Multi-omics allows the systematic understanding of the information flow across different
omics layers, while single omics can mainly reflect one aspect of the biological system. The …

Data analysis often entails a multitude of heterogeneous steps, from the application of
various command line tools to the usage of scripting languages like R or Python for the …

The broad research use of organoids from high-grade serous ovarian cancer (HGSC) has
been hampered by low culture success rates and limited availability of fresh tumor material …

Ovarian high-grade serous carcinoma (HGSC) is typically diagnosed at an advanced stage,
with multiple genetically heterogeneous clones existing in the tumors long before …

Copy-number alterations (CNAs) are a hallmark of cancer and can regulate cancer cell
states via altered gene expression values. Herein, we have developed a copy-number …

Motivation A major challenge in analyzing cancer patient transcriptomes is that the tumors
are inherently heterogeneous and evolving. We analyzed 214 bulk RNA samples of a …

Next-generation sequencing (NGS) has been a widely-used technology in biomedical
research for understanding the role of molecular genetics of cells in health and disease. A …

Diffuse large B-cell lymphoma (DLBCL) is a biologically and clinically heterogeneous
disease whose personalized clinical management requires robust molecular stratification …

Anti-tumor immunity is crucial for high-grade serous ovarian cancer (HGSC) prognosis, yet
its adaptation upon standard chemotherapy remains poorly understood. Here, we conduct …

We describe an integrative approach to improve contiguity and haploidy of a reference
genome assembly and demonstrate its impact with practical examples. With two novel …