The Cancer Genome Atlas (TCGA) provides an unprecedented opportunity to take an integrated approach toward a systems level understanding of regulatory disruptions in cancer. Such disruptions and their consequences are intertwined within complex dynamical networks through a multitude of interactions among different types of molecules. Understanding such relationships requires multivariate analysis methods that can be effective in the context of highly heterogeneous data, measurement uncertainty, and missing data.


Development of novel computational approaches for analyzing large-scale heterogeneous data.

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Cancer Studies

Our participation and contribution to multiple TCGA tumor Analysis Working Groups.

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Web-based interactive visualization and exploratory tools that promote collaborative research.

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News & Events

May 2016

The TCGA Research Network published a study on adrenocortical carcinoma (ACC) in Cancer Cell. The study describes the comprehensive analysis of 91 ACC specimens from four continents using state of the art genomic technologies and computational methods. In addition to identification of novel ACC driver genes, pathways and refined subtypes, the AWG analysis revealed whole genome doubling (WGD) as a milestone in disease progression. We performed integrated analysis across different data types for this study and captured statistical associations in Regulome Explorer.

November 2015

The TCGA Research Network published a study on primary Prostate Cancer in Cell. The study described a molecular taxonomy in which 74% of the tumors belonged to one of seven subtypes. This study revealed additional molecular heterogeneity among primary prostate cancers and molecular defects which may be therapeutically actionable. We performed integrated analysis across different data types for this study. Associations for the 333 tumor dataset can be viewed in Regulome Explorer.

June 2015

The TCGA Research Network published a study on diffuse lower-grade gliomas (LGG) in The New England Journal of Medicine. The study concluded that there were three molecular classes of LGG. The majority of LGGs without an IDH mutation exhibited similar molecular and clinical properties to glioblastoma. Associations for the LGG dataset can be viewed in Regulome Explorer.

We also participated in the TCGA study of cutaneous melanoma published in Cell. The multidimensional study looked at 331 patients and identified immune signatures associated with improved survival.

October 2014

The TCGA Research Network published a study on Papillary Thyroid Cancer (PTC) in Cell. The study concluded that the subgroups of PTC differ in their molecular alterations as well as signaling and differentiation characteristics. The paper proposes a refined classification of PTC to reflect these differences and to better inform clinical management of the disease. We made significant contributions to this study by performing integrated analysis across different data types. Associations for the full tumor dataset and the BRAFV600E tumor dataset can be viewed in Regulome Explorer.

July 2014

The TCGA Research Network published a study on Gastric Cancer in Nature with substantial contributions from members of our center. Dr. Shmulevich served as one of the co-chairs of the study group. One of the main results of the paper is that gastric tumors tend to fall into one of four subtypes. The treatment of gastric cancer may improve with therapy targeted against specific subtypes. Associations within the dataset of 295 tumors can be viewed in Regulome Explorer.

October 2013

A position paper is published in Nature Genetics describing The Pan-Cancer initiative, which compares the first 12 tumor types profiled by The Cancer Genome Atlas (TCGA) project. The data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. Nature also created a focused resource with threads and links to 18 pan-cancer papers. A related article also appeared in the Los Angeles Times.

We took part in the TCGA study of glioblastoma, published in Cell. The project released a new catalog of genetic-mutation data for nearly 600 glioblastoma cases. We also developed a companion open-access software tool (Micro) that allows researchers to study the correlations between microRNAs and proteins in detail.

September 2013

We have been awarded a grant from Washington State's Life Sciences Discovery Fund to develop web-based tools for analyzing cancer genetic data to advance understanding of tumor biology, accelerate new discoveries, and in the long term, facilitate personalized therapy. Here is the Press Release from LSDF. There was also an article on GenomeWeb about this award.

May 2013

New paper published in Nature on "Integrated genomic characterization of endometrial carcinoma" as part of the TCGA network.

April 2013

We were awarded the first prize in the YarcData Graph Analytics Challenge. The topic of our entry was drug repurposing for cancer and uses data from TCGA, PubMed, and other databases.

February 2013

Investigators from our GDAC have published the discovery and characterization of FGFR3-TACC3 fusion in 8% of glioblastoma in "The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma".

New paper published in Cancer Cell on "Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer" as part of the TCGA network. The cover of Cancer Cell features the article, with a graphic depicting the analysis.

November 2012

Researchers at our center attended and presented at the 2nd Annual TCGA Scientific Symposium. The symposium was co-chaired by Dr Ilya Shmulevich. Dr Brady Bernard and Hector Rovira gave a talk on Genespot: A Portal for Interactive Gene-Centric Exploration of The Cancer Genome Atlas. Dick Kreisberg presented a workshop on Regulome Explorer.

October 2012

New paper published in Nature on "Comprehensive molecular portraits of human breast tumours" as a part of the TCGA network. An article related to the work was published in the New York Times.

September 2012

The TCGA project published a Case Study on "The New Genomic Bottleneck and How the Cloud Might Widen It" in which Dr Ilya Shmulevich is interviewed on his lab’s efforts to analyze genomic information using large computational clusters with cloud infrastructure on demand.

July 2012

New paper published in Nature on "Comprehensive molecular characterization of human colon and rectal cancer" as part of the TCGA network. An article related to the work was featured on the home page of the New York Times.

June 2012

Our work was featured during the Compute Engine keynote presentation at the Google I/O 2012 conference.

The keynote, delivered by Urs Hölzle, Senior Vice President of Infrastructure at Google, introduced Google Compute Engine. He demonstrated how RF-ACE, a machine learning algorithm that learns associations among genomic and clinical features, can be scaled to 600,000 cores across Google’s global data centers and the results visualized using a version of Regulome Explorer. A case study published by Google discusses the integration with Compute Engine.

May 2012

Regulome Explorer is featured in this article where ISB founder Dr. Leroy Hood talks about the application of mathematics to biological research.

March 2012

Regulome Explorer is covered in this story about online tools available for analyzing TCGA data.

December 2011

Addama described in this technology feature on adaptive technologies for systems biology data integration.

October 2011

New paper published in the Journal of the American Medical Association on "Association of BRCA1 and BRCA2 Mutations With Survival, Chemotherapy Sensitivity, and Gene Mutator Phenotype in Patients With Ovarian Cancer" showing that women with high-grade ovarian cancer live longer and respond better to platinum-based chemotherapy when their tumors have BRCA2 genetic mutations.

There was also a related editorial published in JAMA.