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Nature - February 20, 2019

The single-cell transcriptional landscape of mammalian organogenesis

Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transcriptomes of around 2 million cells derived from 61 embryos staged between 9.5 and 13.5 days of gestation, in a single experiment.

Nature Genetics - August 29, 2018

Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape

The rapid generation and expanding the accessibility of clinical and molecular data is shifting the bottleneck in cancer research from data acquisition to data aggregation and interpretation. Many tools have been developed to address various aspects of this need1,2,3,4,5. To overcome the persistent challenges in cohort discovery and analysis for translational research and prospective clinical-decision support in precision medicine, we developed Oncoscape, an online open-access data-analysis and visualization platform (see URLs) that empowers researchers and clinicians to discover novel patterns and relationships between linked clinical and molecular data.

Acta Neuropathologica Communications - May 22, 2017

Multidimensional scaling of diffuse gliomas

Using the web-based platform Oncoscape as a tool, we applied multidimensional scaling-derived molecular groups to the 2D visualization of the 2016 WHO classification of diffuse gliomas. Here we show that molecular multidimensional scaling of TCGA data provides 2D clustering that represents the 2016 WHO classification of diffuse gliomas. Additionally, we used this platform to successfully identify and define novel copy-number alteration-based molecular subtypes, which are independent of WHO grading, as well as predictive of clinical outcome.

Paired Tumor Normal Sample Distributionss Linked By Clinical


2019 Cambia Grove Innovator Fellowship

In collaboration with Cambia Grove, Fred Hutch Data Visualization accepted its inaugural fellowship cohort to develop a biological data catalog to expose valuable clinical and molecular data through consistent web-optimized application programming interfaces (APIs). These efforts will help researchers worldwide find effective treatments or even cures to cancer.

Brotman Baty Collaboration

We recently partnered with Brotman Baty and UW Genome Sciences to develop a multispecies organogenesis atlas featuring scRNA and ATAC Seq data. Together we are reimagining how to best share and visualize single cell data.