News

TCGA, ISB Researchers Identify Potential Drug Targets for Leading Form of Deadly Liver Cancer

June 19, 2017 Researchers in ISB’s Shmulevich Lab and their colleagues in The Cancer Genome Atlas Research Network performed the first large-scale, multi-platform analysis of hepatocellular carcinoma, the predominant form of liver cancer. Study was published on June 15, 2017, in the journal Cell. 3 Bullets: Liver cancer is the second most common cause of death from cancer worldwide. ISB researchers and colleagues from The Cancer Genome Atlas Research Network…

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ISB Consilience: Museum of Awe

The Museum of Awe is all around us; you just have to find a door. Attendees of the 2017 Consilience event, including ISB’s Dr. Ilya Shmulevich (center), examine a mini “pop-up” experience created by NASA JPL visual strategists Dan Goods and David Delgado. The tank allows people to see particles that have come down to earth from outer space. The experience is designed as a simple reminder of the gift…

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ISB Q&A: David Gibbs, Research Scientist

You have to have fun. ISB founder Dr. Lee Hood always reminds staff that it’s important to do great work, and it’s also important to have fun. In that spirit, we feature CatterPlots, a “silly idea” that brought a smile to many scientists. Q: What is CatterPlots and how is it used? David Gibbs: The R programming environment is organized around a large collection of software packages. Many packages are…

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William Poole, 2013 undergrad intern

Former Undergrad Intern Publishes Algorithm in PLOS Computational Biology

Posted March 1, 2017 In a study published in PLoS Computational Biology, researchers at Institute for Systems Biology (ISB) have developed a multiscale mutation clustering algorithm (M2C) that identifies variable length regions with high mutation density in cancer genes. The M2C algorithm was developed by William Poole (first author on the paper), who started as a summer intern in 2013 as part of ISB’s Center for Systems Biology internship program….

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Sanger Institute’s COSMIC database expands cancer cloud capabilities at the Institute for Systems Biology

The Wellcome Trust Sanger Institute released this news on Feb. 20, 2017. See original release… FOR IMMEDIATE RELEASE The Wellcome Trust Sanger Institute’s Catalog of Somatic Mutations in Cancer (COSMIC) team announces a new agreement to provide their data to the U.S.-based Institute for Systems Biology (ISB). COSMIC is an expert-curated cancer mutation database, and is the world’s largest and most comprehensive resource for exploring the impact of somatic mutations…

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Comprehensive study of esophageal cancer reveals several molecular subtypes, provides new insight into increasingly prevalent disease

The Cancer Genome Atlas Research Network recommends clinical trials organizers and drug manufacturers focus on newly discovered molecular subtypes GRAND RAPIDS, Mich., Jan. 4, 2017 –– A comprehensive analysis of 559 esophageal and gastric cancer samples, collected from patients around the world, suggests the two main types of esophageal cancer differ markedly in their molecular characteristics and should be considered separate diseases. The study, published today in Nature from The…

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ISB Gets $3.4M NIH Extension for Cancer Genomics Cloud

FOR IMMEDIATE RELEASE ISB Receives $3.4 Million Extension to NIH Contract to Continue Development of ‘Cancer Genomics Cloud’ with Google and CSRA SEATTLE, Oct. 21, 2016 – Institute for Systems Biology (ISB) has received a $3.4 million, one-year extension to an existing federally-funded contract from the National Cancer Institute (NCI), National Institutes of Health (NIH). This follows the completion of the initial two-year, $6.5 million contract during which ISB developed…

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Vice President Biden Gives Cancer Moonshot Update

This week, Vice President Biden delivered an extensive update on the progress of the Cancer Moonshot initiative. ISB was mentioned in relation to the Cancer Genomics Cloud project. Learn more about ISB CGC at isb-cgc.org. Excerpt from the official White House press release: Official White House press release Full Cancer Moonshot Report Puget Sound Business Journal article

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A Landscape of Pharmacogenomic Interactions in Cancer

The journal Cell published a study today (July 7) about the integrated analysis of drug response in 1,001 cancer cell lines. This study was undertaken by a large international group of researchers including ISB Senior Research Scientist Theo Knijnenburg. The researchers integrated heterogeneous molecular data of 11,215 tumors and 1,001 cell lines in order to study the drug response of these cell lines to 265 anti-cancer drugs. They uncovered numerous…

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Not Just About Collecting Data

Genetic Engineering & Biotechnology News interviewed ISB’s Dr. Ilya Shmulevich for a feature article on systems biology. “Systems biology is not just about measuring as many things as possible,” says Ilya Shmulevich, PhD, a professor at the Institute for Systems Biology. “It is also about using mathematical and computational modeling to make predictions about the system.” READ THE ARTICLE: http://www.genengnews.com/…/systems-biology-digs-deep…/5775/

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Systems Biology Digs Deep, Aims High

Dr. Ilya Shmulevich was recently interviewed for the following article in Genetic Engineering & Biotechnology News. Read more here.

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New Publication in ‘Cancer Cell’

As part of The Cancer Genome Atlas project, the Shmuelvich Lab and colleagues published a paper in the journal Cancer Cell related to the rare cancer adrenocortical carcinoma. Read the summary: 3 Bullets: Adrenocortical carcinoma (ACC) is a rare, under-researched endocrine cancer with limited therapeutic options and overall poor outcome. TCGA researchers performed comprehensive analysis of 91 ACC samples to gain better understanding of potential genetic causes of the cancer….

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Dr. Nyasha Chambwe, a postdoctoral fellow in the Shmulevich Lab at Institute for Systems Biology, discusses some data analysis with colleague Summer Elasady.

In the News: Basketball and Biology

Congratulations to Dr. Nyasha Chambwe on being featured in the May 20 issue of Puget Sound Business Journal’s “People in Research” column. The profile reveals Dr. Chambwe’s path to ISB, starting with a full-ride scholarship to Jackson State University. She has been working on a study on pre-term birth and soon will be moving to projects related to glioblastoma and leukemia. Read the PSBJ article… Photo above: Dr. Nyasha Chambwe,…

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New TCGA publication on adrenocortical carcinoma

Our group has contributed to a recent paper published by the TCGA Research Network on a study about 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…

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Bio-IT features Sheila Reynolds

Congrats to Sheila Reynolds on being featured on the Bio-IT World Conference site for her presentation on ISB’s Cancer Genomics Cloud project. Read the Q&A here.

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Ilya Shmulevich at GCPNext

Using Google Cloud Platform to Give Researchers Easier Access to Cancer Data

ISB’s Dr. Ilya Shmulevich attended Google Cloud Platform’s GCPNext conference in San Francisco and presented on ISB’s Cancer Genomics Cloud project. He explains how his team used GCP to create better access for a broad range of researchers to cancer genomics data (from The Cancer Genomics Atlas) and the tools with which to explore that data. Watch Dr. Shmulevich’s talk below.

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ISB Spotlight: Lisa Iype

Dr. Lisa Iype (Ilya Shmulevich group) has been promoted to Senior Bioinformatics Scientist. She has experience in biochemistry, software and website development, and data analysis. She works with high-dimensional cancer data sets and looks for significant patterns which may provide insight into cancer development and progression. Dr. Shmulevich commented: “Lisa has made major contributions to The Cancer Genome Atlas project through her participation in tumor working groups, including thyroid carcinoma…

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Event: Cancer Think Tank

Cure First is hosting the forum “Cancer Think Tank.” Speakers include ISB’s Dr. Ilya Shmulevich and Dr. Brady Bernard. Date: January 21, 2016 Time: 1-5:30 p.m. MED talks, breakout sessions, and panel discussion; 6-8 p.m. networking with wine and dinner Why: To jump start innovative collaborations in cancer research with the goal to submit proposals for funding to accelerate the discovery of new, less toxic and targeted therapies. Who: This…

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