil Protection.
    Beschreibung: Published
    Beschreibung: 7376–7395
    Beschreibung: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): Stromboli volcano ; thermal imaging ; multidisciplinary study ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    facet.materialart.
    Unbekannt
    American Geophysical Union
    Publikationsdatum: 2017-04-04
    Beschreibung: An array of nine three-component broadband seismometers was deployed in two different configurations on Stromboli volcano. The analysis of the seismic wavefield related to volcanic explosions revealed some observations which offer a completely new insight into the internal dynamics of a volcano. These new observations are restricted to the low-frequency range below 1 Hz and underline, therefore, the superiority of broadband recordings over conventional short-period observations. Surprisingly simple wavelets indicate an initially contracting source mechanism. Gas-jets that could not be seen in a short-period seismic record at all, generate a clear dilatational wavelet in a broadband recording suggesting the same contracting source mechanism. The analysis of particle motion and seismic array techniques permits a location of the seismic source. We find low-frequency signals of 3s and 6s period that are not related to eruptions and do not share a common source with the eruption-related events. A video recording of visible volcanic activity at the crater region allows one to correlate precisely eruptive features with seismic signals.
    Beschreibung: Published
    Beschreibung: 749-752
    Beschreibung: 5V. Sorveglianza vulcanica ed emergenze
    Beschreibung: N/A or not JCR
    Beschreibung: restricted
    Schlagwort(e): Stromboli ; volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Publikationsdatum: 2017-04-04
    Beschreibung: High-speed imaging of explosive eruptions at Stromboli (Italy), Fuego (Guatemala), and Yasur (Vanuatu) volcanoes allowed visualization of pressure waves from seconds-long explosions. From the explosion jets, waves radiate with variable geometry, timing, and apparent direction and velocity. Both the explosion jets and their wave fields are replicated well by numerical simulations of supersonic jets impulsively released from a pressurized vessel. The scaled acoustic signal from one explosion at Stromboli displays a frequency pattern with an excellent match to those from the simulated jets. We conclude that both the observed waves and the audible sound from the explosions are jet noise, i.e., the typical acoustic field radiating from high-velocity jets. Volcanic jet noise was previously quantified only in the infrasonic emissions from large, sub-Plinian to Plinian eruptions. Our combined approach allows us to define the spatial and temporal evolution of audible jet noise from supersonic jets in small-scale volcanic eruptions.
    Beschreibung: INGV-DPC “V2” and “Paroxysm,” FIRB-MIUR “Research and Development of New Technologies for Protection and Defense of Territory from Natural Risks,” and FP7-PEOPLE-IEF-2008–235328 “NEMOH” ITN projects
    Beschreibung: Published
    Beschreibung: 3096–3102
    Beschreibung: 3V. Dinamiche e scenari eruttivi
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): jet noise ; volcano acoustics ; Stromboli ; Yasur ; Fuego ; strombolian eruption ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 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::05.02.03. Volcanic eruptions
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2017-04-04
    Beschreibung: The fumarolic gas output has not been quantified for any of the currently deforming calderas worldwide, due to the lack of suitable gas flux sensing techniques. In view of resumption of ground uplift (since 2005) and the associated variations in gas chemistry, Campi Flegrei, in southern Italy, is one of the restless calderas where gas flux observations are especially necessary. Here we report the first ever obtained estimate of the Campi Flegrei fumarolic gas output, based on a set of MultiGAS surveys (performed in 2012 and 2013) with an ad-hoc-designed measurement setup. We estimate that the current Campi Flegrei fumarolic sulphur (S) flux is low, on the order of 1.5–2.2 tons/day, suggesting substantial scrubbing of magmatic S by the hydrothermal system. However, the fumarolic carbon dioxide (CO2) output is ∼460±160 tons/day (mean±SD), which is surprisingly high for a dormant volcano in the hydrothermal stage of activity, and results in a combined (fumaroles + soil) CO2 output of ∼1560 tons/day. Assuming magma to be the predominant source, we propose that the current CO2 output can be supplied by either (i) a large (0.6–4.6 km3), deeply stored (〉7 km) magmatic source with low CO2 contents (0.05–0.1 wt%) or (ii) by a small to medium-sized (∼0.01–0.1 km3) but CO2-rich (2 wt%) magma, possibly stored at pressures of ∼100 to 120 MPa. Independent geophysical evidence (e.g., inferred from geodetic and gravity data) is needed to distinguish between these two possibilities.
    Beschreibung: Published
    Beschreibung: 4153–4169
    Beschreibung: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): Campi Flegrei ; calderas ; gas output ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2017-04-04
    Beschreibung: The interpretation of dynamic processes that occur in volcanic calderas is not simple. The ground deformations and the local seismicity, which in other volcanic contexts are usually regarded as precursors to eruption, in caldera environment in many cases are not followed by any eruption. We formulate a general hypothesis that can explain these behaviors. Our hypothesis is that the intrusion of a sill can be responsible for the dynamics observed during unrest at calderas. In order to investigate the reliability of this hypothesis, we developed a dynamic model of sill intrusion in a shallow volcanic environment. In our model, the sill, fed by a deeper magma reservoir, intrudes below a horizontal elastic plate, representing the overlying rocks, and expands with axisymmetric geometry. The model is based on the numerical solution of the equation for the elastic plate, coupled with a Navier-Stokes equation for simulating the dynamics of the sill intrusion. We performed a number of simulations, with the objective of showing the main features of the model. In the experiments, when the feeding process stops, the vertical movement reverses its trend and the area of maximum uplift undergoes subsidence. Under certain conditions the subsidence can occur even during the intrusion of the sill. The stress field produced by the intrusion is mainly concentrated in a circular zone that follows the sill intrusion front. The features predicted by the model are consistent with many observations carried out on different calderas as reported in the scientific literature.
    Beschreibung: Published
    Beschreibung: 3986–4000
    Beschreibung: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Beschreibung: 3V. Dinamiche e scenari eruttivi
    Beschreibung: 5V. Sorveglianza vulcanica ed emergenze
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): sill intrusion ; caldera ; volcano geodesy ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.05. Mathematical geophysics::05.05.99. General or miscellaneous
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Publikationsdatum: 2017-04-04
    Beschreibung: Mt Etna volcano (Italy) typically generates lava fountains and Strombolian eruptions from the summit craters, producing significant emissions of tephra which may cause moderate to high impact both in the atmosphere and on the ground. However, we have also witnessed a number of minor ash emissions that, although far less powerful, may pose considerable volcanic hazards. In this paper, we deal with three ash emissions occurring in 2010 (8 April at Southeast Crater, 25 August at Bocca Nuova, and 14–15 November at Northeast Crater), correlating their volcanological features with the associated seismoacoustic signals. We provide details regarding the chronology, eruption column, dispersal of the deposit, and texture (grain size, componentry and morphology) of the emitted ash. Each eruptive episode has also been characterized by means of seismo-acoustic analyses evaluating the volcanic acoustic-seismic ratio (VASR). Furthermore, the source of volcanic tremor recorded from March to December 2010 was localized. The joint volcanological and seismo-acoustic analyses allowed distinguishing two main kinds of ash emissions: types a (8 April and 25 August) and b (14–15 November). Regarding the former, the accumulation of gas below a dense cap rock obstructing the conduit vent, giving rise, with the uncorking, to impulsive explosivity, was hypothesized. The latter type instead is characterized by a longer-lasting and less explosivity, likely due to the existence of open conduit conditions. Therefore, type b ash emissions are less hazardous than type a. This simple model, regarding minor explosive activity, may constitute a starting point to assess the volcanic risk from unexpected explosions.
    Beschreibung: Published
    Beschreibung: 51-70
    Beschreibung: 3V. Dinamiche e scenari eruttivi
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): Mt Etna ; seismo-acoustic signals ; ash emissions ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Publikationsdatum: 2017-04-04
    Beschreibung: Between January 2011 and April 2013, Mt. Etna's eruptive activity consisted of episodic intra-crater strombolian explosions and paroxysms from Bocca Nuova, Voragine, and the New South-East (NSEC) summit craters, respectively. Eruptions from NSEC consisted of initial increasing strombolian activity and lava flow output, passing to short-lasting lava fountaining. In this study we present seismic, infrasound, radiometric, plume SO2 and HCl fluxes and geodetic data collected by the INGV monitoring system between May 2012 and April 2013. The multi-parametric approach enabled characterization of NSEC eruptive activity at both daily and monthly time scales and tracking of magma movement within Mt. Etna's plumbing system. While seismic, infrasound and radiometric signals give insight on the energy and features of the 13 paroxysms fed by NSEC, SO2 and halogen fluxes shed light on the likely mechanisms triggering the eruptive phenomena. GPS data provided clear evidence of pressurization of Mt. Etna's plumbing system from May 2012 to middle February 2013 and depressurization during the February-April 2013 eruptive activity. Taking into account geochemical data, we propose that the paroxysms' sequence represented the climax of a waxing-waning phase of degassing that had started as early as December 2012, and eventually ended in April 2013. Integration of the multidisciplinary observations suggests that the February-April 2013 eruptive activity reflects a phase of release of a volatile-rich batch of magma that had been stored in the shallow volcano plumbing system at least four months before, and with the majority of gas released between February and March 2013. This article is protected by copyright. All rights reserved.
    Beschreibung: European FP7 MED-SUV (MEditerranean SUpersite Volcanoes). Grant Number: 308665 European Research Council European FP7 (FP/2007-2013)/ERC. Grant Number: 279802 SIGMA (Sistema Integrato di sensori in ambiente cloud per la Gestione Multirischio Avanzata)
    Beschreibung: Published
    Beschreibung: 1932–1949
    Beschreibung: 3V. Dinamiche e scenari eruttivi
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): Mt. Etna ; paroxysmal activity ; SO2 and HCl fluxes ; infrasound and seismic signals ; radiometry ; ground deformation ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 11
    Publikationsdatum: 2017-04-04
    Beschreibung: We present the results of laboratory experiments on the aggregation and disaggregation of colliding volcanic ash particles. Ash particles of different composition and size 〈90 µm were held in turbulent suspension and filmed in high speed while colliding, aggregating, and disaggregating, forming a growing layer of electrostatically bound particles along a vertical plate. At room conditions and regardless of composition, 60–80% of the colliding particles smaller than 32 µm remained aggregated. In contrast, aggregation of particles larger than 63 µm was negligible, and, when a layer formed, periods when disaggregation (mainly by collisions or drag) exceeded aggregation occurred twice as frequently than for smaller particles. An empirical relationship linking the aggregation index, i.e., the effective fraction of aggregated particles surviving disaggregation, to the mean particle collision kinetic energy is provided. Our results have potential implications on the dynamics of volcanic plumes and ash mobility in the environment.
    Beschreibung: INGV-DPC project V1 “Probabilistic evaluation of volcanic hazard”; EU Seventh Programme FP7 “MED-SUV” grant agreement 308665
    Beschreibung: Published
    Beschreibung: 1068–1075
    Beschreibung: 3V. Dinamiche e scenari eruttivi
    Beschreibung: 2IT. Laboratori sperimentali e analitici
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): volcanic ash ; disaggregation ; experimental modeling ; volcanic plumes ; aggregation processes ; colliding particles ; sticking rate ; 01. Atmosphere::01.01. Atmosphere::01.01.07. Volcanic effects ; 04. Solid Earth::04.08. Volcanology::04.08.02. Experimental volcanism ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 12
    Publikationsdatum: 2021-12-15
    Beschreibung: Relationships between frequency and intensity of volcanic eruptions are actively sought by geophysicists for both monitoring and research purposes. By analyzing surveillance videos of persistent volcanic activity at Stromboli (Italy), we derived the frequency and jet height of 〉4000 explosions that occurred in 72 h-long time windows sampled yearly from 2005 to 2009. We found a positive relationship linking explosion frequency and jet height (linked to eruption intensity) when averaging the two parameters over time intervals from hours to days, with a stronger correlation for longer intervals. We interpret this behavior as the response of the magmatic system to variable influx of magma and gas at depth, increased flux at depth causing more frequent and stronger explosions at the surface. This relationship entails concurrent control of source processes over explosion frequency and intensity, directly impacting modeling of explosion sources at persistently active volcanoes in general and hazard assessment at Stromboli in particular.
    Beschreibung: DPC-INGV Project V2 “Paroxysm”
    Beschreibung: Published
    Beschreibung: 1–5
    Beschreibung: 3V. Dinamiche e scenari eruttivi
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): Stromboli ; Strombolian frequency ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 13
    Publikationsdatum: 2023-01-19
    Beschreibung: In situ measurements have been the basis for monitoring volcanic gas emissions for many years and—being complemented by remote sensing techniques—still play an important role to date. Concerning in situ techniques for sampling a dilute plume, an increase in accuracy and a reduction of detection limits are still necessary for most gases (e.g., CO2, SO2, HCl, HF, HBr, HI). In this work, the Raschig-Tube technique (RT) is modified and utilized for application on volcanic plumes. The theoretical and experimental absorption properties of the RT and the Drechsel bottle (DB) setups are characterized and both are applied simultaneously to the well-established Filter packs technique (FP) in the field (on Stromboli Island and Mount Etna). The comparison points out that FPs are the most practical to apply but the results are errorprone compared to RT and DB, whereas the RT results in up to 13 times higher analyte concentrations than the DB in the same sampling time. An optimization of the analytical procedure, including sample pretreatment and analysis by titration, Ion Chromatography, and Inductively Coupled Plasma Mass Spectrometry, led to a comprehensive data set covering a wide range of compounds. In particular, less abundant species were quantified more accurately and iodine was detected for the first time in Stromboli’s plume. Simultaneously applying Multiaxis Differential Optical Absorption Spectroscopy (MAX-DOAS) the chemical transformation of emitted bromide into bromine monoxide (BrO) from Stromboli and Etna was determined to 3–6% and 7%, respectively, within less than 5 min after the gas release from the active vents.
    Beschreibung: Published
    Beschreibung: 2797–2820
    Beschreibung: 5V. Sorveglianza vulcanica ed emergenze
    Beschreibung: JCR Journal
    Beschreibung: restricted
    Schlagwort(e): plume ; volcano ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
    Standort Signatur Erwartet Verfügbarkeit
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  • 14
    Publikationsdatum: 2015-09-19
    Beschreibung: Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data ( 3DBG ), and a 3D genome browser to visualize and explore 3D genome structures ( 3DGB ). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/ .
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 15
    Publikationsdatum: 2015-05-29
    Beschreibung: Identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-specific RNA-seq (ssRNA-seq) datasets collected under two experimental conditions to derive the genomic TU organization of Clostridium thermocellum using a machine-learning approach. Our method accurately predicted the genomic boundaries of individual TUs based on two sets of parameters measuring the RNA-seq expression patterns across the genome: expression-level continuity and variance. A total of 2590 distinct TUs are predicted based on the four RNA-seq datasets. Among the predicted TUs, 44% have multiple genes. We assessed our prediction method on an independent set of RNA-seq data with longer reads. The evaluation confirmed the high quality of the predicted TUs. Functional enrichment analyses on a selected subset of the predicted TUs revealed interesting biology. To demonstrate the generality of the prediction method, we have also applied the method to RNA-seq data collected on Escherichia coli and achieved high prediction accuracies. The TU prediction program named SeqTU is publicly available at https://code.google.com/p/seqtu/ . We expect that the predicted TUs can serve as the baseline information for studying transcriptional and post-transcriptional regulation in C. thermocellum and other bacteria.
    Schlagwort(e): Computational Methods, Genomics
    Print ISSN: 0305-1048
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    Publiziert von Oxford University Press
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  • 16
    Publikationsdatum: 2015-05-29
    Beschreibung: Detecting genetic variation is one of the main applications of high-throughput sequencing, but is still challenging wherever aligning short reads poses ambiguities. Current state-of-the-art variant calling approaches avoid such regions, arguing that it is necessary to sacrifice detection sensitivity to limit false discovery. We developed a method that links candidate variant positions within repetitive genomic regions into clusters. The technique relies on a resource, a thesaurus of genetic variation, that enumerates genomic regions with similar sequence. The resource is computationally intensive to generate, but once compiled can be applied efficiently to annotate and prioritize variants in repetitive regions. We show that thesaurus annotation can reduce the rate of false variant calls due to mappability by up to three orders of magnitude. We apply the technique to whole genome datasets and establish that called variants in low mappability regions annotated using the thesaurus can be experimentally validated. We then extend the analysis to a large panel of exomes to show that the annotation technique opens possibilities to study variation in hereto hidden and under-studied parts of the genome.
    Schlagwort(e): Computational Methods, Genomics
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  • 17
    Publikationsdatum: 2015-05-03
    Beschreibung: Inversion polymorphisms have important phenotypic and evolutionary consequences in humans. Two different methodologies have been used to infer inversions from SNP dense data, enabling the use of large cohorts for their study. One approach relies on the differences in linkage disequilibrium across breakpoints; the other one captures the internal haplotype groups that tag the inversion status of chromosomes. In this article, we assessed the convergence of the two methods in the detection of 20 human inversions that have been reported in the literature. The methods converged in four inversions including inv-8p23, for which we studied its association with low-BMI in American children. Using a novel haplotype tagging method with control on inversion ancestry, we computed the frequency of inv-8p23 in two American cohorts and observed inversion haplotype admixture. Accounting for haplotype ancestry, we found that the European inverted allele in children carries a recessive risk of underweight, validated in an independent Spanish cohort (combined: OR= 2.00, P = 0.001). While the footprints of inversions on SNP data are complex, we show that systematic analyses, such as convergence of different methods and controlling for ancestry, can reveal the contribution of inversions to the ancestral composition of populations and to the heritability of human disease.
    Schlagwort(e): Computational Methods, Genomics
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  • 18
    Publikationsdatum: 2015-05-03
    Beschreibung: The Metabolic Models Reconstruction Using Genome-Scale Information ( merlin ) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin .
    Schlagwort(e): Computational Methods, Genomics
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  • 19
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    Oxford University Press
    Publikationsdatum: 2015-05-03
    Beschreibung: For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen .
    Schlagwort(e): Computational Methods, Genomics
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  • 20
    Publikationsdatum: 2015-05-03
    Beschreibung: Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF–DNA binding specificities (‘motifs’). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF–DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of ~200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays.
    Schlagwort(e): Computational Methods, Genomics
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  • 21
    Publikationsdatum: 2015-06-24
    Beschreibung: Much of the inter-individual variation in gene expression is triggered via perturbations of signaling networks by DNA variants. We present a novel probabilistic approach for identifying the particular pathways by which DNA variants perturb the signaling network. Our procedure, called PINE, relies on a systematic integration of established biological knowledge of signaling networks with data on transcriptional responses to various experimental conditions. Unlike previous approaches, PINE provides statistical aspects that are critical for prioritizing hypotheses for followup experiments. Using simulated data, we show that higher accuracy is attained with PINE than with existing methods. We used PINE to analyze transcriptional responses of immune dendritic cells to several pathogenic stimulations. PINE identified statistically significant genetic perturbations in the pathogen-sensing signaling network, suggesting previously uncharacterized regulatory mechanisms for functional DNA variants.
    Schlagwort(e): Computational Methods, Genomics
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  • 22
    Publikationsdatum: 2015-08-29
    Beschreibung: Variations in sample quality are frequently encountered in small RNA-sequencing experiments, and pose a major challenge in a differential expression analysis. Removal of high variation samples reduces noise, but at a cost of reducing power, thus limiting our ability to detect biologically meaningful changes. Similarly, retaining these samples in the analysis may not reveal any statistically significant changes due to the higher noise level. A compromise is to use all available data, but to down-weight the observations from more variable samples. We describe a statistical approach that facilitates this by modelling heterogeneity at both the sample and observational levels as part of the differential expression analysis. At the sample level this is achieved by fitting a log-linear variance model that includes common sample-specific or group-specific parameters that are shared between genes. The estimated sample variance factors are then converted to weights and combined with observational level weights obtained from the mean–variance relationship of the log-counts-per-million using ‘voom’. A comprehensive analysis involving both simulations and experimental RNA-sequencing data demonstrates that this strategy leads to a universally more powerful analysis and fewer false discoveries when compared to conventional approaches. This methodology has wide application and is implemented in the open-source ‘limma’ package.
    Schlagwort(e): Computational Methods, Genomics
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  • 23
    Publikationsdatum: 2015-08-29
    Beschreibung: Most mammalian genes have mRNA variants due to alternative promoter usage, alternative splicing, and alternative cleavage and polyadenylation. Expression of alternative RNA isoforms has been found to be associated with tumorigenesis, proliferation and differentiation. Detection of condition-associated transcription variation requires association methods. Traditional association methods such as Pearson chi-square test and Fisher Exact test are single test methods and do not work on count data with replicates. Although the Cochran Mantel Haenszel (CMH) approach can handle replicated count data, our simulations showed that multiple CMH tests still had very low power. To identify condition-associated variation of transcription, we here proposed a ranking analysis of chi-squares (RAX2) for large-scale association analysis. RAX2 is a nonparametric method and has accurate and conservative estimation of FDR profile. Simulations demonstrated that RAX2 performs well in finding condition-associated transcription variants. We applied RAX2 to primary T-cell transcriptomic data and identified 1610 (16.3%) tags associated in transcription with immune stimulation at FDR 〈 0.05. Most of these tags also had differential expression. Analysis of two and three tags within genes revealed that under immune stimulation short RNA isoforms were preferably used.
    Schlagwort(e): Computational Methods, Genomics
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  • 24
    Publikationsdatum: 2015-12-16
    Beschreibung: To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of 〉300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, 〉500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (〈25%) of transposon families comprise the majority (〉70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.
    Schlagwort(e): Computational Methods, Genomics
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  • 25
    Publikationsdatum: 2015-04-21
    Beschreibung: Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free ( de novo ) assembly of short overlapping sequence reads into larger contigs. We describe an ensemble strategy that integrates the sequential use of various de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approach. We also proposed new quality metrics that are suitable for evaluating metagenome de novo assembly. We demonstrate that this new ensemble strategy tested using in silico spike-in, clinical and environmental NGS datasets achieved significantly better contigs than current approaches.
    Schlagwort(e): Computational Methods, Genomics
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  • 26
    Publikationsdatum: 2015-04-21
    Beschreibung: Distinguishing between promoter-like sequences in bacteria that belong to true or abortive promoters, or to those that do not initiate transcription at all, is one of the important challenges in transcriptomics. To address this problem, we have studied the genome-reduced bacterium Mycoplasma pneumoniae , for which the RNAs associated with transcriptional start sites have been recently experimentally identified. We determined the contribution to transcription events of different genomic features: the –10, extended –10 and –35 boxes, the UP element, the bases surrounding the –10 box and the nearest-neighbor free energy of the promoter region. Using a random forest classifier and the aforementioned features transformed into scores, we could distinguish between true, abortive promoters and non-promoters with good –10 box sequences. The methods used in this characterization of promoters can be extended to other bacteria and have important applications for promoter design in bacterial genome engineering.
    Schlagwort(e): Computational Methods, Genomics
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  • 27
    Publikationsdatum: 2015-04-21
    Beschreibung: MicroRNAs (miRNAs) are involved in the regulation of gene expression at a post-transcriptional level. As such, monitoring miRNA expression has been increasingly used to assess their role in regulatory mechanisms of biological processes. In large scale studies, once miRNAs of interest have been identified, the target genes they regulate are often inferred using algorithms or databases. A pathway analysis is then often performed in order to generate hypotheses about the relevant biological functions controlled by the miRNA signature. Here we show that the method widely used in scientific literature to identify these pathways is biased and leads to inaccurate results. In addition to describing the bias and its origin we present an alternative strategy to identify potential biological functions specifically impacted by a miRNA signature. More generally, our study exemplifies the crucial need of relevant negative controls when developing, and using, bioinformatics methods.
    Schlagwort(e): Computational Methods, Genomics
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  • 28
    Publikationsdatum: 2015-09-30
    Beschreibung: In cancer research, background models for mutation rates have been extensively calibrated in coding regions, leading to the identification of many driver genes, recurrently mutated more than expected. Noncoding regions are also associated with disease; however, background models for them have not been investigated in as much detail. This is partially due to limited noncoding functional annotation. Also, great mutation heterogeneity and potential correlations between neighboring sites give rise to substantial overdispersion in mutation count, resulting in problematic background rate estimation. Here, we address these issues with a new computational framework called LARVA. It integrates variants with a comprehensive set of noncoding functional elements, modeling the mutation counts of the elements with a β-binomial distribution to handle overdispersion. LARVA, moreover, uses regional genomic features such as replication timing to better estimate local mutation rates and mutational hotspots. We demonstrate LARVA's effectiveness on 760 whole-genome tumor sequences, showing that it identifies well-known noncoding drivers, such as mutations in the TERT promoter. Furthermore, LARVA highlights several novel highly mutated regulatory sites that could potentially be noncoding drivers. We make LARVA available as a software tool and release our highly mutated annotations as an online resource ( larva.gersteinlab.org ).
    Schlagwort(e): Computational Methods, Genomics
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  • 29
    Publikationsdatum: 2015-12-02
    Beschreibung: Alu insertions have contributed to 〉11% of the human genome and ~30–35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means to reconstruct the full sequence of insertion events from Illumina paired end reads. Comparison with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at the cost of reduced sensitivity due to the colocation of reference and non-reference repeats. We generate a highly accurate call set of 1614 completely assembled Alu variants from 53 samples from the Human Genome Diversity Project (HGDP) panel. We utilize the reconstructed alternative insertion haplotypes to genotype 1010 fully assembled insertions, obtaining 〉99% agreement with genotypes obtained by PCR. In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5' truncation in 16% of Alu Ya5 and Alu Yb8 insertions. The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5' truncations. Additionally, we identified variable Alu J and Alu S elements that likely arose due to non-retrotransposition mechanisms.
    Schlagwort(e): Computational Methods, Genomics
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  • 30
    Publikationsdatum: 2015-03-14
    Beschreibung: Mutual information (MI), a quantity describing the nonlinear dependence between two random variables, has been widely used to construct gene regulatory networks (GRNs). Despite its good performance, MI cannot separate the direct regulations from indirect ones among genes. Although the conditional mutual information (CMI) is able to identify the direct regulations, it generally underestimates the regulation strength, i.e. it may result in false negatives when inferring gene regulations. In this work, to overcome the problems, we propose a novel concept, namely conditional mutual inclusive information (CMI2), to describe the regulations between genes. Furthermore, with CMI2, we develop a new approach, namely CMI2NI (CMI2-based network inference), for reverse-engineering GRNs. In CMI2NI, CMI2 is used to quantify the mutual information between two genes given a third one through calculating the Kullback–Leibler divergence between the postulated distributions of including and excluding the edge between the two genes. The benchmark results on the GRNs from DREAM challenge as well as the SOS DNA repair network in Escherichia coli demonstrate the superior performance of CMI2NI. Specifically, even for gene expression data with small sample size, CMI2NI can not only infer the correct topology of the regulation networks but also accurately quantify the regulation strength between genes. As a case study, CMI2NI was also used to reconstruct cancer-specific GRNs using gene expression data from The Cancer Genome Atlas (TCGA). CMI2NI is freely accessible at http://www.comp-sysbio.org/cmi2ni .
    Schlagwort(e): Computational Methods, Genomics
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  • 31
    Publikationsdatum: 2015-04-02
    Beschreibung: High-throughput sequencing of DNA coding regions has become a common way of assaying genomic variation in the study of human diseases. Copy number variation (CNV) is an important type of genomic variation, but detecting and characterizing CNV from exome sequencing is challenging due to the high level of biases and artifacts. We propose CODEX, a normalization and CNV calling procedure for whole exome sequencing data. The Poisson latent factor model in CODEX includes terms that specifically remove biases due to GC content, exon capture and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data. CODEX is compared to existing methods on a population analysis of HapMap samples from the 1000 Genomes Project, and shown to be more accurate on three microarray-based validation data sets. We further evaluate performance on 222 neuroblastoma samples with matched normals and focus on a well-studied rare somatic CNV within the ATRX gene. We show that the cross-sample normalization procedure of CODEX removes more noise than normalizing the tumor against the matched normal and that the segmentation procedure performs well in detecting CNVs with nested structures.
    Schlagwort(e): Computational Methods, Genomics
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  • 32
    Publikationsdatum: 2015-01-10
    Beschreibung: Comprehensive motif discovery under experimental conditions is critical for the global understanding of gene regulation. To generate a nearly complete list of human DNA motifs under given conditions, we employed a novel approach to de novo discover significant co-occurring DNA motifs in 349 human DNase I hypersensitive site datasets. We predicted 845 to 1325 motifs in each dataset, for a total of 2684 non-redundant motifs. These 2684 motifs contained 54.02 to 75.95% of the known motifs in seven large collections including TRANSFAC. In each dataset, we also discovered 43 663 to 2 013 288 motif modules, groups of motifs with their binding sites co-occurring in a significant number of short DNA regions. Compared with known interacting transcription factors in eight resources, the predicted motif modules on average included 84.23% of known interacting motifs. We further showed new features of the predicted motifs, such as motifs enriched in proximal regions rarely overlapped with motifs enriched in distal regions, motifs enriched in 5' distal regions were often enriched in 3' distal regions, etc. Finally, we observed that the 2684 predicted motifs classified the cell or tissue types of the datasets with an accuracy of 81.29%. The resources generated in this study are available at http://server.cs.ucf.edu/predrem/ .
    Schlagwort(e): Computational Methods, Genomics
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  • 33
    Publikationsdatum: 2015-11-17
    Beschreibung: The prediction of novel pre-microRNA (miRNA) from genomic sequence has received considerable attention recently. However, the majority of studies have focused on the human genome. Previous studies have demonstrated that sensitivity (correctly detecting true miRNA) is sustained when human-trained methods are applied to other species, however they have failed to report the dramatic drop in specificity (the ability to correctly reject non-miRNA sequences) in non-human genomes. Considering the ratio of true miRNA sequences to pseudo-miRNA sequences is on the order of 1:1000, such low specificity prevents the application of most existing tools to non-human genomes, as the number of false positives overwhelms the true predictions. We here introduce a framework (SMIRP) for creating species-specific miRNA prediction systems, leveraging sequence conservation and phylogenetic distance information. Substantial improvements in specificity and precision are obtained for four non-human test species when our framework is applied to three different prediction systems representing two types of classifiers (support vector machine and Random Forest), based on three different feature sets, with both human-specific and taxon-wide training data. The SMIRP framework is potentially applicable to all miRNA prediction systems and we expect substantial improvement in precision and specificity, while sustaining sensitivity, independent of the machine learning technique chosen.
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  • 34
    Publikationsdatum: 2015-08-29
    Beschreibung: Statistical network modeling techniques are increasingly important tools to analyze cancer genomics data. However, current tools and resources are not designed to work across multiple diagnoses and technical platforms, thus limiting their applicability to comprehensive pan-cancer datasets such as The Cancer Genome Atlas (TCGA). To address this, we describe a new data driven modeling method, based on generalized Sparse Inverse Covariance Selection (SICS). The method integrates genetic, epigenetic and transcriptional data from multiple cancers, to define links that are present in multiple cancers, a subset of cancers, or a single cancer. It is shown to be statistically robust and effective at detecting direct pathway links in data from TCGA. To facilitate interpretation of the results, we introduce a publicly accessible tool ( cancerlandscapes.org ), in which the derived networks are explored as interactive web content, linked to several pathway and pharmacological databases. To evaluate the performance of the method, we constructed a model for eight TCGA cancers, using data from 3900 patients. The model rediscovered known mechanisms and contained interesting predictions. Possible applications include prediction of regulatory relationships, comparison of network modules across multiple forms of cancer and identification of drug targets.
    Schlagwort(e): Computational Methods, Genomics
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  • 35
    Publikationsdatum: 2015-07-25
    Beschreibung: Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis , rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants. Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/
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  • 36
    Publikationsdatum: 2015-03-01
    Beschreibung: RNA-Seq is gradually becoming the standard tool for transcriptomic expression studies in biological research. Although considerable progress has been recorded in the development of statistical algorithms for the detection of differentially expressed genes using RNA-Seq data, the list of detected genes can differ significantly between algorithms. We present a new method (PANDORA) that combines multiple algorithms toward a summarized result, more efficiently reflecting true experimental outcomes. This is achieved through the systematic combination of several analysis algorithms, by weighting their outcomes according to their performance with realistically simulated data sets generated from real data. Results supported by the analysis of both simulated and real data from different organisms as well as correlation with PolII occupancy demonstrate that PANDORA improves the detection of differential expression. It accomplishes this by optimizing the tradeoff between standard performance measurements, such as precision and sensitivity.
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  • 37
    Publikationsdatum: 2015-02-18
    Beschreibung: We define a new category of candidate tumor drivers in cancer genome evolution: ‘selected expression regulators’ (SERs)—genes driving dysregulated transcriptional programs in cancer evolution. The SERs are identified from genome-wide tumor expression data with a novel method, namely SPARROW ( SPAR se selected exp R essi O n regulators identified W ith penalized regression). SPARROW uncovers a previously unknown connection between cancer expression variation and driver events, by using a novel sparse regression technique. Our results indicate that SPARROW is a powerful complementary approach to identify candidate genes containing driver events that are hard to detect from sequence data, due to a large number of passenger mutations and lack of comprehensive sequence information from a sufficiently large number of samples. SERs identified by SPARROW reveal known driver mutations in multiple human cancers, along with known cancer-associated processes and survival-associated genes, better than popular methods for inferring gene expression networks. We demonstrate that when applied to acute myeloid leukemia expression data, SPARROW identifies an apoptotic biomarker ( PYCARD ) for an investigational drug obatoclax. The PYCARD and obatoclax association is validated in 30 AML patient samples.
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