Biometry Commons^™

Biological And Practical Implications Of Genome-Wide Association Study Of Schizophrenia Using Bayesian Variable Selection, Benazir Rowe, Xiangning Chen, Zuoheng Wang, Jingchun Chen, Amei Amei

School of Medicine Faculty Publications

Genome-wide association studies (GWAS) have identified over 100 loci associated with schizophrenia. Most of these studies test genetic variants for association one at a time. In this study, we performed GWAS of the molecular genetics of schizophrenia (MGS) dataset with 5334 subjects using multivariate Bayesian variable selection (BVS) method Posterior Inference via Model Averaging and Subset Selection (piMASS) and compared our results with the previous univariate analysis of the MGS dataset. We showed that piMASS can improve the power of detecting schizophrenia-associated SNPs, potentially leading to new discoveries from existing data without increasing the sample size. We tested SNPs in …

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …

A Statistical Method For The Conservative Adjustment Of False Discovery Rate (Q-Value), Yinglei Lai

Epidemiology Faculty Publications

Background

q-value is a widely used statistical method for estimating false discovery rate (FDR), which is a conventional significance measure in the analysis of genome-wide expression data. q-value is a random variable and it may underestimate FDR in practice. An underestimated FDR can lead to unexpected false discoveries in the follow-up validation experiments. This issue has not been well addressed in literature, especially in the situation when the permutation procedure is necessary for p-value calculation.

Results

We proposed a statistical method for the conservative adjustment of q-value. In practice, it is usually necessary to calculate p …

Hpcnmf: A High-Performance Toolbox For Non-Negative Matrix Factorization, Karthik Devarajan, Guoli Wang

COBRA Preprint Series

Non-negative matrix factorization (NMF) is a widely used machine learning algorithm for dimension reduction of large-scale data. It has found successful applications in a variety of fields such as computational biology, neuroscience, natural language processing, information retrieval, image processing and speech recognition. In bioinformatics, for example, it has been used to extract patterns and profiles from genomic and text-mining data as well as in protein sequence and structure analysis. While the scientific performance of NMF is very promising in dealing with high dimensional data sets and complex data structures, its computational cost is high and sometimes could be critical for …

Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret

UW Biostatistics Working Paper Series

We have frequently implemented crossover studies to evaluate new therapeutic interventions for genital herpes simplex virus infection. The outcome measured to assess the efficacy of interventions on herpes disease severity is the viral shedding rate, defined as the frequency of detection of HSV on the genital skin and mucosa. We performed a simulation study to ascertain whether our standard model, which we have used previously, was appropriately considering all the necessary features of the shedding data to provide correct inference. We simulated shedding data under our standard, validated assumptions and assessed the ability of 5 different models to reproduce the …

Mixtures Of Self-Modelling Regressions, Rhonda D. Szczesniak, Kert Viele, Robin L. Cooper

Statistics Faculty Publications

A shape invariant model for functions f₁,...,f_n specifies that each individual function f_i can be related to a common shape function g through the relation f_i(x) = a_ig(c_ix + d_i) + b_i. We consider a flexible mixture model that allows multiple shape functions g₁,...,g_K, where each f_i is a shape invariant transformation of one of those g_K. We derive an MCMC algorithm for fitting the model using Bayesian Adaptive Regression Splines (BARS), propose …

Missing At Random And Ignorability For Inferences About Subsets Of Parameters With Missing Data, Roderick J. Little, Sahar Zanganeh

The University of Michigan Department of Biostatistics Working Paper Series

For likelihood-based inferences from data with missing values, Rubin (1976) showed that the missing data mechanism can be ignored when (a) the missing data are missing at random (MAR), in the sense that missingness does not depend on the missing values after conditioning on the observed data, and (b) the parameters of the data model and the missing-data mechanism are distinct; that is, there are no a priori ties, via parameter space restrictions or prior distributions, between the parameters of the data model and the parameters of the model for the mechanism. Rubin described (a) and (b) as the "weakest …

Approximating Confidence Intervals About Discrete Time Survival/Cumulative Incidence Estimates Using The Delta Method, Alexis Dinno, Jong-Sung Kim

Community Health Faculty Publications and Presentations

Poster focuses on answering the questions whether and when and event will happen in a population at risk.

Behavior And Habitat Use Of Roseate Terns (Sterna Dougallii) Before And After Construction Of An Erosion Control Revetment, Corey Grinnell

Masters Theses 1911 - February 2014

An erosion control revetment was constructed at the Falkner Island Unit of the Stewart B. McKinney National Wildlife Refuge, Connecticut during the winter of 2000–2001. At the time, Falkner Island was the fifth largest breeding colony site for the federally endangered Roseate Tern. This study measures and describes some baseline information regarding Roseate Tern nesting, behavior, and habitat use at Falkner Island during the three breeding seasons prior to revetment construction (1998–2000). This baseline information is then compared to similar information from the first breeding season following revetment construction (2001).

For Roseate Tern adults, this study examined changes in pre-nesting …

Understanding The Physical Properties That Control Protein Crystallization By Analysis Of Largescale Experimental Data, W. Nicholson Price Ii, Yang Chen, Samuel K. Handelman, Helen Neely, Philip Manor, Richard Karlin, Rajesh Nair, Jinfeng Liu, Michael Baran, John Everett, Saichiu N. Tong, Farhad Forouhar, Swarup S. Swaminathan, Thomas Acton, Rong Xiao, Joseph R. Luft, Angela Lauricella, George T. Detitta, Burkhard Rost, Gaetano T. Montelione, John T. Hunt

Law Faculty Scholarship

Crystallization is the most serious bottleneck in high-throughput protein-structure determination by diffraction methods. We have used data mining of the large-scale experimental results of the Northeast Structural Genomics Consortium and experimental folding studies to characterize the biophysical properties that control protein crystallization. This analysis leads to the conclusion that crystallization propensity depends primarily on the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. We identify specific sequence features that correlate with crystallization propensity and that can be used to estimate the crystallization probability of a given construct. Analyses of …

Statistical Services, Jane Speijers, Australian Co-Operation With The National Agricultural Research Project, Thailand.

All other publications

2. TERMS OF REFERENCE

To achieve familiarity with the existing resources for biometrical work within the Department of Agriculture both at Bangkhen and at the regional centres - and to gain an understanding of the present systems whereby biometricians are involved in designing experiments and analysing results. This will involve visits to research stations and discussions with both research directors and scientists.

2.1 To become informed on the planned improvements in biometrical services for regional research centres to be carried out through the Thai/World Bank, National Agricultural Research Project (NARP).

2.2 Against the background of items 2.1 and 2.2 above, …