TITLE: "PCA outperforms popular hidden variable inference methods for QTL mapping." ABSTRACT: Estimating and accounting for hidden variables is widely practiced as an important step in quantitative trait locus (QTL) analysis for improving the power of QTL identification. However, few benchmark studies have been performed to evaluate the efficacy of the various methods developed for […]
TITLE: "Stochastic Model and Optimization of SELEX." ABSTRACT: Systematic Evolution of Ligands by EXponential enrichment (SELEX) is a process to select the best aptamer sequence in a huge aptamer library that binds a specified target molecule with the highest affinity. There has been a deterministic model of SELEX, and we develop a fully discrete stochastic […]
TITLE: "Tensor Factorization for Interpreting the Mechanisms of MRSA Persistence." ABSTRACT: Methicillin-resistant Staphylococcus aureus (MRSA) bacteria is an increasingly common and life-threatening infection. While some antibiotics resolve MRSA infections in vitro, these same antibiotics often fail to clear an infection when used to treat patients, suggesting that MRSA persistence is a confluence of both host […]
TITLE: "Baseline MEthylation Patterns prior to flu vaccination." ABSTRACT: Influenza affects millions worldwide each year with responses varying from individual to individual. Influenza can be broken down into subtypes specifically H1N1, H3N2, Yamagata, and Victoria. One way to measure the immune response to influenza is to measure a person’s antibody response to influenza. To measure how […]
TITLE: "Universal annotation of the human genome through integration of over a thousand epigenomic datasets." ABSTRACT: Genome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states […]
TITLE: "Model driven design and analysis of functional screens" ABSTRACT: A little over a decade ago biomedicine was revolutionized by a conceptually simple insight: DNA sequencers could be used as molecular counting machines to measure a multitude of molecules beyond DNA. Through the years, sequencing has continued to become cheaper and more efficient (faster than […]
TITLE: "Evolutionary dynamics in the human gut microbiome from infancy through adulthood." ABSTRACT: While the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about the evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from >700 infants and their mothers over the first […]
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 […]
