TITLE: "Exercise and tumor genomic landscapes in 2,702 patients with cancer" ABSTRACT: Approximately two-thirds of cancer diagnoses globally are attributed to modifiable lifestyle factors such as smoking, diet and inactivity. Conversely, regular exercise is linked to decreased risk of multiple cancers. However, the underlying molecular mechanisms are not fully elucidated. Specifically, how exercise impacts tumor genomic […]

TITLE: “Automatic analysis of cryo-electron tomography using computer vision and machine learning.”

TITLE: "Multi-tissue single-cell level understanding of Alzheimer’s disease points to the therapeutic potential of nutritional and metabolic modulation." ABSTRACT: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by extracellular amyloid plaque deposition and intracellular neurofibrillary tangles. The direct cause of abnormal protein accumulation and aggregation is largely unknown, and no treatments exist to effectively delay […]

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 […]