Life Sciences Commons^™

Statistical Contributions To Bioinformatics: Design, Modeling, Structure Learning, And Integration, Jeffrey S. Morris, Veera Baladandayuthapani

Jeffrey S. Morris

Robust Optimization Of Biological Protocols, Patrick Flaherty, Ronald W. Davis

Mathematics and Statistics Department Faculty Publication Series

When conducting high-throughput biological experiments, it is often necessary to develop a protocol that is both inexpensive and robust. Standard approaches are either not cost-effective or arrive at an optimized protocol that is sensitive to experimental variations. Here, we describe a novel approach that directly minimizes the cost of the protocol while ensuring the protocol is robust to experimental variation. Our approach uses a risk-averse conditional value-at-risk criterion in a robust parameter design framework. We demonstrate this approach on a polymerase chain reaction protocol and show that our improved protocol is less expensive than the standard protocol and more robust …

Microproteomics: Analysis Of Protein Diversity In Small Samples, Howard B. Gutstein, Jeffrey S. Morris, Suresh P. Annangudi, Jonathan V. Sweedler

Jeffrey S. Morris

Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The …

Statistical Issues In Proteomic Research, Jeffrey S. Morris

Jeffrey S. Morris

No abstract provided.

Laser Capture Sampling And Analytical Issues In Proteomics, Howard Gutstein, Jeffrey S. Morris

Jeffrey S. Morris

Proteomics holds the promise of evaluating global changes in protein expression and post-translational modificaiton in response to environmental stimuli. However, difficulties in achieving cellular anatomic resolution and extracting specific types of proteins from cells have limited the efficacy of these techniques. Laser capture microdissection has provided a solution to the problem of anatomical resolution in tissues. New extraction methodologies have expanded the range of proteins identified in subsequent analyses. This review will examine the application of laser capture microdissection to proteomic tissue sampling, and subsequent extraction of these samples for differential expression analysis. Statistical and other quantitative issues important for …

Designing And Conducting Experiments For Range Beef Cows, Don C. Adams, Merlyn K. Nielsen, Walter H. Schacht, Richard T. Clark

Department of Animal Science: Faculty Publications

Designing and conducting effective research for range beef systems involves analysis of intended application of the results, identification of factors affecting variation, and selection of appropriate research methods so that precise inferences can be made. Variances associated with time, location, animal, and error in grazing research can be high. Variation due to treatment × location and treatment × time interactions is reduced by increasing the number of locations and periods tested. Random error is reduced by increasing the total number of observations. Animals, pastures, and weather are significant sources of variation in grazing studies. Factors that influence nutrient requirements or …

Statistical Design And Analysis Of Dairy Nutrition Experiments To Improve Detection Of Milk Response Differences, Stephen R. Lowry

Conference on Applied Statistics in Agriculture

The objective of many dairy nutrition experiments is to determine the effect of certain dietary treatments on milk production and quality responses. However, milk responses are quite variable and cows (experimental units) are expensive and have substantial maintenance costs. This manuscript reviews principles for planning to obtain good data relevant to the hypothesis, experimental design to control inherent variation, and interpreted analyses to facilitate understanding of dairy relationships. Emphasis is placed on assurance that milk response differences due to dietary treatments will have a high probability of being detected as significant. Guidelines addressing these principles along with suggested computer programs …