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Barnett, Ian

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Barnett

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Barnett, Ian
Author's Publications: search.filters.isAuthorOfPublication.714b24a9-7878-4a39-92cf-bd20ecf4cb7a

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    SNP-set Tests for Sequencing and Genome-Wide Association Studies
    (2014-06-06) Barnett, Ian; Lin, Xihong; Lin, Xihong; Kraft, Peter; Robins, James
    In this dissertation we propose methodology for testing SNP-sets for genetic associations, both for sequencing and genome-wide association studies. Due to the large scale of this kind of data, there is an emphasis on producing methodology that is not only accurate and powerful, but also computationally efficient.
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    Heart rate variability and DNA methylation levels are altered after short-term metal fume exposure among occupational welders: a repeated-measures panel study
    (BioMed Central, 2014) Fan, Tianteng; Fang, Shona C; Cavallari, Jennifer M; Barnett, Ian; Wang, Zhaoxi; Su, Li; Byun, Hyang-Min; Lin, Xihong; Baccarelli, Andrea; Christiani, David
    Background: In occupational settings, boilermakers are exposed to high levels of metallic fine particulate matter (PM2.5) generated during the welding process. The effect of welding PM2.5 on heart rate variability (HRV) has been described, but the relationship between PM2.5, DNA methylation, and HRV is not known. Methods: In this repeated-measures panel study, we recorded resting HRV and measured DNA methylation levels in transposable elements Alu and long interspersed nuclear element-1 (LINE-1) in peripheral blood leukocytes under ambient conditions (pre-shift) and right after a welding task (post-shift) among 66 welders. We also monitored personal PM2.5 level in the ambient environment and during the welding procedure. Results: The concentration of welding PM2.5 was significantly higher than background levels in the union hall (0.43 mg/m3 vs. 0.11 mg/m3, p < 0.0001). The natural log of transformed power in the high frequency range (ln HF) had a significantly negative association with PM2.5 exposure (β = -0.76, p = 0.035). pNN10 and pNN20 also had a negative association with PM2.5 exposure (β = -0.16%, p = 0.006 and β = -0.13%, p = 0.030, respectively). PM2.5 was positively associated with LINE-1 methylation [β = 0.79%, 5-methylcytosince (%mC), p = 0.013]; adjusted for covariates. LINE-1 methylation did not show an independent association with HRV. Conclusions: Acute decline of HRV was observed following exposure to welding PM2.5 and evidence for an epigenetic response of transposable elements to short-term exposure to high-level metal-rich particulates was reported. Electronic supplementary material The online version of this article (doi:10.1186/1471-2458-14-1279) contains supplementary material, which is available to authorized users.
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    Change Point Detection in Correlation Networks
    (Nature Publishing Group, 2016) Barnett, Ian; Onnela, Jukka-Pekka
    Many systems of interacting elements can be conceptualized as networks, where network nodes represent the elements and network ties represent interactions between the elements. In systems where the underlying network evolves, it is useful to determine the points in time where the network structure changes significantly as these may correspond to functional change points. We propose a method for detecting change points in correlation networks that, unlike previous change point detection methods designed for time series data, requires minimal distributional assumptions. We investigate the difficulty of change point detection near the boundaries of the time series in correlation networks and study the power of our method and competing methods through simulation. We also show the generalizable nature of the method by applying it to stock price data as well as fMRI data.
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    Social and Spatial Clustering of People at Humanity’s Largest Gathering
    (Public Library of Science, 2016) Barnett, Ian; Khanna, Tarun; Onnela, Jukka-Pekka
    Macroscopic behavior of scientific and societal systems results from the aggregation of microscopic behaviors of their constituent elements, but connecting the macroscopic with the microscopic in human behavior has traditionally been difficult. Manifestations of homophily, the notion that individuals tend to interact with others who resemble them, have been observed in many small and intermediate size settings. However, whether this behavior translates to truly macroscopic levels, and what its consequences may be, remains unknown. Here, we use call detail records (CDRs) to examine the population dynamics and manifestations of social and spatial homophily at a macroscopic level among the residents of 23 states of India at the Kumbh Mela, a 3-month-long Hindu festival. We estimate that the festival was attended by 61 million people, making it the largest gathering in the history of humanity. While we find strong overall evidence for both types of homophily for residents of different states, participants from low-representation states show considerably stronger propensity for both social and spatial homophily than those from high-representation states. These manifestations of homophily are amplified on crowded days, such as the peak day of the festival, which we estimate was attended by 25 million people. Our findings confirm that homophily, which here likely arises from social influence, permeates all scales of human behavior.