Time filter

Source Type

Thornwood, NY, United States

Hunter S.R.,Purdue University | McClosky B.,Nature Source Genetics
IIE Transactions (Institute of Industrial Engineers) | Year: 2016

Commercial plant breeders improve economically important traits by selectively mating individuals from a given breeding population. Potential pairings are evaluated before the growing season using Monte Carlo simulation, and a mating design is created to allocate a fixed breeding budget across the parent pairs to achieve desired population outcomes. We introduce a novel objective function for this mating design problem that accurately models the goals of a certain class of breeding experiments. The resulting mating design problem is a computationally burdensome simulation optimization problem on a combinatorially large set of feasible points. We propose a two-step solution to this problem: (i) simulate to estimate the performance of each parent pair and (ii) solve an estimated version of the mating design problem, which is an integer program, using the simulation output. To reduce the computational burden when implementing steps (i) and (ii), we analytically identify a Pareto set of parent pairs that will receive the entire breeding budget at optimality. Since we wish to estimate the Pareto set in step (i) as input to step (ii), we derive an asymptotically optimal simulation budget allocation to estimate the Pareto set that, in our numerical experiments, out-performs Multi-objective Optimal Computing Budget Allocation in reducing misclassifications. Given the estimated Pareto set, we provide a branch-and-bound algorithm to solve the estimated mating design problem. Our approach dramatically reduces the computational effort required to solve the mating design problem when compared with naïve methods. Copyright © 2016 “IIE” Source

McClosky B.,Nature Source Genetics | Simms A.,University of Maryland Baltimore County | Hicks I.V.,Rice University
Journal of Combinatorial Optimization | Year: 2011

This paper offers a generalization of the independence polynomial, the co-k-plex polynomial. The resulting family of polynomials carries combinatorial information on a class of independence systems defined over the vertex set of a finite graph. Specifically, we offer a recursion formula and examples of the co-2-plex polynomial on certain graphs. In addition, we characterize the class of graphs whose co-2-plex polynomial will have all real roots. © 2010 Springer Science+Business Media, LLC. Source

Sheehan M.J.,Nature Source Genetics | Pawlowski W.P.,Cornell University
Methods in Enzymology | Year: 2012

Progression of meiosis has been traditionally reconstructed from microscopic images collected from fixed cells. This approach has clear shortcomings in accurately portraying the dynamics of meiotic processes. Studies conducted in recent years mostly in unicellular fungi have shown that chromosomes in meiotic prophase exhibit dynamic motility that cannot be accurately examined using fixed cell imaging. However, in contrast to yeast, research on meiotic chromosome dynamics in multicellular eukaryotes has been lagging. This was in part because meiocytes in multicellular eukaryotes reside deep within reproductive organs and are often refractory to culturing. Here, we describe a method in which intact, live-plant reproductive organs (anthers) are cultured to enable monitoring chromosome dynamics of meiocytes using multiphoton excitation (MPE) microscopy. The method was developed for use in maize but can be applied to other plant species and adapted for use in other taxa in which meiocytes are embedded in multicellular reproductive structures. MPE microscopy allows visualization of meiocytes embedded within native tissue in planta and thus meiocytes remain intact for the entire imaging procedure. We detail the kinds of time-lapse movies that can be captured and analyzed using this technique and also highlight software packages that can be utilized for analysis of movies chromosome dynamic in live meiocytes. © 2012 Elsevier Inc. Source

Almudevar A.,University of Rochester | Lacombe J.,Nature Source Genetics
IEEE Transactions on Signal Processing | Year: 2012

A signal processing algorithm for the estimation of the trajectory of amobile transmitter in a wireless network, based on RSSI measurements, was proposed in [A. Almudevar, "Approximate calibration-free trajectory reconstruction in a wireless network," IEEE Trans. Signal Process., vol. 56, no. 7, pp. 3081-3088, 2008]. The problem of explicit transmission source location estimation is bypassed, producing instead an estimation of the trajectory shape which does not require a translation of RSSI measurements into transmission distance estimates. It was proven for the case of k = 3 receivers that the resulting mapping of the source to an estimation region is 1 - 1 and continuous while preserving directionality and providing robustness to measurement distortion. The purpose of this correspondence is to extend these results to the general k ≥ 3 case. The method is demonstrated using a commercial RSSI home monitoring system using k = 4 receivers. © 2012 IEEE. Source

LaCombe J.,Nature Source Genetics
G3 (Bethesda, Md.) | Year: 2012

The Churchill-Doerge approach toward constructing empirical thresholds has received widespread use in the genetic mapping literature through the past 16 years. The method is valued for both its simplicity and its ability to preserve the genome-wide error rate at a prespecified level. However, the Churchill-Doerge method is not designed to maintain the local (comparison-wise) error rate at a constant level except in situations that are unlikely to occur in practice. In this article, we introduce the objective of preserving the local error rate at a constant level in the context of mapping quantitative trait loci in linkage populations. We derive a method that preserves the local error rate at a constant level, provide an application via simulation on a Hordeum vulgare population, and demonstrate evidence of the relationship between recombination and location bias. Furthermore, we indicate that this method is equivalent to the Churchill-Doerge method when several assumptions are satisfied. Source

Discover hidden collaborations