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 publicly available data where […]

TITLE: "Swab-Seq: Detecting COVID-19 with Genomic Sequencing: From bench to vending machine." ABSTRACT: At UCLA we developed one of the only novel technologies for COVID-19 diagnostic testing that was deployed on a large scale.  The assay, which we named SwabSeq, performs genomic sequencing of pooled samples tagged with sample-specific molecular barcodes and then uses computational […]

TITLE: “Integrative systems analysis, applications, and challenges of single cell multiomics.” 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 resolution. However, integrative analysis across single cell […]

TITLE: "Predicting Biological Aging from Epigenetics." ABSTRACT: Epigenetics are a proven measure of cellular health. Therefore, a field of research has emerged that utilizes epigenetics to measure, treat, and potentially reverse biological age in humans. Specifically, DNA methylation, responsible for cell differentiation and gene expression, has the potential to be a barcode for measuring biological […]

TITLE: "Comprehensive study of gene expression outliers and their regulation mechanisms in pan-cancer." ABSTRACT: Cancer is a disease characterized by remarkable heterogeneity. Gene expression varies drastically between tumours and within cells of a single. This variability can generate extreme outliers: transcripts that show atypically high gene expression in a small percentage of cancers. These outliers […]

TITLE: "Heterogeneity in cell states: Is it important whether cell states are heritable or change rapidly?" ABSTRACT: Cells of the same cell type show molecular and phenotypic heterogeneity. Is the particular cell state of a given cell heritable from one generation to the next?  Previous work in liver cancer cells indicates that the molecular network […]

TITLE: "scReadSim: a single-cell RNA-seq and ATAC-seq read simulator." ABSTRACT: Rapid advances of single-cell RNA-seq and ATAC-seq technologies have propelled the development of many computational tools, benchmarking of which demands realistic simulators. However, few simulators can generate sequencing reads, and none of the existing read simulators aim to mimic real cells, hindering the benchmarking of […]

TITLE: "Proteogenomic characterization of the molecular determinants of prostate cancer radioresistance." ABSTRACT: Prostate Cancer (PC), the second most common cause of cancer death in men, is frequently treated using radiotherapy with curative intent. Despite its effectiveness, radiotherapy often results in aggressive PC relapse characterized by radioresistance. The diversity in therapeutic response to radiotherapy, and the molecular […]

TITLE: "Supervised capacity preserving mapping: a clustering guided visualization method for scRNA-seq data." ABSTRACT: Recently, various computational methods have been developed to analyze the scRNAseq data, such as clustering and visualization. However, current visualization methods, including t-SNE and UMAP, are challenged by the limited accuracy of rendering the geometric relationship of populations with distinct functional […]

TITLE: "Statistics, Biology and Applications of Human Mutation.”