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  1. Article: Approximation Bayesian Computation.

    Marjoram, Paul

    OA genetics

    2014  Volume 1, Issue 3, Page(s) 853

    Abstract: Approximation Bayesian computation [ABC] is an analysis approach that has arisen in response to the recent trend to collect data that is of a magnitude far higher than has been historically the case. This has led to many existing methods become ... ...

    Abstract Approximation Bayesian computation [ABC] is an analysis approach that has arisen in response to the recent trend to collect data that is of a magnitude far higher than has been historically the case. This has led to many existing methods become intractable because of difficulties in calculating the likelihood function. ABC circumvents this issue by replacing calculation of the likelihood with a simulation step in which it is estimated in one way or another. In this review we give an overview of the ABC approach, giving examples of some of the more popular specific forms of ABC. We then discuss some of the areas of most active research and application in the field, specifically, choice of low-dimensional summaries of complex datasets and metrics for measuring similarity between observed and simulated data. Next, we consider the question of how to do model selection in an ABC context. Finally, we discuss an area of growing prominence in the ABC world, use of ABC methods in genetic pathway inference.
    Language English
    Publishing date 2014-12-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2742971-4
    ISSN 2054-197X
    ISSN 2054-197X
    DOI 10.13172/2054-197x-1-1-853
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Longitudinal hierarchical Bayesian models of covariate effects on airway and alveolar nitric oxide.

    Weng, Jingying / Molshatzki, Noa / Marjoram, Paul / Gauderman, W James / Gilliland, Frank D / Eckel, Sandrah P

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 5346

    Abstract: Biomarkers such as exhaled nitric oxide (FeNO), a marker of airway inflammation, have applications in the study of chronic respiratory disease where longitudinal studies of within-participant changes in the biomarker are particularly relevant. A cutting- ... ...

    Abstract Biomarkers such as exhaled nitric oxide (FeNO), a marker of airway inflammation, have applications in the study of chronic respiratory disease where longitudinal studies of within-participant changes in the biomarker are particularly relevant. A cutting-edge approach to assessing FeNO, called multiple flow FeNO, repeatedly assesses FeNO across a range of expiratory flow rates at a single visit and combines these data with a deterministic model of lower respiratory tract NO to estimate parameters quantifying airway wall and alveolar NO sources. Previous methodological work for multiple flow FeNO has focused on methods for data from a single participant or from cross-sectional studies. Performance of existing ad hoc two-stage methods for longitudinal multiple flow FeNO in cohort or panel studies has not been evaluated. In this paper, we present a novel longitudinal extension to a unified hierarchical Bayesian (L_U_HB) model relating longitudinally assessed multiple flow FeNO to covariates. In several simulation study scenarios, we compare the L_U_HB method to other unified and two-stage frequentist methods. In general, L_U_HB produced unbiased estimates, had good power, and its performance was not sensitive to the magnitude of the association with a covariate and correlations between NO parameters. In an application relating height to longitudinal multiple flow FeNO in schoolchildren without asthma, unified analysis methods estimated positive, statistically significant associations of height with airway and alveolar NO concentrations and negative associations with airway wall diffusivity while estimates from two-stage methods were smaller in magnitude and sometimes non-significant.
    MeSH term(s) Humans ; Child ; Nitric Oxide/analysis ; Bayes Theorem ; Cross-Sectional Studies ; Asthma ; Bronchi/chemistry ; Exhalation ; Breath Tests/methods ; Biomarkers
    Chemical Substances Nitric Oxide (31C4KY9ESH) ; Biomarkers
    Language English
    Publishing date 2023-04-01
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-31774-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Functional human genes typically exhibit epigenetic conservation.

    Rud, Daniel / Marjoram, Paul / Siegmund, Kimberly / Shibata, Darryl

    PloS one

    2021  Volume 16, Issue 9, Page(s) e0253250

    Abstract: Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap ... ...

    Abstract Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.
    MeSH term(s) Cell Culture Techniques/methods ; Cell Line, Tumor ; DNA Methylation ; Epigenesis, Genetic ; Gene Expression Regulation ; Genes, Essential ; Genetic Drift ; Humans
    Language English
    Publishing date 2021-09-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0253250
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Functional human genes typically exhibit epigenetic conservation.

    Daniel Rud / Paul Marjoram / Kimberly Siegmund / Darryl Shibata

    PLoS ONE, Vol 16, Iss 9, p e

    2021  Volume 0253250

    Abstract: Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap ... ...

    Abstract Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: fmcmc: A friendly MCMC framework.

    Vega Yon, George G / Marjoram, Paul

    Journal of open source software

    2019  Volume 4, Issue 39

    Language English
    Publishing date 2019-07-09
    Publishing country United States
    Document type Journal Article
    ISSN 2475-9066
    ISSN 2475-9066
    DOI 10.21105/joss.01427
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: slurmR: A lightweight wrapper for HPC with Slurm.

    Vega Yon, George G / Marjoram, Paul

    Journal of open source software

    2019  Volume 4, Issue 42

    Language English
    Publishing date 2019-10-08
    Publishing country United States
    Document type Journal Article
    ISSN 2475-9066
    ISSN 2475-9066
    DOI 10.21105/joss.01493
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Sure enough: efficient Bayesian learning and choice.

    Foley, Brad R / Marjoram, Paul

    Animal cognition

    2017  Volume 20, Issue 5, Page(s) 867–880

    Abstract: Probabilistic decision-making is a general phenomenon in animal behavior, and has often been interpreted to reflect the relative certainty of animals' beliefs. Extensive neurological and behavioral results increasingly suggest that animal beliefs may be ... ...

    Abstract Probabilistic decision-making is a general phenomenon in animal behavior, and has often been interpreted to reflect the relative certainty of animals' beliefs. Extensive neurological and behavioral results increasingly suggest that animal beliefs may be represented as probability distributions, with explicit accounting of uncertainty. Accordingly, we develop a model that describes decision-making in a manner consistent with this understanding of neuronal function in learning and conditioning. This first-order Markov, recursive Bayesian algorithm is as parsimonious as its minimalist point-estimate, Rescorla-Wagner analogue. We show that the Bayesian algorithm can reproduce naturalistic patterns of probabilistic foraging, in simulations of an experiment in bumblebees. We go on to show that the Bayesian algorithm can efficiently describe the behavior of several heuristic models of decision-making, and is consistent with the ubiquitous variation in choice that we observe within and between individuals in implementing heuristic decision-making. By describing learning and decision-making in a single Bayesian framework, we believe we can realistically unify descriptions of behavior across contexts and organisms. A unified cognitive model of this kind may facilitate descriptions of behavioral evolution.
    MeSH term(s) Algorithms ; Animals ; Appetitive Behavior ; Bayes Theorem ; Bees/physiology ; Choice Behavior ; Decision Making ; Learning ; Models, Theoretical
    Language English
    Publishing date 2017-07-01
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1466332-6
    ISSN 1435-9456 ; 1435-9448
    ISSN (online) 1435-9456
    ISSN 1435-9448
    DOI 10.1007/s10071-017-1107-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: iMutSig

    Yang, Zhi / Pandey, Priyatama / Marjoram, Paul / Siegmund, Kimberly D

    F1000Research

    2020  Volume 9, Page(s) 586

    Abstract: There are two frameworks for characterizing mutational signatures which are commonly used to describe the nucleotide patterns that arise from mutational processes. Estimated mutational signatures from fitting these two methods in human cancer can be ... ...

    Abstract There are two frameworks for characterizing mutational signatures which are commonly used to describe the nucleotide patterns that arise from mutational processes. Estimated mutational signatures from fitting these two methods in human cancer can be found online, in the Catalogue Of Somatic Mutations In Cancer (COSMIC) website or a GitHub repository. The two frameworks make differing assumptions regarding independence of base pairs and for that reason may produce different results. Consequently, there is a need to compare and contrast the results of the two methods, but no such tool currently exists. In this paper, we provide a simple and intuitive interface that allows comparisons of pairs of mutational signatures to be easily performed. Cosine similarity measures the extent of signature similarity. To compare mutational signatures of different formats, one signature type (COSMIC or
    MeSH term(s) DNA Mutational Analysis ; Humans ; Internet ; Mutation ; Neoplasms/genetics ; Software
    Language English
    Publishing date 2020-06-10
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.24435.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Hierarchical Bayesian estimation of covariate effects on airway and alveolar nitric oxide.

    Weng, Jingying / Molshatzki, Noa / Marjoram, Paul / Gauderman, W James / Gilliland, Frank D / Eckel, Sandrah P

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 17180

    Abstract: Exhaled breath biomarkers are an important emerging field. The fractional concentration of exhaled nitric oxide (FeNO) is a marker of airway inflammation with clinical and epidemiological applications (e.g., air pollution health effects studies). Systems ...

    Abstract Exhaled breath biomarkers are an important emerging field. The fractional concentration of exhaled nitric oxide (FeNO) is a marker of airway inflammation with clinical and epidemiological applications (e.g., air pollution health effects studies). Systems of differential equations describe FeNO-measured non-invasively at the mouth-as a function of exhalation flow rate and parameters representing airway and alveolar sources of NO in the airway. Traditionally, NO parameters have been estimated separately for each study participant (Stage I) and then related to covariates (Stage II). Statistical properties of these two-step approaches have not been investigated. In simulation studies, we evaluated finite sample properties of existing two-step methods as well as a novel Unified Hierarchical Bayesian (U-HB) model. The U-HB is a one-step estimation method developed with the goal of properly propagating uncertainty as well as increasing power and reducing type I error for estimating associations of covariates with NO parameters. We demonstrated the U-HB method in an analysis of data from the southern California Children's Health Study relating traffic-related air pollution exposure to airway and alveolar airway inflammation.
    MeSH term(s) Asthma/epidemiology ; Asthma/etiology ; Bayes Theorem ; Biomarkers/metabolism ; Breath Tests ; Child ; Data Interpretation, Statistical ; Exhalation ; Humans ; Inhalation Exposure/statistics & numerical data ; Models, Theoretical ; Nitric Oxide/metabolism ; Pulmonary Alveoli/metabolism ; Respiratory Mucosa/metabolism ; Vehicle Emissions/toxicity
    Chemical Substances Biomarkers ; Vehicle Emissions ; Nitric Oxide (31C4KY9ESH)
    Language English
    Publishing date 2021-08-25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-96176-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Longitudinal hierarchical Bayesian models of covariate effects on airway and alveolar nitric oxide

    Jingying Weng / Noa Molshatzki / Paul Marjoram / W. James Gauderman / Frank D. Gilliland / Sandrah P. Eckel

    Scientific Reports, Vol 13, Iss 1, Pp 1-

    2023  Volume 10

    Abstract: Abstract Biomarkers such as exhaled nitric oxide (FeNO), a marker of airway inflammation, have applications in the study of chronic respiratory disease where longitudinal studies of within-participant changes in the biomarker are particularly relevant. A ...

    Abstract Abstract Biomarkers such as exhaled nitric oxide (FeNO), a marker of airway inflammation, have applications in the study of chronic respiratory disease where longitudinal studies of within-participant changes in the biomarker are particularly relevant. A cutting-edge approach to assessing FeNO, called multiple flow FeNO, repeatedly assesses FeNO across a range of expiratory flow rates at a single visit and combines these data with a deterministic model of lower respiratory tract NO to estimate parameters quantifying airway wall and alveolar NO sources. Previous methodological work for multiple flow FeNO has focused on methods for data from a single participant or from cross-sectional studies. Performance of existing ad hoc two-stage methods for longitudinal multiple flow FeNO in cohort or panel studies has not been evaluated. In this paper, we present a novel longitudinal extension to a unified hierarchical Bayesian (L_U_HB) model relating longitudinally assessed multiple flow FeNO to covariates. In several simulation study scenarios, we compare the L_U_HB method to other unified and two-stage frequentist methods. In general, L_U_HB produced unbiased estimates, had good power, and its performance was not sensitive to the magnitude of the association with a covariate and correlations between NO parameters. In an application relating height to longitudinal multiple flow FeNO in schoolchildren without asthma, unified analysis methods estimated positive, statistically significant associations of height with airway and alveolar NO concentrations and negative associations with airway wall diffusivity while estimates from two-stage methods were smaller in magnitude and sometimes non-significant.
    Keywords Medicine ; R ; Science ; Q
    Subject code 310
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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