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Jaeger J.,University Pompeu Fabra | Manu,University of Chicago | Reinitz J.,University of Chicago | Reinitz J.,Institute of Genomics and Systems Biology
Current Opinion in Genetics and Development | Year: 2012

The Drosophila blastoderm embryo is a classic model for the study of the genetics of pattern formation. In recent years, quantitative empirical approaches have been employed extensively in the study of blastoderm pattern formation. This quantitative work has enabled the development of a number of data-driven computational models. More than in other systems, these models have been experimentally validated, and have informed new empirical work. They have led to insights into the establishment of morphogen gradients, the interpretation and transduction of positional information by downstream transcriptional networks, and the mechanisms by which spatial scaling and robustness of gene expression are achieved. Here we review the latest developments in the field. © 2012 Elsevier Ltd.

Yang X.,University of Chicago | Lee Y.,University of Chicago | Huang Y.,University of Chicago | Chen J.L.,University of Chicago | And 3 more authors.
BMC Bioinformatics | Year: 2010

Background: Mouse xenograft models, in which human cancer cells are implanted in immune-suppressed mice, have been popular for studying the mechanisms of novel therapeutic targets, tumor progression and metastasis. We hypothesized that we could exploit the interspecies genetic differences in these experiments. Our purpose is to elucidate stromal microenvironment signals from probes on human arrays unintentionally cross-hybridizing with mouse homologous genes in xenograft tumor models.Results: By identifying cross-species hybridizing probes from sequence alignment and cross-species hybridization experiment for the human whole-genome arrays, deregulated stromal genes can be identified and then their biological significance were predicted from enrichment studies. Comparing these results with those found by the laser capture microdissection of stromal cells from tumor specimens resulted in the discovery of significantly enriched stromal biological processes.Conclusions: Using this method, in addition to their primary endpoints, researchers can leverage xenograft experiments to better characterize the tumor microenvironment without additional costs. The Xhyb probes and R script are available at © 2010 Xing et al; licensee BioMed Central Ltd.

Liu Y.,Institute of Genomics and Systems Biology | Zhou J.,Institute of Genomics and Systems Biology | Zhou J.,University of Chicago | White K.P.,Institute of Genomics and Systems Biology | White K.P.,University of Chicago
Bioinformatics | Year: 2014

Motivation: RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources.Results: We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. In the human cell line MCF7, adding more sequencing depth after 10 M reads gives diminishing returns on power to detect DE genes, whereas adding biological replicates improves power significantly regardless of sequencing depth. We also propose a cost-effectiveness metric for guiding the design of large-scale RNA-seq DE studies. Our analysis showed that sequencing less reads and performing more biological replication is an effective strategy to increase power and accuracy in large-scale differential expression RNA-seq studies, and provided new insights into efficient experiment design of RNA-seq studies. © 2013 The Author 2013.

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