Related papers: Topological Data Analysis of copy number alteratio…
We present a new method for exploring cancer gene expression data based on tools from algebraic topology. Our method selects a small relevant subset from tens of thousands of genes while simultaneously identifying nontrivial higher order…
Changes in the number of copies of certain parts of the genome, known as copy number alterations (CNAs), due to somatic mutation processes are a hallmark of many cancers. This genomic complexity is known to be associated with poorer…
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…
While we once thought of cancer as single monolithic diseases affecting a specific organ site, we now understand that there are many subtypes of cancer defined by unique patterns of gene mutations. These gene mutational data, which can be…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
Recent advances in types and extent of medical imaging technologies has led to proliferation of multimodal quantitative imaging data in cancer. Quantitative medical imaging data refer to numerical representations derived from medical…
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
Statistical inference on the cancer-site specificities of collective ultra-rare whole genome somatic mutations is an open problem. Traditional statistical methods cannot handle whole-genome mutation data due to their…
DNA copy number aberrations (CNAs) can be found in the majority of cancer genomes, and are crucial for understanding the potential mechanisms underlying tumor initiation and progression. Since the first release in 2001, the Progenetix…
Identifying genes underlying cancer development is critical to cancer biology and has important implications across prevention, diagnosis and treatment. Cancer sequencing studies aim at discovering genes with high frequencies of somatic…
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of…
With the advanced imaging technology, digital pathology imaging of tumor tissue slides is becoming a routine clinical procedure for cancer diagnosis. This process produces massive imaging data that capture histological details in high…
In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and…
Microscopic examination of slides prepared from tissue samples is the primary tool for detecting and classifying cancerous lesions, a process that is time-consuming and requires the expertise of experienced pathologists. Recent advances in…
Copy number alterations (CNAs) are thought to account for 85% of the variation in gene expression observed among breast tumours. The expression of cis-associated genes is impacted by CNAs occurring at proximal loci of these genes, whereas…
Sequence data, such as DNA, RNA, and protein sequences, exhibit intricate, multi-scale structures that pose significant challenges for conventional analysis methods, particularly those relying on alignment or purely statistical…
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…
Cancer is a complex disease driven by dynamic regulatory shifts that cannot be fully captured by individual molecular profiling. We employ a data-driven approach to construct a coarse-grained dynamic network model based on hallmark…
Healthcare data from patient or population cohorts are often characterized by sparsity, high missingness and relatively small sample sizes. In addition, being able to quantify uncertainty is often important in a medical context. To address…