In the Addona et al. paper (Nature Biotechnology 2009), a large-scale multi-site study was performed to quantify Multiple Reaction Monitoring (MRM) measurements of proteins spiked in human plasma. The unlabeled signature peptides derived from the seven target proteins were measured at nine different concentration levels, and their isotopic counterparts were served as the internal standards.

%B PLoS1 %V 6 %P e14590 %G eng %R 10.1371/journal.pone.0014590 %0 Journal Article %J Computational Statistics and Data Analysis %D 2009 %T Verification servers: enabling analysts to assess the quality of inferences from public use data %A J. P. Reiter %A A. Oganyan %A A. F. Karr %XTo protect confidentiality, statistical agencies typically alter data before releasing them to the public. Ideally, although generally not done, the agency also provides a way for secondary data analysts to assess the quality of inferences obtained with the released data. Quality measures can help secondary data analysts to identify inaccurate conclusions resulting from the disclosure limitation procedures, as well as have confidence in accurate conclusions. We propose a framework for an interactive, web-based system that analysts can query for measures of inferential quality. As we illustrate, agencies seeking to build such systems must consider the additional disclosure risks from releasing quality measures. We suggest some avenues of research on limiting these risks.

%B Computational Statistics and Data Analysis %V 53 %P 1475-1482 %G eng %0 Journal Article %J Journal of Regional Science %D 2003 %T Validation of multiclass urban travel forecasting models combining origin-destination, mode, and route choices %A Bar-Gera, H. %A Boyce, D. E. %B Journal of Regional Science %V 43 %P 517-540 %G eng %& 517 %0 Journal Article %J Transportation Research Record C %D 2002 %T Variability of travel times on arterial streets: effects of signals and volume %A A. F. Karr %A T.L. Graves %A A. Mockus %A P. Schuster %B Transportation Research Record C %V 10 %P 000-000 %G eng %0 Journal Article %J Journal Comp. Graphical Statistics %D 2002 %T Visual Scalability %A A. F. Karr %A S. G. Eick %B Journal Comp. Graphical Statistics %V 11 %P 22-43 %G eng %0 Journal Article %J INTERACTIONS %D 2002 %T Visualizing Software Changes %A Stephen G. Eick %A Paul Schuster %A Audris Mockus %A Todd L. Graves %A Alan F. Karr %B INTERACTIONS %V 17 %P 29–31 %G eng %0 Journal Article %J Advances in Applied Probability %D 2000 %T Variance Reducing Modifications for Estimators of Standardized Moments of Random Sets %A Jeffrey D. Picka %XIn the statistical analysis of random sets, it is useful to have simple statistics that can be used to describe the realizations of these sets. The cumulants and several other standardized moments such as the correlation and second cumulant can be used for this purpose, but their estimators can be excessively variable if the most straightforward estimation strategy is used. Through exploitation of similarities between this estimation problem and a similar one for a point process statistic, two modifications are proposed. Analytical results concerning the effects of these modifications are found through use of a specialized asymptotic regime. Simulation results establish that the modifications are highly effective at reducing estimator standard deviations for Boolean models. The results suggest that the reductions in variance result from a balanced use of information in the estimation of the first and second moments, through eliminating the use of observations that are not used in second moment estimation.

%B Advances in Applied Probability %V 32 %P 682-700 %G eng %0 Journal Article %J International Transactions in Operational Research %D 1999 %T Variances of link travel time estimates: Implications for optimal routes %A A. F. Karr %A A. Sen %A P. Thakuriah %A X. Zhu %K Advanced Traveler Information System %K Covariance of travel times %K Dependence in travel time observations %K Intelligent Transportation System %K Probe vehicles %K Variance of travel time estimates %K Vehicle simulation model %XIn this paper, we explore the consequences of using link travel time estimates with high variance to compute the minimum travel time route between an origin and destination pair. Because of platoon formation or for other reasons, vehicles on a link separated by small headways tend to have similar travel times. In other words, the covariance of link travel times of distinct vehicles which are close together may not be zero. It follows that the variance of the mean of travel times obtained from a sample of n vehicles on a same link over small time intervals is of the form a+b/n where a and b would usually be positive. This result has an important implication for the quality of road network travel time information given by Intelligent Transportation Systems (ITS)?that the variance of the estimate of mean travel time does not go to zero with increasing n. Thus the quality of information disseminated by ITS is not necessarily improved by increasing the market penetration of vehicles monitoring the system with the necessary equipment (termed probe vehicles). Estimates of a and b for a set of links are presented in the paper and consequences for probe-based ITS are explored by means of a simulation of such a system which is operational on an actual network.

%B International Transactions in Operational Research %V 6 %P 75-87 %8 January %G eng %R 10.1111/j.1475-3995.1999.tb00144.x %0 Conference Proceedings %B Transportation Networks: Recent Methodological Advances. Selected Proceedings of the 4th EURO Transportation Meeting %D 1999 %T Variational inequality Model of Ideal Dynamic User-Optimal Route Choice %A Boyce, D. E. %A Lee, D.-H. %A Janson, B.N. %K Advanced traffic management systems %K Advanced Traveler Information Systems %K Links (Networks) %K Route choice %K Variational inequalities (Mathematics) %XAn ideal dynamic user-optimal (DUO) route choice model is described for predicting dynamic traffic conditions, as required for off-line evaluation of Advanced Traffic Management Systems and Advanced Traveler Information Systems. The model is formulated as a variational inequality (VI), a general way of describing a dynamic network equilibrium. Although route-based VI models have an intuitive interpretation, their computational complexity makes them intractable for real applications. Consequently, the proposed model is formulated as a link-based variational inequality for use in large-scale implementations. Using the diagonalization technique with discrete time intervals, the model is solved to a specified level of convergence. Computational results for a real, large-scale traffic network are presented.

%B Transportation Networks: Recent Methodological Advances. Selected Proceedings of the 4th EURO Transportation Meeting %C Newcastle, England %P 289-302 %G eng %0 Book Section %B Dynamic Urban Transportation Network Models %D 1994 %T Variational Inequality Models of Ideal Dynamic User-Optimal Route Choice Problems %A Ran, Bin %A Boyce, David E. %XIn this chapter, we present both route-based and link-based variational inequality models for the ideal dynamic user-optimal route choice problem. In Section 13.1, a route-time-based VI model for ideal DUO route choice is proposed. This model is the most straight-forward formulation of route-time-based, ideal DUO route choice conditions. In Section 13.2, a multi-group route-time-based VI model is developed. In this model, each group of travelers is associated with a disutility function. Thus, the route-based ideal DUO route choice conditions are defined for each group of travelers on the basis of travel disutilities instead of travel times only.

%B Dynamic Urban Transportation Network Models %S Lecture Notes in Economics and Mathematical Systems %I Springer Berlin Heidelberg %V 417 %P 267-290 %@ 978-3-540-58360-8 %G eng %U http://dx.doi.org/10.1007/978-3-662-00773-0_13 %R 10.1007/978-3-662-00773-0_13