TITLE: "XIST controls X chromosome dampening and autosomal genes in early human development" ABSTRACT: Female human pre-implantation embryos and naïve human pluripotent stem cells (hPSCs) equalize X-linked gene expression with males via X-chromosome dampening (XCD), a unique strategy of dosage compensation in mammals. The mechanisms controlling XCD are unknown. Here, we show that the long non-coding […]
TITLE: "Fast estimation of genetic correlation for Biobank-scale data" ABSTRACT: Genetic correlation is an important parameter in understanding the shared genetic basis across pairs of complex traits with applications ranging across disease subtyping, genetic prediction, and causal inference. The availability of genome-wide genetic data has led to a number of methods that aim to estimate genetic […]
TITLE: "Determining mRNA nuclear export kinetics reveals a wide range of values associated with innate immune response genes" ABSTRACT: The abundance and stimulus-responsiveness of mature mRNA is known to be determined by nuclear synthesis and cytoplasmic decay. However, nuclear processing and export events and may also contribute. Here, we investigated the role nuclear export rates […]
TITLE: "Oncogenic alterations in the p53 pathway abolish oscillatory competence" ABSTRACT: The tumor suppressor p53 displays concentration oscillations in response to DNA damage, a behavior that has been suggested to be essential to its anti-cancer function. Many genetic alterations in the p53 pathway have been shown to be oncogenic, whether by experiment or by clinical associations […]
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 […]
