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Articles 1 - 30 of 52

Full-Text Articles in Biometry

Mixtures Of Self-Modelling Regressions, Rhonda D. Szczesniak, Kert Viele, Robin L. Cooper Mar 2019

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

Robin L. Cooper

A shape invariant model for functions f1,...,fn specifies that each individual function fi can be related to a common shape function g through the relation fi(x) = aig(cix + di) + bi. We consider a flexible mixture model that allows multiple shape functions g1,...,gK, where each fi is a shape invariant transformation of one of those gK. We derive an MCMC algorithm for fitting the model using Bayesian Adaptive Regression Splines (BARS), propose a strategy to improve its mixing properties and utilize existing model selection ...


Reassessment Of The Red Drum Stock In Mississippi Coastal Waters: The Role Of Ages 3-5 Year-Class Fish, Emily Satterfield Dec 2017

Reassessment Of The Red Drum Stock In Mississippi Coastal Waters: The Role Of Ages 3-5 Year-Class Fish, Emily Satterfield

Master's Theses

Red Drum, Sciaenops ocellatus, are highly sought after by sport fishermen in Mississippi coastal waters. In 2016, Mississippi anglers made over 180,000 fishing trips targeting Red Drum, making it the second most targeted marine species. The current Fishery Management Plan of the Gulf of Mexico Fishery Management Council, prohibits harvest of Red Drum in federal waters. Monitoring of the stock in Mississippi state waters occurs at sites that are almost exclusively estuarine, using gear types selective for juvenile fish. Additional samples come from the for-hire-industry that typically targets larger Red Drum. This project’s goal was to target age ...


Adaptation Of The Genetic Risk Prediction Model Brcapro For Primary Care Settings, Philamer M. Atienza May 2017

Adaptation Of The Genetic Risk Prediction Model Brcapro For Primary Care Settings, Philamer M. Atienza

Theses and Dissertations

Identifying women at high risks of carrying the breast cancer susceptibility genes is crucial for providing timely surveillance and necessary health management interventions. BRCAPRO is one of the most widely used statistical models for breast cancer risk prediction in genetic counseling. It provides carrier probabilities of BRCA1/2 mutations and calculates the risks of developing breast and ovarian cancers. This calculation requires extensive personal and family history information, which makes it difficult to use in primary care where a wider population could be reached. Thus, we developed a two-stage approach for the genetic risk prediction of BRCA1/2 mutation. In ...


A Statistical Method For The Conservative Adjustment Of False Discovery Rate (Q-Value), Yinglei Lai Mar 2017

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

Epidemiology and Biostatistics 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 ...


Estimating The Effects Of Overstory Retention, Vegetative Competition, And Site Quality On The Height Growth Of Small Ponderosa Pine Trees Using Regression Quantiles, Colin P. Kirkmire Jan 2017

Estimating The Effects Of Overstory Retention, Vegetative Competition, And Site Quality On The Height Growth Of Small Ponderosa Pine Trees Using Regression Quantiles, Colin P. Kirkmire

Graduate Student Theses, Dissertations, & Professional Papers

Ponderosa pine (Pinus ponderosa C. Lawson) forests in the Inland Northwestern region of the US are increasingly managed under multi-aged silvicultural systems that provide stand structure for wildlife habitat, timber production, enhanced aesthetic, or restoration of presettlement conditions (O'Hara 2005). Partial retention harvest, where an element of the previous stand's overstory structure is retained, is commonly used to achieve a multi-aged stand structure. However, little is known about how ponderosa pine trees in the understory respond to overstory and understory competitive factors following partial retention harvest. The height growth of small trees was hypothesized to be influenced by ...


Juvenile Remains: Predicting Body Mass And Stature In Modern American Populations, Erin F E Pinkston Jan 2017

Juvenile Remains: Predicting Body Mass And Stature In Modern American Populations, Erin F E Pinkston

Theses and projects

There are increasing numbers of unidentified persons in the U.S. and abroad. To generate positive identifications, forensic anthropologists and others working in the medicolegal field employ a variety of methods to produce biological profiles to match to case files and missing persons databases. Body mass, and stature are two important components of a biological profile, and both can be estimated using regression formulae derived from skeletal metrics. In cases of unidentified juvenile remains, these are particularly important metrics, as it is difficult or impossible to determine sex in prepubescent remains, and the quality of ancestry estimation is currently under ...


Hpcnmf: A High-Performance Toolbox For Non-Negative Matrix Factorization, Karthik Devarajan, Guoli Wang Feb 2016

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 Jan 2016

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 ...


Macrobenthic Communities In The Northern Gulf Of Mexico Hypoxic Zone: Testing The Pearson-Rosenberg Model, Shivakumar Shivarudrappa Dec 2015

Macrobenthic Communities In The Northern Gulf Of Mexico Hypoxic Zone: Testing The Pearson-Rosenberg Model, Shivakumar Shivarudrappa

Dissertations

The Pearson and Rosenberg (P-R) conceptual model of macrobenthic succession was used to assess the impact of hypoxia (dissolved oxygen [DO] ≤ 2 mg/L) on the macrobenthic community on the continental shelf of northern Gulf of Mexico for the first time. The model uses a stress-response relationship between environmental parameters and the macrobenthic community to determine the ecological condition of the benthic habitat. The ecological significance of dissolved oxygen in a benthic habitat is well understood. In addition, the annual recurrence of bottom-water hypoxia on the Louisiana/Texas shelf during summer months is well documented.

The P-R model illustrates the ...


Individual Tree Measurements From Three-Dimensional Point Clouds, Elias Ayrey Aug 2015

Individual Tree Measurements From Three-Dimensional Point Clouds, Elias Ayrey

Electronic Theses and Dissertations

This study develops and tests novel methodologies for measuring the attributes of individual trees from three-dimensional point clouds generated from an aerial platform. Recently, advancements in technology have allowed for the acquisition of very high resolution three-dimensional point clouds that can be used to map the forest in a virtual environment. These point clouds can be interpreted to produce valuable forest attributes across entire landscapes with minimal field labor, which can then aid forest managers in their planning and decision making.

Biometrics derived from point clouds are often generated on a plot level, with estimates spanning many meters (rather than ...


Evaluating The Long-Term Effects Of Logging Residue Removals In Great Lakes Aspen Forests, Michael I. Premer Jan 2015

Evaluating The Long-Term Effects Of Logging Residue Removals In Great Lakes Aspen Forests, Michael I. Premer

Dissertations, Master's Theses and Master's Reports

Commercial aspen (Populus spp.) forests of the Great Lakes region are primarily managed for timber products such as pulp fiber and panel board, but logging residues (topwood and non-merchantable bolewood) are potentially important for utilization in the bioenergy market. In some regions, pulp and paper mills already utilize residues as fuel in combustion for heat and electricity, and progressive energy policies will likely cause an increase in biomass feedstock demand. The effects of removing residues, which have a comparatively high concentration of macronutrients, is poorly understood when evaluating long-term site productivity, future timber yields, plant diversity, stand dynamics, and consequently ...


Mixtures Of Self-Modelling Regressions, Rhonda D. Szczesniak, Kert Viele, Robin L. Cooper Aug 2014

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

Statistics Faculty Publications

A shape invariant model for functions f1,...,fn specifies that each individual function fi can be related to a common shape function g through the relation fi(x) = aig(cix + di) + bi. We consider a flexible mixture model that allows multiple shape functions g1,...,gK, where each fi is a shape invariant transformation of one of those gK. We derive an MCMC algorithm for fitting the model using Bayesian Adaptive Regression Splines (BARS), propose a strategy to improve its mixing properties and utilize existing model selection ...


Spectral Density Shrinkage For High-Dimensional Time Series, Mark Fiecas, Rainer Von Sachs Dec 2013

Spectral Density Shrinkage For High-Dimensional Time Series, Mark Fiecas, Rainer Von Sachs

Mark Fiecas

Time series data obtained from neurophysiological signals is often high-dimensional and the length of the time series is often short relative to the number of dimensions. Thus, it is difficult or sometimes impossible to compute statistics that are based on the spectral density matrix because these matrices are numerically unstable. In this work, we discuss the importance of regularization for spectral analysis of high-dimensional time series and propose shrinkage estimation for estimating high-dimensional spectral density matrices. The shrinkage estimator is derived from a penalized log-likelihood, and the optimal penalty parameter has a closed-form solution, which can be estimated using the ...


Adaptive Mechanisms Of Campylobacter Jejuni To Erythromycin Treatment, Qingqing Xia, Wayne T. Muraoka, Zhangqi Shen, Orhan Sahin, Hongning Wang, Zuowei Wu, Peng Liu, Qijing Zhang Jun 2013

Adaptive Mechanisms Of Campylobacter Jejuni To Erythromycin Treatment, Qingqing Xia, Wayne T. Muraoka, Zhangqi Shen, Orhan Sahin, Hongning Wang, Zuowei Wu, Peng Liu, Qijing Zhang

Veterinary Microbiology and Preventive Medicine Publications

Background
Macrolide is the drug of choice to treat human campylobacteriosis, but Campylobacter resistance to this antibiotic is rising. The mechanisms employed by Campylobacter jejuni to adapt to erythromycin treatment remain unknown and are examined in this study. The transcriptomic response of C. jejuni NCTC 11168 to erythromycin (Ery) treatment was determined by competitive microarray hybridizations. Representative genes identified to be differentially expressed were further characterized by constructing mutants and assessing their involvement in antimicrobial susceptibility, oxidative stress tolerance, and chicken colonization.

Results
Following the treatment with an inhibitory dose of Ery, 139 genes were up-regulated and 119 were down-regulated ...


Missing At Random And Ignorability For Inferences About Subsets Of Parameters With Missing Data, Roderick J. Little, Sahar Zanganeh Feb 2013

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 ...


Global Quantitative Assessment Of The Colorectal Polyp Burden In Familial Adenomatous Polyposis Using A Web-Based Tool, Patrick M. Lynch, Jeffrey S. Morris, William A. Ross, Miguel A. Rodriguez-Bigas, Juan Posadas, Rossa Khalaf, Diane M. Weber, Valerie O. Sepeda, Bernard Levin, Imad Shureiqi Jan 2013

Global Quantitative Assessment Of The Colorectal Polyp Burden In Familial Adenomatous Polyposis Using A Web-Based Tool, Patrick M. Lynch, Jeffrey S. Morris, William A. Ross, Miguel A. Rodriguez-Bigas, Juan Posadas, Rossa Khalaf, Diane M. Weber, Valerie O. Sepeda, Bernard Levin, Imad Shureiqi

Jeffrey S. Morris

Background: Accurate measures of the total polyp burden in familial adenomatous polyposis (FAP) are lacking. Current assessment tools include polyp quantitation in limited-field photographs and qualitative total colorectal polyp burden by video.

Objective: To develop global quantitative tools of the FAP colorectal adenoma burden.

Design: A single-arm, phase II trial.

Patients: Twenty-seven patients with FAP.

Intervention: Treatment with celecoxib for 6 months, with before-treatment and after-treatment videos posted to an intranet with an interactive site for scoring.

Main Outcome Measurements: Global adenoma counts and sizes (grouped into categories: less than 2 mm, 2-4 mm, and greater than 4 mm) were ...


A Field Comes Of Age: Geometric Morphometrics In The 21st Century, Dean C. Adams, F. James Rohlf, Dennis E. Slice Jan 2013

A Field Comes Of Age: Geometric Morphometrics In The 21st Century, Dean C. Adams, F. James Rohlf, Dennis E. Slice

Ecology, Evolution and Organismal Biology Publications

Twenty years ago, Rohlf and Marcus proclaimed that a "revolution in morphometrics" was underway, where classic analyses based on sets of linear distances were being supplanted by geometric approaches making use of the coordinates of anatomical landmarks. Since that time the field of geometric morphometrics has matured into a rich and cohesive discipline for the study of shape variation and covariation. The development of the field is identified with the Procrustes paradigm, a methodological approach to shape analysis arising from the intersection of the statistical shape theory and analytical procedures for obtaining shape variables from landmark data. In this review ...


Statistical Methods For Proteomic Biomarker Discovery Based On Feature Extraction Or Functional Modeling Approaches, Jeffrey S. Morris Jan 2012

Statistical Methods For Proteomic Biomarker Discovery Based On Feature Extraction Or Functional Modeling Approaches, Jeffrey S. Morris

Jeffrey S. Morris

In recent years, developments in molecular biotechnology have led to the increased promise of detecting and validating biomarkers, or molecular markers that relate to various biological or medical outcomes. Proteomics, the direct study of proteins in biological samples, plays an important role in the biomarker discovery process. These technologies produce complex, high dimensional functional and image data that present many analytical challenges that must be addressed properly for effective comparative proteomics studies that can yield potential biomarkers. Specific challenges include experimental design, preprocessing, feature extraction, and statistical analysis accounting for the inherent multiple testing issues. This paper reviews various computational ...


Integrative Bayesian Analysis Of High-Dimensional Multi-Platform Genomics Data, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju C. Manyam, Kim-Anh Do Jan 2012

Integrative Bayesian Analysis Of High-Dimensional Multi-Platform Genomics Data, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju C. Manyam, Kim-Anh Do

Jeffrey S. Morris

Motivation: Analyzing data from multi-platform genomics experiments combined with patients’ clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current integration approaches that treat the data are limited in that they do not consider the fundamental biological relationships that exist among the data from platforms.

Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes/biomarkers that are associated with clinical outcome. This framework uses a hierarchical modeling technique to combine the data obtained from multiple ...


R Code: A Non-Iterative Implementation Of Tango's Score Confidence Interval For A Paired Difference Of Proportions, Zhao Yang Jan 2012

R Code: A Non-Iterative Implementation Of Tango's Score Confidence Interval For A Paired Difference Of Proportions, Zhao Yang

Zhao (Tony) Yang, Ph.D.

For matched-pair binary data, a variety of approaches have been proposed for the construction of a confidence interval (CI) for the difference of marginal probabilities between two procedures. The score-based approximate CI has been shown to outperform other asymptotic CIs. Tango’s method provides a score CI by inverting a score test statistic using an iterative procedure. In the developed R code, we propose an efficient non-iterative method with closed-form expression to calculate Tango’s CIs. Examples illustrate the practical application of the new approach.


Kinetics Of Uv254 Inactivation Of Selected Viral Pathogens In A Static System, T. Cutler, C. Wang, Q. Qin, F. Zhou, K. Warren, K.-J. Yoon, S. J. Hoff, J. Ridpath, J. Zimmerman Aug 2011

Kinetics Of Uv254 Inactivation Of Selected Viral Pathogens In A Static System, T. Cutler, C. Wang, Q. Qin, F. Zhou, K. Warren, K.-J. Yoon, S. J. Hoff, J. Ridpath, J. Zimmerman

Veterinary Diagnostic and Production Animal Medicine Publications

Aims:  The objective of this study was to estimate UV254 inactivation constants for four viral pathogens: influenza virus type A, porcine respiratory and reproductive syndrome virus (PRRSV), bovine viral diarrhoea virus (BVDV) and reovirus.

Methods and Results:  Viruses in culture medium were exposed to one of nine doses of UV254 and then titrated for infectious virus. Analysis showed that viral inactivation by UV254 was more accurately described by a two-stage inactivation model vs a standard one-stage inactivation model.

Conclusions:  The results provided evidence for the existence of two heterogeneous viral subpopulations among the viruses tested, one highly ...


Statistical Analysis In Empirical Bayes And In Causal Inference, Hui Nie May 2011

Statistical Analysis In Empirical Bayes And In Causal Inference, Hui Nie

Publicly Accessible Penn Dissertations

In Part I titled Empirical Bayes Estimation, we discuss the estimation of a heteroscedastic multivariate normal mean in terms of the ensemble risk. We first derive the ensemble minimax properties of various estimators that shrink towards zero through the empirical Bayes method. We then generalize our results to the case where the variances are given as a common unknown but estimable chi-squared random variable scaled by different known factors. We further provide a class of ensemble minimax estimators that shrink towards the common mean. We also make comparison and show differences between results from the heteroscedastic case and those from ...


Approximating Confidence Intervals About Discrete Time Survival/Cumulative Incidence Estimates Using The Delta Method, Alexis Dinno, Jong-Sung Kim Jan 2011

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.


A Bayesian Approach To Dose-Response Assessment And Drug-Drug Interaction Analysis: Application To In Vitro Studies, Violeta G. Hennessey Aug 2010

A Bayesian Approach To Dose-Response Assessment And Drug-Drug Interaction Analysis: Application To In Vitro Studies, Violeta G. Hennessey

UT GSBS Dissertations and Theses (Open Access)

The considerable search for synergistic agents in cancer research is motivated by the therapeutic benefits achieved by combining anti-cancer agents. Synergistic agents make it possible to reduce dosage while maintaining or enhancing a desired effect. Other favorable outcomes of synergistic agents include reduction in toxicity and minimizing or delaying drug resistance. Dose-response assessment and drug-drug interaction analysis play an important part in the drug discovery process, however analysis are often poorly done. This dissertation is an effort to notably improve dose-response assessment and drug-drug interaction analysis.

The most commonly used method in published analysis is the Median-Effect Principle/Combination Index ...


Gene Expression In Hypothalamus, Liver, And Adipose Tissues And Food Intake Response To Melanocortin-4 Receptor Agonist In Pigs Expressing Melanocortin-4 Receptor Mutations, C. Richard Barb, Gary J. Hausman, Romdhane Rekaya, Clay A. Lents, Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P. Couture, Lloyd L. Anderson, Jack C. M. Dekkers, Christopher K. Tuggle May 2010

Gene Expression In Hypothalamus, Liver, And Adipose Tissues And Food Intake Response To Melanocortin-4 Receptor Agonist In Pigs Expressing Melanocortin-4 Receptor Mutations, C. Richard Barb, Gary J. Hausman, Romdhane Rekaya, Clay A. Lents, Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P. Couture, Lloyd L. Anderson, Jack C. M. Dekkers, Christopher K. Tuggle

Animal Science Publications

Transcriptional profiling was used to identify genes and pathways that responded to intracerebroventricular injection of melanocortin-4 receptor (MC4R) agonist [Nle4, D-Phe7]-α-melanocyte stimulating hormone (NDP-MSH) in pigs homozygous for the missense mutation in the MC4R, D298 allele (n = 12), N298 allele (n = 12), or heterozygous (n = 12). Food intake (FI) was measured at 12 and 24 h after treatment. All pigs were killed at 24 h after treatment, and hypothalamus, liver, and back-fat tissue was collected. NDP-MSH suppressed (P < 0.004) FI at 12 and 24 h in all animals after treatment. In response to NDP-MSH, 278 genes in hypothalamus (q ≤ 0.07, P ≤ 0.001), 249 genes in liver (q ≤ 0.07, P ≤ 0.001), and 5,066 genes in ...


Gene Expression Profiling Of The Short-Term Adaptive Response To Acute Caloric Restriction In Liver And Adipose Tissues Of Pigs Differing In Feed Efficiency, Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P. Couture, C. Richard Barb, Gary J. Hausman, Dan Nettleton, Lloyd L. Anderson, Jack C. M. Dekkers, Christopher K. Tuggle Feb 2010

Gene Expression Profiling Of The Short-Term Adaptive Response To Acute Caloric Restriction In Liver And Adipose Tissues Of Pigs Differing In Feed Efficiency, Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P. Couture, C. Richard Barb, Gary J. Hausman, Dan Nettleton, Lloyd L. Anderson, Jack C. M. Dekkers, Christopher K. Tuggle

Animal Science Publications

Residual feed intake (RFI) is a measure of feed efficiency, in which low RFI denotes improved feed efficiency. Caloric restriction (CR) is associated with feed efficiency in livestock species and to human health benefits, such as longevity and cancer prevention. We have developed pig lines that differ in RFI, and we are interested in identifying the genes and pathways that underlie feed efficiency. Prepubertal Yorkshire gilts with low RFI (n = 10) or high RFI (n = 10) were fed ad libitum or fed at restricted intake of 80% of maintenance energy requirements for 8 days. We measured serum metabolites and hormones ...


Wavelet-Based Functional Linear Mixed Models: An Application To Measurement Error–Corrected Distributed Lag Models, Elizabeth J. Malloy, Jeffrey S. Morris, Sara D. Adar, Helen Suh, Diane R. Gold, Brent A. Coull Jan 2010

Wavelet-Based Functional Linear Mixed Models: An Application To Measurement Error–Corrected Distributed Lag Models, Elizabeth J. Malloy, Jeffrey S. Morris, Sara D. Adar, Helen Suh, Diane R. Gold, Brent A. Coull

Jeffrey S. Morris

Frequently, exposure data are measured over time on a grid of discrete values that collectively define a functional observation. In many applications, researchers are interested in using these measurements as covariates to predict a scalar response in a regression setting, with interest focusing on the most biologically relevant time window of exposure. One example is in panel studies of the health effects of particulate matter (PM), where particle levels are measured over time. In such studies, there are many more values of the functional data than observations in the data set so that regularization of the corresponding functional regression coefficient ...


Members’ Discoveries: Fatal Flaws In Cancer Research, Jeffrey S. Morris Jan 2010

Members’ Discoveries: Fatal Flaws In Cancer Research, Jeffrey S. Morris

Jeffrey S. Morris

A recent article published in The Annals of Applied Statistics (AOAS) by two MD Anderson researchers—Keith Baggerly and Kevin Coombes—dissects results from a highly-influential series of medical papers involving genomics-driven personalized cancer therapy, and outlines a series of simple yet fatal flaws that raises serious questions about the veracity of the original results. Having immediate and strong impact, this paper, along with related work, is providing the impetus for new standards of reproducibility in scientific research.


Statistical Contributions To Proteomic Research, Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, Kevin R. Coombes Jan 2010

Statistical Contributions To Proteomic Research, Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, Kevin R. Coombes

Jeffrey S. Morris

Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the ...


Informatics And Statistics For Analyzing 2-D Gel Electrophoresis Images, Andrew W. Dowsey, Jeffrey S. Morris, Howard G. Gutstein, Guang Z. Yang Jan 2010

Informatics And Statistics For Analyzing 2-D Gel Electrophoresis Images, Andrew W. Dowsey, Jeffrey S. Morris, Howard G. Gutstein, Guang Z. Yang

Jeffrey S. Morris

Whilst recent progress in ‘shotgun’ peptide separation by integrated liquid chromatography and mass spectrometry (LC/MS) has enabled its use as a sensitive analytical technique, proteome coverage and reproducibility is still limited and obtaining enough replicate runs for biomarker discovery is a challenge. For these reasons, recent research demonstrates the continuing need for protein separation by two-dimensional gel electrophoresis (2-DE). However, with traditional 2-DE informatics, the digitized images are reduced to symbolic data though spot detection and quantification before proteins are compared for differential expression by spot matching. Recently, a more robust and automated paradigm has emerged where gels are ...