Related papers: Multiple testing of local maxima for detection of …

A topological multiple testing scheme is presented for detecting peaks in images under stationary ergodic Gaussian noise, where tests are performed at local maxima of the smoothed observed signals. The procedure generalizes the…

A topological multiple testing scheme for one-dimensional domains is proposed where, rather than testing every spatial or temporal location for the presence of a signal, tests are performed only at the local maxima of the smoothed observed…

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data…

A new approach to detect change points based on differential smoothing and multiple testing is presented for long data sequences modeled as piecewise constant functions plus stationary ergodic Gaussian noise. As an application of the STEM…

Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which method and what parameters are optimal for any given data set. In contrast, peaks can easily be located by visual inspection of…

This paper considers the problem of detecting equal-shaped non-overlapping unimodal peaks in the presence of Gaussian ergodic stationary noise, where the number, location and heights of the peaks are unknown. A multiple testing approach is…

ChIP-seq, which combines chromatin immunoprecipitation with massively parallel short-read sequencing, can profile in vivo genome-wide transcription factor-DNA association with higher sensitivity, specificity and spatial resolution than…

Motivation: Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing…

Joint peak detection is a central problem when comparing samples in genomic data analysis, but current algorithms for this task are unsupervised and limited to at most 2 sample types. We propose PeakSegJoint, a new constrained maximum…

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…

Classical and more recent tests for detecting distributional changes in multivariate time series often lack power against alternatives that involve changes in the cross-sectional dependence structure. To be able to detect such changes…

Evolution in its course found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underlying structure on…

The detection of local genomic signals using high-throughput DNA sequencing data can be cast as a problem of scanning a Poisson random field for local changes in the rate of the process. We propose a likelihood-based framework for for such…

In this paper, we propose a new generic method for detecting the number and locations of structural breaks or change points in piecewise linear models under stationary Gaussian noise. Our method transforms the change point detection problem…

In a multiple testing framework, we propose a method that identifies the interval with the highest estimated false discovery rate of P-values and rejects the corresponding null hypotheses. Unlike the Benjamini-Hochberg method, which does…

Peak inference concerns the use of local maxima ("peaks") of a noisy random field to detect and localize regions where underlying signal is present. We propose a peak inference method that first subjects observed peaks to a significance…

We consider the problem of testing positively dependent multiple hypotheses assuming that a prior information about the dependence structure is available. We propose two-step multiple comparisons procedures that exploit the prior…

Estimating and testing for differences in molecular phenotypes (e.g. gene expression, chromatin accessibility, transcription factor binding) across conditions is an important part of understanding the molecular basis of gene regulation.…

Phenomenological (P-type) bifurcations are qualitative changes in stochastic dynamical systems whereby the stationary probability density function (PDF) changes its topology. The current state of the art for detecting these bifurcations…

In this paper, we study statistical inference of change-points (CPs) in multi-dimensional sequence. In CP detection from a multi-dimensional sequence, it is often desirable not only to detect the location, but also to identify the subset of…