TITLE: Structural interrogation of small open reading frame (sORF) encoded proteins ABSTRACT: Advances in genomics and proteomics have unearthed sequences of a startling number of novel proteins. Despite this, our knowledge of their three-dimensional structure and function relies on only a small fraction of the known protein universe. Small open reading frames (sORFs) encoding proteins less […]
Swab-Seq: Massively scaling SARS-CoV-2 testing using genomic sequencing. The COVID-19 Basic, Translational and Clinical Research Task Forces has created a seminar series each Friday at noon. The purpose of these seminars is to bring together people across campus working on SARS-CoV-2 from all angles to form a community and exchange information, both for expert virologists and those new to COVID-19 […]
TITLE: Cis-regulatory divergence between highland and lowland deer mice populations highlight the essential role of pleiotropic genes for high-altitude adaptation. ABSTRACT: Variation in gene expression regulation contributes extensively to phenotypic diversity within and between species and plays a major role in complex trait evolution. However, the characterization of the genetic basis of regulatory variation is […]
TITLE: "scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling." ABSTRACT: Single-cell RNA sequencing (scRNA-seq) captures whole transcriptome information of individual cells. While scRNA-seq measures thousands of genes, researchers are often interested in only dozens to hundreds of genes for a closer study. Then a question is how to […]
TITLE: "A state space model to characterize the phenotypic variation in a panel of drug treatment time course experiments." ABSTRACT: As new technologies enable high throughput collection of marker measurements in drug treatment time course experiments, we are faced with a need to characterize the observed cellular behaviors over time. I will present a model […]
TITLE: The evolution and co-evolution of PRDM9 across vertebrates ABSTRACT: In sexually reproducing organisms, meiotic recombination is initiated by the deliberate infliction of numerous double-strand breaks (DSBs) in the genome, the repair of which yields crossover and non-crossover resolutions. In most mammals, these DSBs are specified through the binding of PRDM9 and the deposition of […]
TITLE: "Linking exposure dose to infectious disease development using mechanistic models" (using SARS-CoV-2 in a mouse model as an illustration) ABSTRACT: Disease development after exposure to a pathogen does not follow […]
TITLE: “Inferring positive selection in the human gut microbiome using signatures of genetic linkage.” ABSTRACT: The human gut microbiome is composed of hundreds of simultaneously evolving species that can affect human […]
TITLE: "Quantifying response-specificity to diverse immune threats from single cell transcriptomes" ABSTRACT: Innate immune sentinel cells such as macrophages upregulate over a thousand genes in the minutes to hours following an […]
TITLE: "Efficient variance components analysis across millions of genomes." ABSTRACT: While variance components analysis has emerged as a powerful tool in complex trait genetics, existing methods for fitting variance components do […]
