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We present an integrated approach to identify genetic mechanisms that control self-renewal in mouse embryonic stem cells. We use short hairpin RNA (shRNA) loss-of-function techniques to downregulate a set of gene products whose expression patterns suggest self-renewal regulatory functions. We focus on transcriptional regulators and identify seven genes for(More)
Molecular regulation of embryonic stem cell (ESC) fate involves a coordinated interaction between epigenetic, transcriptional and translational mechanisms. It is unclear how these different molecular regulatory mechanisms interact to regulate changes in stem cell fate. Here we present a dynamic systems-level study of cell fate change in murine ESCs(More)
A new air quality modeling system, the surface meteorology and ozone generation (SMOG) model, is used to investigate the evolution and properties of air pollution in the Los Angeles basin during the southern California air quality study (SCAQS) intensive field program. The SMOG model includes four major components: a meteorological model, a tracer transport(More)
Disentangling cellular heterogeneity is a challenge in many fields, particularly in the stem cell and cancer biology fields. Here we demonstrate how to combine viral genetic barcoding with high-throughput sequencing to track single cells in a heterogeneous population. We use this technique to track the in vivo differentiation of unitary hematopoietic stem(More)
Establishing a functional network is invaluable to our understanding of gene function, pathways, and systems-level properties of an organism and can be a powerful resource in directing targeted experiments. In this study, we present a functional network for the laboratory mouse based on a Bayesian integration of diverse genetic and functional genomic data.(More)
Specularities on surfaces with tangential hairs or grooves are readily observable in nature. Examples of such phenomena are the arched or looped highlights observed on horses and on human heads and the linear or curved specularities observed on parts of industrial machinery that have tangential grooves. We investigate the geometry of curvilinear(More)
This paper focuses on the problem of discovering users' topics of interest on Twitter. While previous efforts in modeling users' topics of interest on Twitter have focused on building a "bag-of-words" profile for each user based on his tweets, they overlooked the fact that Twitter users usually publish noisy posts about their lives or create conversation(More)
Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works, must be obtained from the IEEE. Abstract Abstract ––(More)
BACKGROUND Salmonella infection is a common public health problem that can become chronic and increase the risk of inflammatory bowel diseases and cancer. AvrA is a Salmonella bacterial type III secretion effector protein. Increasing evidence demonstrates that AvrA is a multi-functional enzyme with critical roles in inhibiting inflammation, regulating(More)
To quantify spatial protein-protein proximity (colocalization) in paired microscopic images of two sets of proteins labeled by distinct fluorophores, we showed that the cross-correlation and the autocorrelation functions of image intensity consisted of fast and slowly decaying components. The fast component resulted from clusters of proteins specifically(More)