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Standardized benchmarking in the quest for orthologs
(2016)Nature MethodsAchieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision–recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish ...Journal Article -
Inferring causal molecular networks: empirical assessment through a community-based effort
(2016)Nature MethodsIt remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than ...Journal Article -
Observation of the rare Bs0 →µ+µ− decay from the combined analysis of CMS and LHCb data
(2015)NatureThe standard model of particle physics describes the fundamental particles and their interactions via the strong, electromagnetic and weak forces. It provides precise predictions for measurable quantities that can be tested experimentally. The probabilities, or branching fractions, of the strange B meson ( ) and the B0 meson decaying into two oppositely charged muons (μ+ and μ−) are especially interesting because of their sensitivity to ...Journal Article -
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
(2014)Nature BiotechnologyThe domestic ferret (Mustela putorius furo) is an important animal model for multiple human respiratory diseases. It is considered the 'gold standard' for modeling human influenza virus infection and transmission. Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps. We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues. We ...Journal Article -
Evidence for the direct decay of the 125 GeV Higgs boson to fermions
(2014)Nature PhysicsThe discovery of a new boson with a mass of approximately 125 GeV in 2012 at the Large Hadron Collider1,2,3 has heralded a new era in understanding the nature of electroweak symmetry breaking and possibly completing the standard model of particle physics4,5,6,7,8,9. Since the first observation in decays to γγ, WW and ZZ boson pairs, an extensive set of measurements of the mass10,11 and couplings to W and Z bosons11,12,13, as well as ...Journal Article -
Determination of Jet Energy Calibration and Transverse Momentum Resolution in CMS
(2011)Journal of InstrumentationMeasurements of the jet energy calibration and transverse momentum resolution in CMS are presented, performed with a data sample collected in proton-proton collisions at a centre-of-mass energy of 7TeV, corresponding to an integrated luminosity of 36pb−1. The transverse momentum balance in dijet and γ/Z+jets events is used to measure the jet energy response in the CMS detector, as well as the transverse momentum resolution. The results ...Journal Article -
Missing transverse energy performance of the CMS detector
(2011)Journal of InstrumentationDuring 2010 the LHC delivered pp collisions with a centre-of-mass energy of 7 TeV. In this paper, the results of comprehensive studies of missing transverse energy as measured by the CMS detector are presented. The results cover the measurements of the scale and resolution for missing transverse energy, and the effects of multiple pp interactions within the same bunch crossings on the scale and resolution. Anomalous measurements of missing ...Journal Article