Related papers: PICS: Probabilistic Inference for ChIP-seq
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…
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…
Background: Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely used technique to investigate the function of chromatin-related proteins in a genome-wide manner. ChIP-Seq generates large quantities of…
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…
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…
Effective training of deep image segmentation models is challenging due to the need for abundant, high-quality annotations. Generating annotations is laborious and time-consuming for human experts, especially in medical image segmentation.…
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…
In the context of biometrics, matching confidence refers to the confidence that a given matching decision is correct. Since many biometric systems operate in critical decision-making processes, such as in forensics investigations,…
Due to its specificity, fluorescence microscopy (FM) has become a quintessential imaging tool in cell biology. However, photobleaching, phototoxicity, and related artifacts continue to limit FM's utility. Recently, it has been shown that…
Complete genome sequences contain valuable information about natural selection, but extracting this information for short, widely scattered noncoding elements remains a challenging problem. Here we introduce a new computational method for…
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…
Phishing, a continuously growing cyber threat, aims to obtain innocent users' credentials by deceiving them via presenting fake web pages which mimic their legitimate targets. To date, various attempts have been carried out in order to…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
CLIP-seq methods are valuable techniques to experimentally determine transcriptome-wide binding sites of RNA-binding proteins. Despite the constant improvement of such techniques (e.g. eCLIP), the results are affected by various types of…
Unsupervised learning plays an important role in many fields, such as artificial intelligence, machine learning, and neuroscience. Compared to static data, methods for extracting low-dimensional structure for dynamic data are lagging. We…
The notion that transcription factors bind DNA only through specific, consensus binding sites has been recently questioned. In a pioneering study by Pugh and Venters no specific consensus motif for the positioning of the human…
Referring image segmentation aims to segment a referent via a natural linguistic expression.Due to the distinct data properties between text and image, it is challenging for a network to well align text and pixel-level features. Existing…
Photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) is an experimental method based on next-generation sequencing for identifying the RNA interaction sites of a given protein. The method deliberately…
Annotation of medical images, such as MRI and CT scans, is crucial for evaluating treatment efficacy and planning radiotherapy. However, the extensive workload of medical professionals limits their ability to annotate large image datasets,…
Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers…