Other Statistics and Probability Commons^™

Practical Guidelines For The Comprehensive Analysis Of Chip-Seq Data, Timonthy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang

Department of Statistics: Faculty Publications

Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE) Project. To this end, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard methodology. Mapping such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only in sample preparation and sequencing but also for computational analysis. Here, we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality …

Drosophila Melanogaster Selection For Survival After Infection With Bacillus Cereus Spores: Evolutionary Genetic And Phenotypic Investigations Of Respiration And Movement, Junjie Ma, Andrew K. Benson, Stephen D. Kachman, Deidra J. Jacobsen, Lawrence G. Harshman

Department of Statistics: Faculty Publications

Laboratory populations of D.melanogaster have been subjected to selection for survival after live spores of B. cereus were introduced as a pathogenic agent. The present study was designed to investigate correlated traits: respiration as ametabolic trait and movement as a behavioral trait.An underlying hypothesiswas that the evolution of increased survival after B. cereus infection exerts ametabolic cost associated with elevated immunity and this would be detected by increased respiration rates. There was support for this hypothesis in the male response to selection, but not for selected-line females. Two phenotypic effects were also observed in the study. Females especially showed a …

The Change In Differing Leukocyte Populations During Vaccination To Bovine Respiratory Disease And Their Correlations With Lung Scores, Health Records, And Average Daily Gain, R. J. Leach, C. G. Chitko-Mckown, G. L. Bennett, S. A. Jones, Stephen D. Kachman, J. W. Keele, K. A. Leymaster, R. M. Thallman, L. A. Kuehn

Department of Statistics: Faculty Publications

Bovine respiratory disease (BRD) is the most economically important disease in U.S. feedlots. Infection can result in morbidity, mortality, and reduced average daily gain. Cheap and reliable genetic methods of prediction and protection from BRD would be highly advantageous to the industry. The immune response may correlate with BRD incidence. Cattle (n = 2,182) were vaccinated against common viral and bacterial pathogens of BRD. Two blood samples were collected, one during booster vaccination and one 21d later, enabling 3 phenotypes for each trait [prebooster (pre), postbooster (post), and delta (post minus pre)]. From the blood samples innate and adaptive responses …

Prediction In M-Complete Problems With Limited Sample Size, Jennifer Lynn Clarke, Bertrand Clarke, Chi-Wai Yu

Department of Statistics: Faculty Publications

We define a new Bayesian predictor called the posterior weighted median (PWM) and compare its performance to several other predictors including the Bayes model average under squared error loss, the Barbieri-Berger median model predictor, the stacking predictor, and the model average predictor based on Akaike's information criterion. We argue that PWM generally gives better performance than other predictors over a range of M-complete problems. This range is between the M-closed-M-complete boundary and the M-complete- M-open boundary. Indeed, as a problem gets closer to M-open, it seems that M-complete predictive methods begin to break down. Our comparisons rest on extensive simulations …

Comparison Of Molecular Breeding Values Based On Within- And Across-Breed Training In Beef Cattle, Stephen D. Kachman, Matthew L. Spangler, Gary L. Bennett, Kathryn J. Hanford, Larry A. Kuehn, Warren M. Snelling, Mark Thallman, Mahdi Saatchi, Dorian J. Garrick, Robert D. Schnabel, Jeremy F. Taylor, E John Pollak

Department of Statistics: Faculty Publications

Background: Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported.

Methods: Molecular breeding values for weaning and yearling weight …