Multiple‐Changepoint Testing for an Alternating Segments Model of a Binary Sequence

Halpern, Aaron L.

doi:10.1111/j.0006-341x.2000.00903.x

Cited by 19 publications

(8 citation statements)

References 18 publications

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“…Some choices of breakpoints will have very little power, further reducing the effective number of tests. A more complex calculation that avoids our conservative approximations is given by Halpern (2000).…”

Section: Determination Of Breakpoint Regionsmentioning

confidence: 99%

Evolution ofChlamydia trachomatisdiversity occurs by widespread interstrain recombination involving hotspots

Gomes¹,

Bruno²,

Nunes³

et al. 2006

Genome Res.

115

132

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Chlamydia trachomatis is an obligate intracellular bacterium of major public health significance, infecting over one-tenth of the world's population and causing blindness and infertility in millions. Mounting evidence supports recombination as a key source of genetic diversity among free-living bacteria. Previous research shows that intracellular bacteria such as Chlamydiaceae may also undergo recombination but whether this plays a significant evolutionary role has not been determined. Here, we examine multiple loci dispersed throughout the chromosome to determine the extent and significance of recombination among 19 laboratory reference strains and 10 present-day ocular and urogenital clinical isolates using phylogenetic reconstructions, compatibility matrices, and statistically based recombination programs. Recombination is widespread; all clinical isolates are recombinant at multiple loci with no two belonging to the same clonal lineage. Several reference strains show nonconcordant phylogenies across loci; one strain is unambiguously identified as recombinantly derived from other reference strain lineages. Frequent recombination contrasts with a low level of point substitution; novel substitutions relative to reference strains occur less than one per kilobase. Hotspots for recombination are identified downstream from ompA, which encodes the major outer membrane protein. This widespread recombination, unexpected for an intracellular bacterium, explains why strain-typing using one or two genes, such as ompA, does not correlate with clinical phenotypes. Our results do not point to specific events that are responsible for different pathogenicities but, instead, suggest a new approach to dissect the genetic basis for clinical strain pathology with implications for evolution, host cell adaptation, and emergence of new chlamydial diseases.

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Section: Determination Of Breakpoint Regionsmentioning

confidence: 99%

Evolution ofChlamydia trachomatisdiversity occurs by widespread interstrain recombination involving hotspots

Gomes¹,

Bruno²,

Nunes³

et al. 2006

Genome Res.

115

132

View full text Add to dashboard Cite

show abstract

“…Later a method for locating multiple change points in a Binomial Sequence was proposed in Halpern (2000). Rozenholc (2001)…”

Section: Nonparametric Change Point Analysismentioning

confidence: 99%

Variance Change Point Detection Under a Smoothly-Changing Mean Trend with Application to Liver Procurement

Gao

Shang

et al. 2018

Journal of the American Statistical Association

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Literature on change point analysis mostly requires a sudden change in the data distribution, either in a few parameters or the distribution as a whole. We are interested in the scenario that the variance of data may make a significant jump while the mean of data changes in a smooth fashion. It is motivated by a liver procurement experiment with organ surface temperature monitoring. Blindly applying the existing change point analysis methods to the example can yield erratic change point estimates since the smoothly-changing mean violates the sudden-change assumption. In my dissertation, we propose a penalized weighted least squares approach with an iterative estimation procedure that naturally integrates variance change point detection and smooth mean function estimation. Given the variance components, the mean function is estimated by smoothing splines as the minimizer of the penalized weighted least squares. Given the mean function, we propose a likelihood ratio test statistic for identifying the variance change point. The null distribution of the test statistic is derived together with the rates of convergence of all the parameter estimates. Simulations show excellent performance of the proposed method. Application analysis offers numerical support to the non-invasive organ viability assessment by surface temperature monitoring.The method above can only yield the variance change point of temperature at a single point on the surface of the organ at a time. In practice, an organ is often transplanted as a whole or in part. Therefore, it is generally of more interest to study the variance change point for a chunk of organ. With this motivation, we extend our method to study variance change point for a chunk of the organ surface. Now the variances become functions on a 2D space of locations (longitude and latitude) and the mean is a function on a 3D space of location and time. We model the variance functions by thin-plate splines and the mean function by the tensor product of thin-plate splines and cubic splines. However, the additional dimensions in these functions incur serious computational problems since the sample size, as a product of the number of locations and the number of sampling time points, becomes too large to run the standard multi-dimensional spline models. To overcome the computational hurdle, we introduce a multi-stages subsampling strategy into our modified iterative algorithm.The strategy involves several down-sampling or subsampling steps educated by preliminary statistical measures. We carry out extensive simulations to show that the new method can efficiently cut down the computational cost and make a practically unsolvable problem solvable with reasonable time and satisfactory parameter estimates. Application of the new method to the liver surface temperature monitoring data shows its effectiveness in providing accurate status change information for a portion of or the whole organ.The viability evaluation is the key issue in the organ transplant operation. The donated organ must be viable a...

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“…Beattie (1962) and Wasserman and Wadworth (1989) formally considered a double CUSUM process. Recent applications can be seen in Avery and Henderson (1996), Fu and Curnow (1994), Halpern (2000) for locating change segments and heterogeneous segments in DNA sequence analysis and Assaf (1997), Khasminskii and Lazareva (1996), Khasminskii, Lazareva and Stapleton (1994) and Yao (1984) from a signal processing point of view. From a system monitoring point of view, Hines (1974) considered using an EWMA process as a classification process.…”

Section: Classification and Segmentationmentioning

confidence: 99%

Inference for Change Point and Post Change Means After a CUSUM Test

Wu¹

2005

Lecture Notes in Statistics

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Multiple‐Changepoint Testing for an Alternating Segments Model of a Binary Sequence

Cited by 19 publications

References 18 publications

Evolution ofChlamydia trachomatisdiversity occurs by widespread interstrain recombination involving hotspots

Evolution ofChlamydia trachomatisdiversity occurs by widespread interstrain recombination involving hotspots

Variance Change Point Detection Under a Smoothly-Changing Mean Trend with Application to Liver Procurement

Inference for Change Point and Post Change Means After a CUSUM Test

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