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Article
Open AccessDifferential gene expression analysis of spatial transcriptomic experiments using spatial mixed models
Spatial transcriptomics (ST) assays represent a revolution in how the architecture of tissues is studied by allowing for the exploration of cells in their spatial context. A common element in the analysis is d...
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Article
Open AccessModeling phenotypic heterogeneity towards evolutionarily inspired osteosarcoma therapy
Osteosarcoma is the most common bone sarcoma in children and young adults. While universally delivered, chemotherapy only benefits roughly half of patients with localized disease. Increasingly, intratumoral he...
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Article
Open AccessA harmonized resource of integrated prostate cancer clinical, -omic, and signature features
Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These data can be used to better characterize the molecular features associated with clinical out...
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Protocol
Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications
In the current era of multi-omics, new sequencing and molecular profiling technologies have facilitated our quest for a deeper and broader understanding of the variations and dynamic regulations in human genom...
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Protocol
Statistics and Machine Learning in Mass Spectrometry-Based Metabolomics Analysis
In this chapter, we review the cutting-edge statistical and machine learning methods for missing value imputation, normalization, and downstream analyses in mass spectrometry metabolomics studies, with illustr...
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Protocol
Statistical Methods for Integrative Clustering of Multi-omics Data
Cancers are heterogeneous diseases caused by accumulated mutations or abnormal alterations at multi-levels of biological processes including genomics, epigenomics, transcriptomics, and proteomics. There is a g...
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Protocol
A Primer on Preprocessing, Visualization, Clustering, and Phenoty** of Barcode-Based Spatial Transcriptomics Data
Recent developments in spatially resolved transcriptomics (ST) have resulted in a large number of studies characterizing the architecture of tissues, the spatial distribution of cell types, and their interacti...
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Article
Open AccessLifetime ovulatory years and ovarian cancer gene expression profiles
Greater ovulatory years is associated with increased ovarian cancer risk. Although ovulation leads to an acute pro-inflammatory local environment, how long-term exposure to ovulation impacts ovarian carcinogen...
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Article
Mitochondrial DNA sequence variation and risk of meningioma
Risk factors for meningioma include female gender, African American race, high body mass index (BMI), and exposure to ionizing radiation. Although genome-wide association studies (GWAS) have identified two nuc...
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Article
“I think that a brief conversation from their provider can go a very long way”: Patient and provider perspectives on barriers and facilitators of genetic testing after ovarian cancer
Identify predisposing, enabling, and reinforcing factors impacting genetic counseling/testing among ovarian cancer patients guided by Green and Kreuter’s PRECEDE-PROCEED model.
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Protocol
Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments
High-throughput sequencing (HTS) has revolutionized researchers’ ability to study the human transcriptome, particularly as it relates to cancer. Recently, HTS technology has advanced to the point where now one...
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Article
Open AccessNonlinear mixed-effects models for modeling in vitro drug response data to determine problematic cancer cell lines
Cancer cell lines (CCLs) have been widely used to study of cancer. Recent studies have called into question the reliability of data collected on CCLs. Hence, we set out to determine CCLs that tend to be overly...
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Article
Heterogeneous expression of cytokines accounts for clinical diversity and refines prognostication in CMML
Chronic myelomonocytic leukemia (CMML) is a clinically heterogeneous neoplasm in which JAK2 inhibition has demonstrated reductions in inflammatory cytokines and promising clinical activity. We hypothesize that...
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Article
Open AccessSubject level clustering using a negative binomial model for small transcriptomic studies
Unsupervised clustering represents one of the most widely applied methods in analysis of high-throughput ‘omics data. A variety of unsupervised model-based or parametric clustering methods and non-parametric c...
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Article
Open AccessIdentification of nine new susceptibility loci for endometrial cancer
Endometrial cancer is the most commonly diagnosed cancer of the female reproductive tract in developed countries. Through genome-wide association studies (GWAS), we have previously identified eight risk loci f...
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Article
Sestrin family of genes and their role in cancer-related fatigue
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Article
Open AccessAdult height is associated with increased risk of ovarian cancer: a Mendelian randomisation study
Observational studies suggest greater height is associated with increased ovarian cancer risk, but cannot exclude bias and/or confounding as explanations for this. Mendelian randomisation (MR) can provide evid...
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Article
Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer
Paul Pharoah and colleagues report the results of a large genome-wide association study of ovarian cancer. They identify new susceptibility loci for different epithelial ovarian cancer histotypes and use integ...
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Article
Open AccessDrug discovery using clinical outcome-based Connectivity Map**: application to ovarian cancer
Epithelial ovarian cancer (EOC) is the fifth leading cause of cancer death among women in the United States (5 % of cancer deaths). The standard treatment for patients with advanced EOC is initial debulking su...
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Article
Open AccessFunctional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus
A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls an...
