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  • Computational Methods  (21)
  • 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring  (14)
  • Oxford University Press  (21)
  • American Geophysical Union  (13)
  • INGV  (1)
  • Molecular Diversity Preservation International
  • 2015-2019  (35)
  • 1990-1994
  • 1945-1949
  • 2015  (35)
  • 1
    Publication Date: 2020-12-14
    Description: 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.
    Description: 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
    Description: Published
    Description: L02301
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: open
    Keywords: 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)
    Type: article
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  • 2
    Publication Date: 2020-12-15
    Description: 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.
    Description: Published
    Description: 1181–1199
    Description: 4T. Fisica dei terremoti e scenari cosismici
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: 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)
    Type: article
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  • 3
    Publication Date: 2017-04-04
    Description: 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.
    Description: Published
    Description: 2235–2243
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: 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)
    Type: article
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  • 4
    Publication Date: 2017-04-04
    Description: The marine sector of the Campi Flegrei caldera has started to be monitored over the long-term with a seafloor equipment deployed in the Gulf of Pozzuoli from 2008. The equipment includes a set of geophysical, oceanographic and environmental sensors integrated in a marine platform that was specifically designed for real-time monitoring. This platform, named CUMAS (Cabled Underwater Multidisciplinary Acquisition System), was installed in the center of the Gulf at about 2.5 km south of Pozzuoli where the sea depth is about 100 m [Iannaccone et al., 2010]. The CUMAS system consists of a seafloor module connected by cable to a buoy (elastic beacon type) equipped with autonomous power supply systems, real-time data- transmission devices and a weather station. The core of CUMAS is the seafloor module that contains geophysical and oceanographic sensors, in particular, a three-component broadband seismometer, a best in class three axis MEMS accelerometer, a low-frequency hydrophone and a high-resolution sea bottom pressure recorder. A single-point acoustic, three-component, water-current meter and a water-temperature sensor were also installed to monitor some water local physical parameters. A set of status sensors, which also included a digital compass and a two-component digital tilt-meter, were added to track the attitude of the module over the course of the experiment. The marine monitoring system transmits the data in real-time and is integrated into the Monitoring Center in Naples managed by INGV-Osservatorio Vesuviano. A continuous GPS station has been installed since the end of 2011 on the top of the buoy. The elastic beacon buoy forms a structure which is rigidly connected by a mechanical cable to the ballast on the sea bottom, a submerged float at the base of the buoy maintains tension on the cable and ensure the overall buoyancy of the system. In this way, any vertical movement of the seafloor propagates rigidly to the emerged part of the buoy itself, allowing measurement of the vertical movement of the sea floor by the GPS station. The analysis of about 17 months of continuous GPS data, from January 2012 to May 2013, revealed an overall uplift of about 3-4 cm allowing a first measurement of vertical seafloor displacement in the Campi Flegrei caldera [De Martino et al., 2014]. A new opportunity to enhance the deployed system was given by a national project, EMSO-MedIT, which is providing the necessary resources to expand the data acquisition to other areas of the Gulf of Pozzuoli. New improved systems similar to CUMAS are going to be deployed in three additional marine sites of the Gulf of Pozzuoli and the existing tide gauges network will be renewed with state-of-art sensors. The overall new monitoring infrastructure will allow to extensively map the seafloor vertical displacement and to improve the interpretative models of the bradyseism phenomenon including a more accurate location of earthquakes in the marine areas and extending to lower magnitude values the detection of the seismic activity.
    Description: INGV, Comune di Nicolosi, Parco dell'Etna, Funivia dell'Etna
    Description: Published
    Description: Nicolosi (Catania) -I TALY
    Description: 1IT. Reti di monitoraggio e Osservazioni
    Description: open
    Keywords: Monitoring System in Marine Sector ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Conference paper
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  • 5
    Publication Date: 2020-02-24
    Description: 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.
    Description: 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.
    Description: Published
    Description: 7376–7395
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: 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)
    Type: article
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  • 6
    Publication Date: 2017-04-04
    Description: 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.
    Description: Published
    Description: 749-752
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: N/A or not JCR
    Description: restricted
    Keywords: Stromboli ; volcano seismology ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2017-04-04
    Description: 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.
    Description: 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
    Description: Published
    Description: 3096–3102
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: 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)
    Type: article
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  • 8
    Publication Date: 2017-04-04
    Description: 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.
    Description: Published
    Description: 4153–4169
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: 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)
    Type: article
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  • 9
    Publication Date: 2017-04-04
    Description: 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.
    Description: Published
    Description: 3986–4000
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: 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)
    Type: article
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  • 10
    Publication Date: 2017-04-04
    Description: 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.
    Description: Published
    Description: 51-70
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: reserved
    Keywords: 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)
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  • 11
    Publication Date: 2017-04-04
    Description: 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.
    Description: 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)
    Description: Published
    Description: 1932–1949
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: 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)
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  • 12
    Publication Date: 2017-04-04
    Description: 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.
    Description: INGV-DPC project V1 “Probabilistic evaluation of volcanic hazard”; EU Seventh Programme FP7 “MED-SUV” grant agreement 308665
    Description: Published
    Description: 1068–1075
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 2IT. Laboratori sperimentali e analitici
    Description: JCR Journal
    Description: restricted
    Keywords: 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)
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  • 13
    Publication Date: 2021-12-15
    Description: 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.
    Description: DPC-INGV Project V2 “Paroxysm”
    Description: Published
    Description: 1–5
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; Strombolian frequency ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
    Publication Date: 2023-01-19
    Description: 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.
    Description: Published
    Description: 2797–2820
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: plume ; volcano ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
    Publication Date: 2015-09-19
    Description: Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 16
    Publication Date: 2015-05-29
    Description: Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models.
    Keywords: Computational Methods
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  • 17
    Publication Date: 2015-05-03
    Description: MicroRNAs (miRNAs) regulate gene expression by binding to partially complementary sequences on target mRNA transcripts, thereby causing their degradation, deadenylation, or inhibiting their translation. Genomic variants can alter miRNA regulation by modifying miRNA target sites, and multiple human disease phenotypes have been linked to such miRNA target site variants (miR-TSVs). However, systematic genome-wide identification of functional miR-TSVs is difficult due to high false positive rates; functional miRNA recognition sequences can be as short as six nucleotides, with the human genome encoding thousands of miRNAs. Furthermore, while large-scale clinical genomic data sets are becoming increasingly commonplace, existing miR-TSV prediction methods are not designed to analyze these data. Here, we present an open-source tool called SubmiRine that is designed to perform efficient miR-TSV prediction systematically on variants identified in novel clinical genomic data sets. Most importantly, SubmiRine allows for the prioritization of predicted miR-TSVs according to their relative probability of being functional. We present the results of SubmiRine using integrated clinical genomic data from a large-scale cohort study on chronic obstructive pulmonary disease (COPD), making a number of high-scoring, novel miR-TSV predictions. We also demonstrate SubmiRine's ability to predict and prioritize known miR-TSVs that have undergone experimental validation in previous studies.
    Keywords: Computational Methods
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  • 18
    Publication Date: 2015-01-24
    Description: Of the ~1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ~1300 Alu loci corresponding to detectable transcripts, with ~120 of them expressed in at least three cell lines. In vitro transcription of selected Alu s did not reflect their in vivo expression properties, and required the native 5'-flanking region in addition to internal promoter. We also identified a cluster of expressed Alu Ya5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu -unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alu s nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.
    Keywords: Computational Methods
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  • 19
    Publication Date: 2015-10-15
    Description: Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro , are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein–protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/
    Keywords: Computational Methods
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  • 20
    Publication Date: 2015-04-21
    Description: limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
    Keywords: Computational Methods
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  • 21
    Publication Date: 2015-02-18
    Description: Protein sequences predicted from metagenomic datasets are annotated by identifying their homologs via sequence comparisons with reference or curated proteins. However, a majority of metagenomic protein sequences are partial-length, arising as a result of identifying genes on sequencing reads or on assembled nucleotide contigs, which themselves are often very fragmented. The fragmented nature of metagenomic protein predictions adversely impacts homology detection and, therefore, the quality of the overall annotation of the dataset. Here we present a novel algorithm called GRASP that accurately identifies the homologs of a given reference protein sequence from a database consisting of partial-length metagenomic proteins. Our homology detection strategy is guided by the reference sequence, and involves the simultaneous search and assembly of overlapping database sequences. GRASP was compared to three commonly used protein sequence search programs (BLASTP, PSI-BLAST and FASTM). Our evaluations using several simulated and real datasets show that GRASP has a significantly higher sensitivity than these programs while maintaining a very high specificity. GRASP can be a very useful program for detecting and quantifying taxonomic and protein family abundances in metagenomic datasets. GRASP is implemented in GNU C++, and is freely available at http://sourceforge.net/projects/grasp-release .
    Keywords: Computational Methods
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  • 22
    Publication Date: 2015-02-18
    Description: Genetic screens of an unprecedented scale have recently been made possible by the availability of high-complexity libraries of synthetic oligonucleotides designed to mediate either gene knockdown or gene knockout, coupled with next-generation sequencing. However, several sources of random noise and statistical biases complicate the interpretation of the resulting high-throughput data. We developed HiTSelect, a comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. We document the superior performance of HiTSelect using data from both genome-wide RNAi and CRISPR/Cas9 screens. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration. Binary executables are available at http://sourceforge.net/projects/hitselect/ , and the source code is available at https://github.com/diazlab/HiTSelect .
    Keywords: Computational Methods
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  • 23
    Publication Date: 2015-01-24
    Description: Integrative analyses of epigenetic data promise a deeper understanding of the epigenome. Epidaurus is a bioinformatics tool used to effectively reveal inter-dataset relevance and differences through data aggregation, integration and visualization. In this study, we demonstrated the utility of Epidaurus in validating hypotheses and generating novel biological insights. In particular, we described the use of Epidaurus to (i) integrate epigenetic data from prostate cancer cell lines to validate the activation function of EZH2 in castration-resistant prostate cancer and to (ii) study the mechanism of androgen receptor ( AR ) binding deregulation induced by the knockdown of FOXA1 . We found that EZH2 's noncanonical activation function was reaffirmed by its association with active histone markers and the lack of association with repressive markers. More importantly, we revealed that the binding of AR was selectively reprogramed to promoter regions, leading to the up-regulation of hundreds of cancer-associated genes including EGFR . The prebuilt epigenetic dataset from commonly used cell lines (LNCaP, VCaP, LNCaP-Abl, MCF7, GM12878, K562, HeLa-S3, A549, HePG2) makes Epidaurus a useful online resource for epigenetic research. As standalone software, Epidaurus is specifically designed to process user customized datasets with both efficiency and convenience.
    Keywords: Computational Methods
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  • 24
    Publication Date: 2015-02-18
    Description: RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation. The experimental methods to solve RNA-protein interaction prediction problem remain expensive and time-consuming. Here, we present the RPI-Pred (RNA-protein interaction predictor), a new support-vector machine-based method, to predict protein-RNA interaction pairs, based on both the sequences and structures. The results show that RPI-Pred can correctly predict RNA-protein interaction pairs with ~94% prediction accuracy when using sequence and experimentally determined protein and RNA structures, and with ~83% when using sequences and predicted protein and RNA structures. Further, our proposed method RPI-Pred was superior to other existing ones by predicting more experimentally validated ncRNA-protein interaction pairs from different organisms. Motivated by the improved performance of RPI-Pred, we further applied our method for reliable construction of ncRNA-protein interaction networks. The RPI-Pred is publicly available at: http://ctsb.is.wfubmc.edu/projects/rpi-pred .
    Keywords: Computational Methods
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  • 25
    Publication Date: 2015-02-18
    Description: Identifying conserved and divergent response patterns in gene networks is becoming increasingly important. A common approach is integrating expression information with gene association networks in order to find groups of connected genes that are activated or repressed. In many cases, researchers are also interested in comparisons across species (or conditions). Finding an active sub-network is a hard problem and applying it across species requires further considerations (e.g. orthology information, expression data and networks from different sources). To address these challenges we devised ModuleBlast, which uses both expression and network topology to search for highly relevant sub-networks. We have applied ModuleBlast to expression and interaction data from mouse, macaque and human to study immune response and aging. The immune response analysis identified several relevant modules, consistent with recent findings on apoptosis and NFB activation following infection. Temporal analysis of these data revealed cascades of modules that are dynamically activated within and across species. We have experimentally validated some of the novel hypotheses resulting from the analysis of the ModuleBlast results leading to new insights into the mechanisms used by a key mammalian aging protein.
    Keywords: Computational Methods
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  • 26
    Publication Date: 2015-02-18
    Description: Here we used discriminative training methods to uncover the chromatin, transcription factor (TF) binding and sequence features of enhancers underlying gene expression in individual cardiac cells. We used machine learning with TF motifs and ChIP data for a core set of cardiogenic TFs and histone modifications to classify Drosophila cell-type-specific cardiac enhancer activity. We show that the classifier models can be used to predict cardiac cell subtype cis -regulatory activities. Associating the predicted enhancers with an expression atlas of cardiac genes further uncovered clusters of genes with transcription and function limited to individual cardiac cell subtypes. Further, the cell-specific enhancer models revealed chromatin, TF binding and sequence features that distinguish enhancer activities in distinct subsets of heart cells. Collectively, our results show that computational modeling combined with empirical testing provides a powerful platform to uncover the enhancers, TF motifs and gene expression profiles which characterize individual cardiac cell fates.
    Keywords: Computational Methods
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  • 27
    Publication Date: 2015-09-30
    Description: A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to be defined. The flanking sequences impact the folding of the functional elements both at the level of computational analyses and when the element is extracted as a transcript for experimental analysis. Here, we analyze how different flanking region lengths impact folding into a constrained structure by computing probabilities of folding for different sizes of flanking regions. Our method, RNAcop (RNA context optimization by probability), is tested on known and de novo predicted structures. In vitro experiments support the computational analysis and suggest that for a number of structures, choosing proper lengths of flanking regions is critical. RNAcop is available as web server and stand-alone software via http://rth.dk/resources/rnacop .
    Keywords: Computational Methods
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  • 28
    Publication Date: 2015-10-31
    Description: Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx .
    Keywords: Computational Methods
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  • 29
    Publication Date: 2015-12-02
    Description: Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone.
    Keywords: Computational Methods
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  • 30
    Publication Date: 2015-12-02
    Description: Sequence variations in regulatory DNA regions are known to cause functionally important consequences for gene expression. DNA sequence variations may have an essential role in determining phenotypes and may be linked to disease; however, their identification through analysis of massive genome-wide sequencing data is a great challenge. In this work, a new computational pipeline, a Bayesian method for protein–DNA interaction with binding affinity ranking (BayesPI-BAR), is proposed for quantifying the effect of sequence variations on protein binding. BayesPI-BAR uses biophysical modeling of protein–DNA interactions to predict single nucleotide polymorphisms (SNPs) that cause significant changes in the binding affinity of a regulatory region for transcription factors (TFs). The method includes two new parameters (TF chemical potentials or protein concentrations and direct TF binding targets) that are neglected by previous methods. The new method is verified on 67 known human regulatory SNPs, of which 47 (70%) have predicted true TFs ranked in the top 10. Importantly, the performance of BayesPI-BAR, which uses principal component analysis to integrate multiple predictions from various TF chemical potentials, is found to be better than that of existing programs, such as sTRAP and is-rSNP, when evaluated on the same SNPs. BayesPI-BAR is a publicly available tool and is able to carry out parallelized computation, which helps to investigate a large number of TFs or SNPs and to detect disease-associated regulatory sequence variations in the sea of genome-wide noncoding regions.
    Keywords: Computational Methods
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  • 31
    Publication Date: 2015-03-14
    Description: The rapid discovery of potential driver mutations through large-scale mutational analyses of human cancers generates a need to characterize their cellular phenotypes. Among the techniques for genome editing, recombinant adeno-associated virus (rAAV)-mediated gene targeting is suited for knock-in of single nucleotide substitutions and to a lesser degree for gene knock-outs. However, the generation of gene targeting constructs and the targeting process is time-consuming and labor-intense. To facilitate rAAV-mediated gene targeting, we developed the first software and complementary automation-friendly vector tools to generate optimized targeting constructs for editing human protein encoding genes. By computational approaches, rAAV constructs for editing ~71% of bases in protein-coding exons were designed. Similarly, ~81% of genes were predicted to be targetable by rAAV-mediated knock-out. A Gateway-based cloning system for facile generation of rAAV constructs suitable for robotic automation was developed and used in successful generation of targeting constructs. Together, these tools enable automated rAAV targeting construct design, generation as well as enrichment and expansion of targeted cells with desired integrations.
    Keywords: Computational Methods
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  • 32
    Publication Date: 2015-03-14
    Description: Degenerate codon (DC) libraries efficiently address the experimental library-size limitations of directed evolution by focusing diversity toward the positions and toward the amino acids (AAs) that are most likely to generate hits; however, manually constructing DC libraries is challenging, error prone and time consuming. This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit, improving on the existing integer-linear programming formulation. It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library. In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits. Surprisingly, the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1; it effectively side-steps the degeneracy of the genetic code. Our algorithm is freely available through our web server and solves most design problems in about a second.
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  • 33
    Publication Date: 2015-01-10
    Description: Transcription regulation in multicellular eukaryotes is orchestrated by a number of DNA functional elements located at gene regulatory regions. Some regulatory regions (e.g. enhancers) are located far away from the gene they affect. Identification of distal regulatory elements is a challenge for the bioinformatics research. Although existing methodologies increased the number of computationally predicted enhancers, performance inconsistency of computational models across different cell-lines, class imbalance within the learning sets and ad hoc rules for selecting enhancer candidates for supervised learning, are some key questions that require further examination. In this study we developed DEEP, a novel ensemble prediction framework. DEEP integrates three components with diverse characteristics that streamline the analysis of enhancer's properties in a great variety of cellular conditions. In our method we train many individual classification models that we combine to classify DNA regions as enhancers or non-enhancers. DEEP uses features derived from histone modification marks or attributes coming from sequence characteristics. Experimental results indicate that DEEP performs better than four state-of-the-art methods on the ENCODE data. We report the first computational enhancer prediction results on FANTOM5 data where DEEP achieves 90.2% accuracy and 90% geometric mean (GM) of specificity and sensitivity across 36 different tissues. We further present results derived using in vivo -derived enhancer data from VISTA database. DEEP-VISTA, when tested on an independent test set, achieved GM of 80.1% and accuracy of 89.64%. DEEP framework is publicly available at http://cbrc.kaust.edu.sa/deep/ .
    Keywords: Computational Methods
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  • 34
    Publication Date: 2015-11-17
    Description: Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/ .
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  • 35
    Publication Date: 2015-07-25
    Description: The cMonkey integrated biclustering algorithm identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of gene co-regulation, and optimizes biclusters to be supported simultaneously by one or more of these prior constraints. The algorithm served as the cornerstone for constructing the first global, predictive Environmental Gene Regulatory Influence Network (EGRIN) model for a free-living cell, and has now been applied to many more organisms. However, due to its computational inefficiencies, long run-time and complexity of various input data types, cMonkey was not readily usable by the wider community. To address these primary concerns, we have significantly updated the cMonkey algorithm and refactored its implementation, improving its usability and extendibility. These improvements provide a fully functioning and user-friendly platform for building co-regulated gene modules and the tools necessary for their exploration and interpretation. We show, via three separate analyses of data for E. coli, M. tuberculosis and H. sapiens , that the updated algorithm and inclusion of novel scoring functions for new data types (e.g. ChIP-seq and transcription factor over-expression [TFOE]) improve discovery of biologically informative co-regulated modules. The complete cMonkey 2 software package, including source code, is available at https://github.com/baliga-lab/cmonkey2 .
    Keywords: Computational Methods
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