Related papers: Increased peak detection accuracy in over-disperse…

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…

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.…

Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) provides insights into both the genomic location occupied by the protein of interest and the difference in DNA occupancy between experimental states. Given that…

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role…

Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein binding sites. In this paper, we present a Markov random field model for the joint analysis of multiple ChIP-seq…

A topological multiple testing approach to peak detection is proposed for the problem of detecting transcription factor binding sites in ChIP-Seq data. After kernel smoothing of the tag counts over the genome, the presence of a peak is…

Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…

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…

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…

We study a statistical procedure based on higher criticism (HC) to address the sparse multi-stream quickest change-point detection problem. Namely, we aim to detect a potential change in the distribution of multiple data streams at some…

Very long and noisy sequence data arise from biological sciences to social science including high throughput data in genomics and stock prices in econometrics. Often such data are collected in order to identify and understand shifts in…

We propose a flexible change-point model for inhomogeneous Poisson Processes, which arise naturally from next-generation DNA sequencing, and derive score and generalized likelihood statistics for shifts in intensity functions. We construct…

In genomics, differential abundance and expression analyses are complicated by the compositional nature of sequence count data, which reflect only relative-not absolute-abundances or expression levels. Many existing methods attempt to…

Motivation: Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expression from histone modification signals are highly desirable for understanding their…

Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing…

Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the…

Changepoint detection is a central problem in time series and genomic data. For some applications, it is natural to impose constraints on the directions of changes. One example is ChIP-seq data, for which adding an up-down constraint…

Although a generalized spike population model has been actively studied in random matrix theory, its application to real data has been rarely explored. We find that most methods for determining the number of spikes based on the Johnstone's…

We describe a new algorithm and R package for peak detection in genomic data sets using constrained changepoint algorithms. These detect changes from background to peak regions by imposing the constraint that the mean should alternately…

Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…