Inferring ecological interactions from dynamics in phage-bacteria communities

Characterizing how viruses interact with microbial hosts is critical to understanding microbial community structure and function. However, existing methods for quantifying bacteria-phage interactions are not widely applicable to natural communities. First, many bacteria are not culturable, preventing direct experimental testing. Second, “-omics” based methods, while high in accuracy and specificity, have been shown to be extremely low in power. Third, inference methods based on time-series or co-occurrence data, while promising, have for the most part not been rigorously tested. This thesis work focuses on this final category of quantification strategies: inference methods. In this thesis, we further our understanding of both the potential and limitations of several inference methods, focusing primarily on time-series data with high time resolution. We emphasize the quantification of efficacy by using time-series data from multi-strain bacteria-phage communities with known infection networks. We employ both in silico simulated bacteria-phage communities as well as an in vitro community experiment. We review existing correlation-based inference methods, extend theory and characterize tradeoffs for model-based inference which uses convex optimization, characterize pairwise interactions in a 5x5 virus-microbe community experiment using Markov chain Monte Carlo, and present analytic tools for microbiome time-series analysis when a dynamical model is unknown. Together, these chapters bridge gaps in existing literature in inference of ecological interactions from time-series data.Ph.D

Search for new physics in the lepton plus missing transverse momentum final state in proton-proton collisions at s\sqrt{s} = 13 TeV

A search for physics beyond the standard model (SM) in final states with an electron or muon and missing transverse momentum is presented. The analysis uses data from proton-proton collisions at a centre-of-mass energy of 13 TeV, collected with the CMS detector at the LHC in 2016-2018 and corresponding to an integrated luminosity of 138 fb$^{-1}$. No significant deviation from the SM prediction is observed. Model-independent limits are set on the production cross section of W' bosons decaying into lepton-plus-neutrino final states. Within the framework of the sequential standard model, with the combined results from the electron and muon decay channels a W' boson with mass less than 5.7 TeV is excluded at 95% confidence level. Results on a SM precision test, the determination of the oblique electroweak $W$ parameter, are presented using LHC data for the first time. These results together with those from the direct W' resonance search are used to extend existing constraints on composite Higgs scenarios. This is the first experimental exclusion on compositeness parameters using results from LHC data other than Higgs boson measurements

Search for new physics in the lepton plus missing transverse momentum final state in proton-proton collisions at s=\sqrt{s} = 13 TeV

International audienceA search for physics beyond the standard model (SM) in final states with an electron or muon and missing transverse momentum is presented. The analysis uses data from proton-proton collisions at a centre-of-mass energy of 13 TeV, collected with the CMS detector at the LHC in 2016-2018 and corresponding to an integrated luminosity of 138 fb$^{-1}$. No significant deviation from the SM prediction is observed. Model-independent limits are set on the production cross section of W' bosons decaying into lepton-plus-neutrino final states. Within the framework of the sequential standard model, with the combined results from the electron and muon decay channels a W' boson with mass less than 5.7 TeV is excluded at 95% confidence level. Results on a SM precision test, the determination of the oblique electroweak $W$ parameter, are presented using LHC data for the first time. These results together with those from the direct W' resonance search are used to extend existing constraints on composite Higgs scenarios. This is the first experimental exclusion on compositeness parameters using results from LHC data other than Higgs boson measurements

Search for new physics in the lepton plus missing transverse momentum final state in proton-proton collisions at s\sqrt{s} = 13 TeV

A search for physics beyond the standard model (SM) in final states with an electron or muon and missing transverse momentum is presented. The analysis uses data from proton-proton collisions at a centre-of-mass energy of 13 TeV, collected with the CMS detector at the LHC in 2016-2018 and corresponding to an integrated luminosity of 138 fb$^{-1}$. No significant deviation from the SM prediction is observed. Model-independent limits are set on the production cross section of W' bosons decaying into lepton-plus-neutrino final states. Within the framework of the sequential standard model, with the combined results from the electron and muon decay channels a W' boson with mass less than 5.7 TeV is excluded at 95% confidence level. Results on a SM precision test, the determination of the oblique electroweak $W$ parameter, are presented using LHC data for the first time. These results together with those from the direct W' resonance search are used to extend existing constraints on composite Higgs scenarios. This is the first experimental exclusion on compositeness parameters using results from LHC data other than Higgs boson measurements