Marco Antonio Tangaro

Marco Antonio Tangaro
Italian National Research Council | CNR · Institute of Biomembrane and Bioenergetics IBBE

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99
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7,854
Citations
Citations since 2016
44 Research Items
6826 Citations
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201620172018201920202021202202004006008001,000

Publications

Publications (99)
Preprint
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Background Galaxy is rapidly becoming a de facto standard among workflow managers for bioinformatics thanks to its rich feature set, overall flexibility, and a thriving community. One of the main advantages of Galaxy consists in making complex analyses, e.g. involving numerous and large data sets, accessible even to users lacking computer proficien...
Preprint
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Motivation: Clinical applications of genome re-sequencing technologies typically generate large amounts of data that need to be carefully annotated and interpreted to identify genetic variants associated with pathological conditions. In this context, accurate and reproducible methods for the functional annotation and prioritization of genetic varia...
Article
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This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources,...
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Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and fast method to measure gene expression. Reproducibility of the analyses is the main limitation of RT-qPCR experiments. Galaxy is an open, web-based, genomic workbench for a reproducible, transparent, and accessible science. Our aim was developing a n...
Article
RNA editing is a widespread post-transcriptional mechanism able to modify transcripts through insertions/deletions or base substitutions. It is prominent in mammals, in which millions of adenosines are deaminated to inosines by members of the ADAR family of enzymes. A-to-I RNA editing has a plethora of biological functions, but its detection in lar...
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The 5′ and 3′ untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Since 1996, we have developed and maintained UTRdb, a specialized database of...
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Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely acc...
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Background Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily act...
Article
DOME is a set of community-wide recommendations for reporting supervised machine learning–based analyses applied to biological studies. Broad adoption of these recommendations will help improve machine learning assessment and reproducibility.
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Motivation: ITSoneWB (ITSone WorkBench) is a Galaxy-based bioinformatic environment where comprehensive and high-quality reference data are connected with established pipelines and new tools in an automated and easy-to-use service targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-t...
Article
In diploid organisms, two copies of each allele are normally inherited from parents. Paternal and maternal alleles can be regulated and expressed unequally, which is referred to as allele-specific expression (ASE). In this work, we present aScan, a novel method for the identification of ASE from the analysis of matched individual genomic and RNA se...
Article
Motivation Clinical applications of genome re-sequencing technologies typically generate large amounts of data that need to be carefully annotated and interpreted to identify genetic variants potentially associated with pathological conditions. In this context, accurate and reproducible methods for the functional annotation and prioritization of ge...
Article
While over 150 thousand genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here we present CorGAT, a novel tool for the functional annotation of SARS-Co...
Article
Full-text available
RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of th...
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Background: The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly availab...
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Background While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios where users can be better served by full administrative control over a private Galaxy instance, including, but not limited to, concerns about data privacy, customisation needs, prioritisation of particula...
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This is an addendum to the article JHEP11 (2015) 205 [1]. The figures 3 (right), 4 (right) and 5 are updated with published results on non-prompt J/ψ-meson production from the CMS collaboration [2]. Open image in new window
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The first study of ϕ-meson production in p–Pb collisions at forward and backward rapidity, at a nucleon–nucleon centre-of-mass energy sNN=5.02 TeV, has been performed with the ALICE apparatus at the LHC. The ϕ-mesons have been identified in the dimuon decay channel in the transverse momentum (pT) range 1<pT<7 GeV/c, both in the p-going (2.03<y<3.53...
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A detailed study of pseudorapidity densities and multiplicity distributions of primary charged particles produced in proton–proton collisions, at \(\sqrt{s} =\) 0.9, 2.36, 2.76, 7 and 8 TeV, in the pseudorapidity range \(|\eta |<2\), was carried out using the ALICE detector. Measurements were obtained for three event classes: inelastic, non-single...
Article
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The measurement of prompt D-meson production as a function of multiplicity in p-Pb collisions at \( \sqrt{s_{\mathrm{NN}}}=5.02 \) TeV with the ALICE detector at the LHC is reported. D0, D+ and D∗+ mesons are reconstructed via their hadronic decay channels in the centre-of-mass rapidity range −0.96 < ycms< 0.04 and transverse momentum interval 1<pT...
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The production of charged pions, kaons and (anti)protons has been measured at mid-rapidity (−0.5<y<0) in p–Pb collisions at sNN=5.02 TeV using the ALICE detector at the LHC. Exploiting particle identification capabilities at high transverse momentum (pT), the previously published pT spectra have been extended to include measurements up to 20 ,GeV/c...
Article
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The pseudorapidity density of charged particles, dN_{ch}/dη, at midrapidity in Pb-Pb collisions has been measured at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02 TeV. For the 5% most central collisions, we measure a value of 1943±54. The rise in dN_{ch}/dη as a function of sqrt[s_{NN}] is steeper than that observed in proton-proton...
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We report on the first measurement of an excess in the yield of J/ψ at very low transverse momentum (p_{T}<0.3 GeV/c) in peripheral hadronic Pb-Pb collisions at sqrt[s_{NN}]=2.76 TeV, performed by ALICE at the CERN LHC. Remarkably, the measured nuclear modification factor of J/ψ in the rapidity range 2.5<y<4 reaches about 7 (2) in the p_{T} range 0...
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Three- and four-pion Bose-Einstein correlations are presented in pp,p-Pb, and Pb-Pb collisions at the LHC. We compare our measured four-pion correlations to the expectation derived from two- and three-pion measurements. Such a comparison provides a method to search for coherent pion emission. We also present mixed-charge correlations in order to de...
Article
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The multi-strange baryon yields in Pb–Pb collisions have been shown to exhibit an enhancement relative to pp reactions. In this work, Ξ and Ω production rates have been measured with the ALICE experiment as a function of transverse momentum, , in p–Pb collisions at a centre-of-mass energy of = 5.02 TeV. The results cover the kinematic ranges 0.6 Ge...
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The production of K∗(892)0 and ϕ(1020) mesons has been measured in p–Pb collisions at sNN= 5.02 TeV. K∗ 0 and ϕ are reconstructed via their decay into charged hadrons with the ALICE detector in the rapidity range - 0.5 < y< 0. The transverse momentum spectra, measured as a function of the multiplicity, have a pT range from 0 to 15 GeV/c for K∗ 0 an...
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The production of J/psi and psi (2S) was studied with the ALICE detector in Pb-Pb collisions at the LHC. The measurement was performed at forward rapidity (2.5 < y < 4) down to zero transverse momentum (p(T)) in the dimuon decay channel. Inclusive J/psi yields were extracted in different centrality classes and the centrality dependence of the avera...
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We report on measurements of a charge-dependent flow using a novel three-particle correlator with ALICE in Pb-Pb collisions at the CERN Large Hadron Collider (LHC), and discuss the implications for observation of local parity violation and the chiral magnetic wave (CMW) in heavy-ion collisions. Charge-dependent flow is reported for different collis...
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We report on the inclusive production cross sections of (Formula presented.) , (Formula presented.) , (Formula presented.) (1S), (Formula presented.) (2S) and (Formula presented.) (3S), measured at forward rapidity with the ALICE detector in (Formula presented.) collisions at a center-of-mass energy (Formula presented.) TeV. The analysis is based o...
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We report on results obtained with the event-shape engineering technique applied to Pb-Pb collisions at sNN=2.76 TeV. By selecting events in the same centrality interval, but with very different average flow, different initial-state conditions can be studied. We find the effect of the event-shape selection on the elliptic flow coefficient v2 to be...
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Transverse momentum (pT) spectra of pions, kaons, and protons up to pT=20GeV/c have been measured in Pb-Pb collisions at sNN=2.76TeV using the ALICE detector for six different centrality classes covering 0%-80%. The proton-to-pion and the kaon-to-pion ratios both show a distinct peak at pT≈3GeV/c in central Pb-Pb collisions that decreases for more...
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The production of prompt D s+ mesons was measured for the first time in collisions of heavy nuclei with the ALICE detector at the LHC. The analysis was performed on a data sample of Pb-Pb collisions at a centre-of-mass energy per nucleon pair, \( \sqrt{s_{\mathrm{NN}}} \) , of 2.76 TeV in two different centrality classes, namely 0–10% and 20–50%. D...
Article
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The production of prompt charmed mesons D0, D+ and D∗+, and their antiparticles, was measured with the ALICE detector in Pb-Pb collisions at the centre-of-mass energy per nucleon pair, \( \sqrt{s_{\mathrm{NN}}} \), of 2.76 TeV. The production yields for rapidity |y| < 0.5 are presented as a function of transverse momentum, p T, in the interval 1–36...
Article
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The production of (anti-)deuteron and (anti-)He3 nuclei in Pb-Pb collisions at sNN=2.76 TeV has been studied using the ALICE detector at the LHC. The spectra exhibit a significant hardening with increasing centrality. Combined blast-wave fits of several particles support the interpretation that this behavior is caused by an increase of radial flow....
Article
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We report on the measurement of freeze-out radii for pairs of identical-charge pions measured in Pb-Pb collisions at sNN=2.76 TeV as a function of collision centrality and the average transverse momentum of the pair kT. Three-dimensional sizes of the system (femtoscopic radii), as well as direction-averaged one-dimensional radii are extracted. The...
Article
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We report on two-particle charge-dependent correlations in pp, p-Pb, and Pb-Pb collisions as a function of the pseudorapidity and azimuthal angle difference, [Formula: see text] and [Formula: see text] respectively. These correlations are studied using the balance function that probes the charge creation time and the development of collectivity in...
Article
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The centrality dependence of the charged–particle pseudorapidity density measured with ALICE in Pb–Pb collisions at over a broad pseudorapidity range is presented. This Letter extends the previous results reported by ALICE to more peripheral collisions. No strong change of the overall shape of charged–particle pseudorapidity density distributions w...
Article
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The production of the hypertriton nuclei and has been measured for the first time in Pb–Pb collisions at with the ALICE experiment at LHC. The -integrated yield in one unity of rapidity, in the 0–10% most central collisions, is consistent with the predictions from a statistical thermal model using the same temperature as for the light hadrons. The...
Article
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Direct photon production at mid-rapidity in Pb–Pb collisions at was studied in the transverse momentum range . Photons were detected with the highly segmented electromagnetic calorimeter PHOS and via conversions in the ALICE detector material with the pair reconstructed in the central tracking system. The results of the two methods were combined an...
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ALICE is one of four large experiments at the CERN Large Hadron Collider near Geneva, specially designed to study particle production in ultra-relativistic heavy-ion collisions. Located 52 meters underground with 28 meters of overburden rock, it has also been used to detect muons produced by cosmic ray interactions in the upper atmosphere. In this...
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The production of electrons from heavy-flavour hadron decays was measured as a function of transverse momentum (pT) in minimum-bias p–Pb collisions at sNN=5.02 TeV using the ALICE detector at the LHC. The measurement covers the pT interval 0.5<pT<12 GeV/c and the rapidity range −1.065<ycms<0.135 in the centre-of-mass reference frame. The contributi...
Article
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The elliptic flow, v2, of muons from heavy-flavour hadron decays at forward rapidity (2.5<y<4) is measured in Pb–Pb collisions at sNN=2.76 TeV with the ALICE detector at the LHC. The scalar product, two- and four-particle Q cumulants and Lee–Yang zeros methods are used. The dependence of the v2 of muons from heavy-flavour hadron decays on the colli...
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We present results of a search for two hypothetical strange dibaryon states, i.e. the H-dibaryon and the possible Λn‾ bound state. The search is performed with the ALICE detector in central (0–10%) Pb–Pb collisions at sNN=2.76 TeV, by invariant mass analysis in the decay modes Λn‾→d‾π+ and H-dibaryon →Λpπ−. No evidence for these bound states is obs...
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The size of the particle emission region in high-energy collisions can be deduced using the femtoscopic correlations of particle pairs at low relative momentum. Such correlations arise due to quantum statistics and Coulomb and strong final state interactions. In this paper, results are presented from femtoscopic analyses of π±π±,K±K±,KS0KS0,pp, and...
Article
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We present a measurement of inclusive J/ψ production in p-Pb collisions at \( \sqrt{s_{\mathrm{NN}}}=5.02 \) TeV as a function of the centrality of the collision, as estimated from the energy deposited in the Zero Degree Calorimeters. The measurement is performed with the ALICE detector down to zero transverse momentum, p T, in the backward (−4.46...
Article
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The nuclear modification factor, R AA, of the prompt charmed mesons D0, D+ and D∗+, and their antiparticles, was measured with the ALICE detector in Pb-Pb collisions at a centre-of-mass energy \( \sqrt{s_{\mathrm{N}\;\mathrm{N}}}=2.76 \) TeV in two transverse momentum intervals, 5 < p T< 8 GeV/c and 8 < p T< 16 GeV/c, and in six collision centralit...
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We report the first measurement at the LHC of coherent photoproduction of ρ 0 mesons in ultra-peripheral Pb-Pb collisions. The invariant mass and transverse momentum distributions for ρ 0 production are studied in the π + π − decay channel at mid-rapidity. The production cross section in the rapidity range |y| < 0.5 is found to be dσ/dy = 425 ± 10(...
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Prompt D meson and non-prompt J/ψ yields are studied as a function of the multiplicity of charged particles produced in inelastic proton-proton collisions at a centre-of-mass energy of √ = 7 TeV. The results are reported as a ratio between yields in a given multiplicity interval normalised to the multiplicity-integrated ones (relative yields). They...
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We report the measurement of a new observable of jet quenching in central Pb-Pb collisions at \( \sqrt{s_{\mathrm{NN}}}=2.76 \) TeV, based on the semi-inclusive rate of charged jets recoiling from a high transverse momentum (high-p T) charged hadron trigger. Jets are measured using collinear-safe jet reconstruction with infrared cutoff for jet cons...
Article
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The transverse momentum (p T) dependence of the nuclear modification factor R AA and the centrality dependence of the average transverse momentum 〈p T〉 for inclusive J/ψ have been measured with ALICE for Pb-Pb collisions at sNN−−−√=2.76 TeV in the e+e− decay channel at mid-rapidity (|y| < 0.8). The 〈p T〉 is significantly smaller than the one observ...
Article
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The elliptic flow coefficient (v 2) of identified particles in Pb-Pb collisions at sNN−−−√=2.76 TeV was measured with the ALICE detector at the Large Hadron Collider (LHC). The results were obtained with the Scalar Product method, a two-particle correlation technique, using a pseudo-rapidity gap of |Δη| > 0.9 between the identified hadron under stu...
Article
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We have studied the transverse-momentum (pT) dependence of the inclusive J/ψ production in p-Pb collisions at sNN$$ \sqrt{s_{\mathrm{NN}}} $$ = 5.02 TeV, in three center-of-mass rapidity (ycms) regions, down to zero pT. Results in the forward and backward rapidity ranges (2.03 < ycms< 3.53 and −4.46 < ycms< −2.96) are obtained by studying the J/ψ d...
Article
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We report measurements of the primary charged-particle pseudorapidity density and transverse momentum distributions in p−Pb collisions at sNN−−−√=5.02TeV and investigate their correlation with experimental observables sensitive to the centrality of the collision. Centrality classes are defined by using different event-activity estimators, i.e., cha...
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The measurement of primary π±, K±, p and p¯ production at mid-rapidity (|y|< 0.5) in proton–proton collisions at s√ = 7 TeV performed with a large ion collider experiment at the large hadron collider (LHC) is reported. Particle identification is performed using the specific ionisation energy-loss and time-of-flight information, the ring-imaging Che...