Related papers: Performance evaluation of DNA copy number segmenta…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
The DNA microarray technology has modernized the approach of biology research in such a way that scientists can now measure the expression levels of thousands of genes simultaneously in a single experiment. Gene expression profiles, which…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
Transcriptional profiling on microarrays to obtain gene expressions has been used to facilitate cancer diagnosis. We propose a deep generative machine learning architecture (called DeepCancer) that learn features from unlabeled microarray…
Cancer detection is one of the key research topics in the medical field. Accurate detection of different cancer types is valuable in providing better treatment facilities and risk minimization for patients. This paper deals with the…
Identifying subgroups and properties of cancer biopsy samples is a crucial step towards obtaining precise diagnoses and being able to perform personalized treatment of cancer patients. Recent data collections provide a comprehensive…
A variety of genome-wide profiling techniques are available to probe complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher-level interactions that cannot be detected…
DNA copy number and mRNA expression are widely used data types in cancer studies, which combined provide more insight than separately. Whereas in existing literature the form of the relationship between these two types of markers is fixed a…
miRNA and gene expression profiles have been proved useful for classifying cancer samples. Efficient classifiers have been recently sought and developed. A number of attempts to classify cancer samples using miRNA/gene expression profiles…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
In this paper, we propose sparse coding-based approaches for segmentation of tumor regions from MR images. Sparse coding with data-adapted dictionaries has been successfully employed in several image recovery and vision problems. The…
DNA microarray gene-expression data has been widely used to identify cancerous gene signatures. Microarray can increase the accuracy of cancer diagnosis and prognosis. However, analyzing the large amount of gene expression data from…
We propose local segmentation of multiple sequences sharing a common time- or location-index, building upon the single sequence local segmentation methods of Niu and Zhang (2012) and Fang, Li and Siegmund (2016). We also propose reverse…
With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis…
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…
In recent years, convolutional neural networks have demonstrated promising performance in a variety of medical image segmentation tasks. However, when a trained segmentation model is deployed into the real clinical world, the model may not…
Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural…
In forensic genetics, short tandem repeats (STRs) are used for human identification (HID). Degraded biological trace samples with low amounts of short DNA fragments (low-quality DNA samples) pose a challenge for STR typing. Predefined…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…