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Full-Text Articles in Life Sciences
Estimation Of A Non-Parametric Variable Importance Measure Of A Continuous Exposure, Chambaz Antoine, Pierre Neuvial, Mark J. Van Der Laan
Estimation Of A Non-Parametric Variable Importance Measure Of A Continuous Exposure, Chambaz Antoine, Pierre Neuvial, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
We define a new measure of variable importance of an exposure on a continuous outcome, accounting for potential confounders. The exposure features a reference level x0 with positive mass and a continuum of other levels. For the purpose of estimating it, we fully develop the semi-parametric estimation methodology called targeted minimum loss estimation methodology (TMLE) [van der Laan & Rubin, 2006; van der Laan & Rose, 2011]. We cover the whole spectrum of its theoretical study (convergence of the iterative procedure which is at the core of the TMLE methodology; consistency and asymptotic normality of the estimator), practical implementation, simulation …
Cellulose- And Xylan-Degrading Thermophilic Anaerobic Bacteria From Biocompost, M. V. Sizova, J. A. Izquierdo, N. S. Panikov, L. R. Lynd
Cellulose- And Xylan-Degrading Thermophilic Anaerobic Bacteria From Biocompost, M. V. Sizova, J. A. Izquierdo, N. S. Panikov, L. R. Lynd
Dartmouth Scholarship
Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S …
A Generalized Approach For Testing The Association Of A Set Of Predictors With An Outcome: A Gene Based Test, Benjamin A. Goldstein, Alan E. Hubbard, Lisa F. Barcellos
A Generalized Approach For Testing The Association Of A Set Of Predictors With An Outcome: A Gene Based Test, Benjamin A. Goldstein, Alan E. Hubbard, Lisa F. Barcellos
U.C. Berkeley Division of Biostatistics Working Paper Series
In many analyses, one has data on one level but desires to draw inference on another level. For example, in genetic association studies, one observes units of DNA referred to as SNPs, but wants to determine whether genes that are comprised of SNPs are associated with disease. While there are some available approaches for addressing this issue, they usually involve making parametric assumptions and are not easily generalizable. A statistical test is proposed for testing the association of a set of variables with an outcome of interest. No assumptions are made about the functional form relating the variables to the …
A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali
A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali
Interdisciplinary Informatics Faculty Proceedings & Presentations
Correlation networks are emerging as a powerful tool for modeling temporal mechanisms within the cell. Particularly useful in examining coexpression within microarray data, studies have determined that correlation networks follow a power law degree distribution and thus manifest properties such as the existence of “hub” nodes and semicliques that potentially correspond to critical cellular structures. Difficulty lies in filtering coincidental relationships from causative structures in these large, noise-heavy networks. As such, computational expenses and algorithm availability limit accurate comparison, making it difficult to identify changes between networks. In this vein, we present our work identifying temporal relationships from microarray data …
Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer
Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer
Mark R Segal
Methods for formally evaluating the clustering of events in space or time, notably the scan statistic, have been richly developed and widely applied. In order to utilize the scan statistic and related approaches, it is necessary to know the extent of the spatial or temporal domains wherein the events arise. Implicit in their usage is that these domains have no “holes”—hereafter “exclusion zones”—regions in which events a priori cannot occur. However, in many contexts, this requirement is not met. When the exclusion zones are known, it is straightforward to correct the scan statistic for their occurrence by simply adjusting the …