TITLE: "Efficient, Multi Sample Inference of Cancer Phylogeny." ABSTRACT: Cancer is characterized by the ongoing accumulation of somatic mutations that may lead to dysregulated cellular proliferation. The selection of advantageous mutations leads to clonal expansions of progressively more aberrant and fit cancer cells. Reconstructing the evolutionary history of a tumor allows us to understand key […]

TITLE: "ClusterDE: a post-clustering differentially expressed (DE) gene identification method robust to false-positive inflation caused by double-dipping" ABSTRACT: In typical single-cell RNA-seq data analysis, first, a clustering algorithm is applied to cluster cells; then, a statistical method is used to identify the differentially expressed (DE) genes between the cell clusters. However, this common procedure uses the same […]

TITLE: "Germline structural variants shape prostate cancer clinical and molecular evolution." ABSTRACT: Inherited genetic variation profoundly influences cancer risk and outcome. While the impact of germline single nucleotide polymorphisms has been well-studied in several cancer types, the effects of germline structural variants (gSVs) on cancer biology and clinical outcomes is largely unknown. From our cohort […]

TITLE: "FastGxC: a statistical framework for mapping context-specific regulatory variants using bulk and single-cell RNA-seq data." ABSTRACT: Recent studies suggest that context-specific eQTLs underlie genetic risk factors for complex diseases. However, methods for identifying them are still nascent, limiting their comprehensive characterization and downstream interpretation of disease-associated variants. In this talk, I will introduce FastGxC, a method to efficiently and powerfully […]

TITLE: "A lack of distinct cellular identities in scRNA-seq data: revisiting Waddington’s landscape." ABSTRACT: Single-cell RNA sequencing is revolutionizing our understanding of development, differentiation and disease. Analysis of this data is often challenging, however, and tasks like clustering cells to uncover distinct cellular identities sometimes yields results that fail to align with existing biological knowledge. We analyzed […]

TITLE: "Single Cell Multiomics Integration to Understand Complex Diseases." ABSTRACT: Recent advances in single cell multiomics technologies such as single cell RNA-seq, single cell ATAC-seq, and spatial transcriptomics have brought enormous opportunities that enable our understanding of the molecular underpinnings of pathophysiology at a single cell or cell type resolution. However, integrative analysis across single […]

TITLE: "Liquid Biopsies for Precision Oncology." ABSTRACT: Liquid biopsies are new diagnostic approaches to profile molecular features of solid tumors by blood, saliva, urine, and other body fluids. Such approaches offer non-invasive options in early cancer detection, tumor sampling, continuous monitoring, and designing personalized therapeutic options. Therefore, liquid biopsies have the potential to transform the […]

TITLE: "Building a tooth from transcriptome to tissue morphogenesis" ABSTRACT: During craniofacial development, the oral epithelium begins as a morphologically homogeneous tissue that gives rise to locally complex structures, including the teeth, salivary glands, and taste buds. How the epithelium is initially patterned and later shaped to generate diverse organ and cell types remains largely […]

TITLE: “Inducible plasmid copy number control and a blueprint for a synthetic genetic feedback optimizer” ABSTRACT: The ability to control gene expression has been paradigm shifting for all areas of biological research, especially for synthetic biology. This talk will focus on two recent advancements in gene expression control. First, TULIP (TUnable Ligand Inducible Plasmid) is presented: a self-contained plasmid with inducible copy […]

TITLE: “Multi-omic and temporal data for rare and common genetic variation”