| 1. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 2. |
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| 3. |
- Aktas, A, et al.
(författare)
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A direct search for stable magnetic monopoles produced in positron-proton collisions at HERA
- 2005
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 41, s. 133-141
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Tidskriftsartikel (refereegranskat)abstract
- A direct search has been made for magnetic monopoles produced in e(+)p collisions at a centre of mass energy of 300 GeV at HERA. The beam pipe surrounding the interaction region in 1995-1997 was investigated using a SQUID magnetometer to look for stopped magnetic monopoles. During this time an integrated luminosity of 62 pb(-1) was delivered. No magnetic monopoles were observed and charge and mass dependent upper limits on the e(+)p production cross section are set.
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| 4. |
- Aktas, A., et al.
(författare)
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Elastic J/psi production at HERA
- 2006
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 46:3, s. 585-603
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Tidskriftsartikel (refereegranskat)abstract
- Cross sections for elastic production of J/psi mesons in photoproduction and electroproduction are measured in electron proton collisions at HERA using an integrated luminosity of 55 pb(-1). Results are presented for photon virtualities Q(2) up to 80 GeV2. The dependence on the photon-proton centre of mass energy W-gamma p is analysed in the range 40 <= W-gamma p <= 305 GeV in photoproduction and 40 <= W-gamma p <= 160 GeV in electroproduction. The W-gamma p dependences of the cross sections do not change significantly with Q(2) and can be described by models based on perturbative QCD. Within such models, the data show a high sensitivity to the gluon density of the proton in the domain of low Bjorken x and low Q(2). Differential cross sections d sigma/dt, where t is the squared four-momentum transfer at the proton vertex, are measured in the range vertical bar t vertical bar < 1.2 GeV2 as functions of W-gamma p and Q(2). Effective Pomeron trajectories are determined for photoproduction and electroproduction. The J/psi production and decay angular distributions are consistent with s-channel helicity conservation. The ratio of the cross sections for longitudinally and transversely polarised photons is measured as a function of Q(2) and is found to be described by perturbative QCD based models.
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| 5. |
- Aktas, A., et al.
(författare)
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Forward jet production in deep inelastic scattering at HERA
- 2006
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 46:1, s. 27-42
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Tidskriftsartikel (refereegranskat)abstract
- The production of forward jets has been measured in deep inelastic ep collisions at HERA. The results are presented in terms of single differential cross sections as a function of the Bjorken scaling variable (xB(j)) and as triple differential cross sections d3 sigma/dx(Bj)dQ(2)dp(t)(,jet)(2), where Q(2) is the four momentum transfer squared and p(t)(,iet)(2) is the squared transverse momentum of the forward jet. Also cross sections for events with a di-jet system in addition to the forward jet are measured as a function of the rapidity separation between the forward jet and the two additional jets. The measurements are compared with next-to-leading order QCD calculations and with the predictions of various QCD-based models.
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| 6. |
- Aktas, A, et al.
(författare)
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Measurement of dijet production at low Q(2) at HERA
- 2004
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 37:2, s. 141-159
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Tidskriftsartikel (refereegranskat)abstract
- Triple differential dijet cross sections in e(+/-)p interactions are presented in the region of photon virtualities 2 < Q(2) < 80 GeV2, inelasticities 0.1 < y < 0.85, jet transverse energies E*(T1) > 7GeV, E*(T2) > 5 GeV, and pseudorapidities - 2.5 < η(1)*, η(2)* < 0. The measurements are made in the gamma*p centre-of-mass frame, using an integrated luminosity of 57 pb(-1). The data are compared with NLO QCD calculations and LO Monte Carlo programs with and without a resolved virtual photon contribution. NLO QCD calculations fail to describe the region of low Q(2) and low jet transverse energies, in contrast to a LO Monte Carlo generator which includes direct and resolved photon interactions with both transversely and longitudinally polarised photons. Initial and final state parton showers are tested as a mechanism for including higher order QCD effects in low E-T jet production.
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| 7. |
- Aktas, A., et al.
(författare)
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Measurement of event shape variables in deep-inelastic scattering at HERA
- 2006
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 46:2, s. 343-356
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Tidskriftsartikel (refereegranskat)abstract
- Deep-inelastic ep scattering data taken with the H1 detector at HERA and corresponding to an integrated luminosity of 106 pb(-1) are used to study the differential distributions of event shape variables. These include thrust, jet broadening, jet mass and the C-parameter. The four-momentum transfer Q is taken to be the relevant energy scale and ranges between 14 GeV and 200 GeV. The event shape distributions are compared with perturbative QCD predictions, which include resummed contributions and analytical power law corrections, the latter accounting for non-perturbative hadronisation effects. The data clearly exhibit the running of the strong coupling alpha(s)(Q) and are consistent with a universal power correction parameter alpha(0) for all event shape variables. A combined QCD fit using all event shape variables yields alpha(s)(m(Z)) = 0.1198 +/- 0.0013 (+0.0056)(-0.0043) and alpha(0) = 0.476 +/- 0.008 (+0.018)(-0.059).
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| 8. |
- Aktas, A., et al.
(författare)
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Photoproduction of dijets with high transverse momenta at HERA
- 2006
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 639:1, s. 21-31
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Tidskriftsartikel (refereegranskat)abstract
- Differential dijet cross sections are measured in photoproduction in the region of photon virtualities Q(2) < 1 GeV2 with the H1 detector at the HERA ep collider using an integrated luminosity of 66.6 pb(-1). Jets are defined with the inclusive k perpendicular to algorithm and a minimum transverse momentum of the leading jet of 25 GeV is required. Dijet cross sections are measured indirect and resolved photon enhanced regions separately. Longitudinal proton momentum fractions up to 0.7 are reached. The data compare well with predictions from Monte Carlo event generators based on leading order QCD and parton showers and with next-to-leading order QCD calculations corrected for hadronisation effects.
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| 9. |
- Adloff, C, et al.
(författare)
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Measurement and QCD analysis of neutral and charged current cross sections at HERA
- 2003
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 30:1, s. 1-32
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Tidskriftsartikel (refereegranskat)abstract
- The inclusive e(+)p single and double differential cross sections for neutral and charged current processes axe measured with the H1 detector at HERA. The data were taken in 1999 and 2000 at a centre-of-mass energy of roots = 319 GeV and correspond to an integrated luminosity of 65.2 pb(-1). The cross sections are measured in the range of four-momentum transfer squared Q(2) between 100 and 30 000 GeV2 and Bjorken x between 0.0013 and 0.65. The neutral current analysis for the new e(+)p data and the earlier e-p data taken in 1998 and 1999 is extended to small energies of the scattered electron and therefore to higher values of inelasticity y, allowing a determination of the longitudinal structure function F-L at high Q(2) (110 - 700 GeV2). A new measurement of the structure function x (F) over tilde (3) is obtained using the new e(+)p and previously published e p neutral current cross section data at high Q(2). These data together with H1 low Q(2) precision data are further used to perform new next-to-leading order QCD analyses in the framework of the Standard Model to extract flavour separated parton distributions in the proton.
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| 10. |
- Aktas, A, et al.
(författare)
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Diffractive photoproduction of J/psi mesons with large momentum transfer at HERA
- 2003
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 568:3-4, s. 205-218
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Tidskriftsartikel (refereegranskat)abstract
- The diffractive photoproduction of J/psi mesons is measured with the HI detector at the ep collider HERA using an integrated luminosity of 78 pb(-1). The differential cross section dsigma(gammap --> J/psiY)/dt is studied in the range 2 < < 30 GeV2, where t is the square of the four-momentum transferred at the proton vertex. The cross section is also presented as a function of the photon-proton centre-of-mass energy W-gammap in three t intervals, spanning the range 50 < W-gammap < 200 GeV. A fast rise of the cross section with W-gammap is observed for each t range and the slope for the effective linear Pomeron trajectory is measured to be alpha' = -0.0135 +/- 0.0074(stat.) +/- 0.0051(syst.) GeV-2. The measurements are compared with perturbative QCD models based on BFKL and DGLAP evolution. The data are found to be compatible with s-channel helicity conservation. (C) 200 Published by Elsevier B.V.
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