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"Whitney, Joseph"
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Genetic Landscape of a Cell
A genome-scale genetic interaction map was constructed by examining 5.4 million gene-gene pairs for synthetic genetic interactions, generating quantitative genetic interaction profiles for approximately 75% of all genes in the budding yeast, Saccharomyces cerevisiae. A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function. The global network identifies functional cross-connections between all bioprocesses, mapping a cellular wiring diagram of pleiotropy. Genetic interaction degree correlated with a number of different gene attributes, which may be informative about genetic network hubs in other organisms. We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification.
Journal Article
Genome-wide detection of tandem DNA repeats that are expanded in autism
Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders
1
. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2–20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)
2
,
3
and population control individuals
4
. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in
DMPK
and
FXN
, which are associated with neuromuscular conditions, and in previously unknown loci such as
FGF14
and
CACNB1
. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.
Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.
Journal Article
Genome-wide detection of tandem DNA repeats expanded in autism
Tandem DNA repeats vary by the size and sequence of each unit (motif). When expanded, they have been associated with >40 monogenic disorders1. Their involvement in complex disorders is largely unknown, as is the extent of their heterogeneity. Here, we interrogated genome-wide characteristics of tandem repeats with 2-20 bp motifs in 17,231 genomes of families with autism2,3 and population controls4. We found extensive polymorphism in motif size and sequence. Many correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated tandem repeat expansions that were rare among population controls were significantly more prevalent among individuals with autism than their unaffected siblings, particularly in exons and near splice junctions and in genes related to nervous system development and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in autism-affected children versus 20.7% in unaffected children, suggesting a collective contribution to autism risk of 2.6%. They included novel autism-linked tandem repeat expansions in DMPK and FXN, known for neuromuscular conditions, and in novel loci such as FGF14 and CACNB1. These were associated with lower IQ and adaptive ability. Our results revealed a strong contribution of tandem DNA repeat expansions to the genetic etiology and phenotypic complexity of autism.
Journal Article
Goats and garbage in Khartoum, Sudan: a study of the urban ecology of animal keeping
Waste management in developing world urban areas is an acute problem which is linked to high growth rates and abatement methods less advanced than in the developed world. Existing neighborhood waste management practices often include the use of organic waste as a feed supplement for urban livestock (mainly goats, but also sheep and cattle). These urban animals bring economic benefits to less affluent residents, who would suffer an economic loss if their supply of urban waste was reduced or eliminated by an organized waste collection and disposal strategy. This paper employs a survey of 319 Greater Khartoum households to derive an estimate of waste intake per urban animal, and illustrate demographic factors (e.g., rural or urban roots, income, education, number of children) which influence animal keeping. A loglinear/logit model is developed to predict animal-keeping households. This model can be applied by waste management planners to estimate the frequency of urban animals in developing world urban areas.
Journal Article
Financing the Transition to a Low-Carbon Future
Climate change is already underway and poses significant perils for both humans and the ecosystems that support us. The relationship of climate change to increased anthropogenic greenhouse gases,² and specifically carbon-dioxide (CO₂) concentrations, has been clearly demonstrated in many studies (see, for example, Richardson, Steffen and Liverman eds. 2011, 3–29). Figure 18.1 shows the global relationship of temperature change and CO₂ concentration over the last 160,000 years using data obtained from ice cores in the Antarctic. Of particular note are the positions on the CO₂ concentration scale of the “current levels,” and the “predicted levels” if countries proceed on
Book Chapter
Graph clustering with overlap
Given a graph G = (V, E), a clustering of G is a set [special characters omitted] of subsets of V which induces a set of subgraphs C1,C2,...,Ck . These subgraphs are known as clusters. The study of graph clustering focuses on finding clusterings such that edges within clusters are maximized and those between different clusters are minimized, so that each cluster represents a grouping of highly interrelated nodes. Traditionally the study of graph clustering has been restricted to the case where every vertex v ∈ V is a member of exactly one cluster. We extend consideration to the case of overlapping clusters, where each vertex may participate in an arbitrary number of clusters. We develop metrics for measuring the quality of an overlapping clustering, and a new stochastic local search algorithm for finding good overlapping clusterings. Finally we obtain experimental results showing the applicability of overlapping-clustering, and our algorithm, to some important applications.
Dissertation
Experimental characterization and dynamic simulation of a quadra link independent rear automotive suspension system
Quantification of the road input spectrum is determined by characterization studies of the various loading conditions (stresses, forces, moments, etc.) at the hard attachment points of an automobile suspension system. The hard attachment points of the suspension system are especially troublesome due to the random nature of the road-input spectrum. The current research details the work and results of a quadra-link rear suspension system characterization study. The study involved the designing of a portable, stand-alone measurement system, as well as, the calibration and installation into the test vehicle where data collection was performed. The characterization study also involved the collection of test data and the design of experiments to characterize fully the response of the suspension system over a broad spectrum of road conditions. Modeling that predicts the loading results experienced from actual road testing provided additional insight. The modeling identifies the response of the suspension system by characterizing the force transfer characteristics at the hard attachment points between the automotive body and the various suspension components. Two methods for modeling a specific case condition are detailed: A four degree of freedom MathCad mathematical model and a Working Model 3D dynamic simulation program model. Both models estimate the expected loads at hard attachment points, as well as the displacement, velocity, and acceleration response of the quadra-link suspension system. Both the MathCad model and the Working Model 3D dynamic simulation model provide authentication and correlation for the collected data as well as a useful tool for parametric design studies of the rear suspension system.
Dissertation