ISB News

ISB’s Computational Teams Play Central Role in Completion of TCGA’s PanCancer Atlas Initiative

ISB’s computational and bioinformatics teams played a central role in the completion of the PanCancer Atlas Initiative, the final phase of TCGA. The culmination of this work is being published in 27 papers this week across the Cell Press research journals, including “The Immune Landscape of Cancer” in Immunity.

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CRI, ISB, Sage Bionetworks Unveil Comprehensive Immunotherapy Tool

Three organizations on the forefront of cancer immunotherapy, systems biology and bioinformatics announced the release of the Cancer Research Institute iAtlas, a comprehensive web-based tool that allows oncologists and researchers to study and analyze interactions between tumors and the immune microenvironment.

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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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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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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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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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ISB Researcher Featured in Bio-IT World

Congrats to Sheila Reynolds (Shmulevich Lab) 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. Excerpt below: Cancer Genome Analysis at the Institute for Systems Biology Q1: How did your background in signal processing and machine learning lead you to work in cancer genome analysis at the Institute for Systems Biology in Seattle, Washington? After working in…

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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’s Cancer Genomics Cloud Team Launches BigQuery Platform

Genomeweb published an article on the Cancer Genomics Cloud pilots. Learn more about ISB’s CGC project. PDF: Cancer Genomics Cloud Pilot Developers Provide Update, Open Up Platforms for Early Testing | GenomeWeb NEW YORK (GenomeWeb) – The developers of the three proposals selected by the National Cancer Institute for the Cancer Genomics Cloud pilots — an effort to build sustainable computing infrastructure for analyzing omics data from the Cancer Genome…

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Into the genetic weeds of hair growth

3 Bullets: ISB researchers used a data-driven mathematical model to identify specific genes associated with hair regeneration Novel methodology paves way for continued research into the molecular basis of this complex cycle as well as other regenerative organs like skin and liver Findings may lead to more precise targets for therapies and genetic markers of hair wellness By Varsha Dhankani Scientists at ISB have identified genes associated with the growth-and-death…

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How Physics and Thermodynamics Help Assess DNA Defects in Cancer

3 Bullets: ‘Big data’ cancer research has revealed a new spectrum of genetic mutations across tumors that need understanding. Existing methods for analyzing DNA defects in cancer are blind to how those mutations actually behave. ISB scientists developed a new approach using physics- and structure-based modeling to systematically assess the spectrum of mutations that arise in several gene regulatory proteins in cancer. By Jake Valenzuela and Justin Ashworth A significant…

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New Details on Thyroid Cancer May Lead to More Precise Therapies

3 Bullets: Papillary thyroid cancer represents 80 percent of all thyroid cancer cases. Integrative analysis resulted in the detection of significant molecular alterations not previously reported in the disease. ISB researchers identified microRNAs which may lead to more precise therapy. By Lisa Iype Papillary thyroid cancer (PTC) is the most common type of thyroid cancer, accounting for 80 percent of all cases. As part of The Cancer Genome Atlas (TCGA)…

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Cancer genomics visualization at ISB

It’s Easier to Go ‘Viral’ When Your Partner Happens to be Google

By ISBUSA Since we announced that we got a $6.5 million contract from NCI to develop the Cancer Genomics Cloud pilot project, we’ve gotten some great press from around the world. It doesn’t hurt that one of our partners is Google, of course. Here are some of the headlines from around the world: Puget Sound Business Journal: Cancer in the cloud: Institute for Systems Biology teams up with Google NBCNews.com:…

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ISB Awarded $6.5 Million NIH Contract to Develop ‘Cancer Genomics Cloud’ with Google and SRA International

PRESS RELEASE Institute for Systems Biology (ISB) has received a $6.5 million, up to two­-year, federally funded contract from the National Cancer Institute (NCI), National Institutes of Health (NIH). ISB is one of three organizations awarded a contract by NCI to develop a cloud-­based platform that will serve as a large­-scale data repository and provide the computational infrastructure necessary to carry out cancer genomics research at unprecedented scales. ISB’s Shmulevich…

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BIOCELLION: New Supercomputer Software Framework Models Biological Systems at Unprecedented Scales

3 Bullets: Computer simulation is a promising way to model multicellular biological systems to help understand complexity underlying health and disease. Biocellion is a high-performance computing (HPC) framework that enables the simulation of billions of cells across multiple scales. Biocellion facilitates researchers without HPC expertise to easily build and simulate large models. By Theo Knijnenburg How do molecular changes, such as a mutation in the DNA or infection by a…

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ISB Researchers Help Identify Four New Subtypes of Gastric Cancer That May Lead to New Targeted Treatments

3 Bullets: Gastric cancer has a high mortality rate, but current classification systems haven’t been effective in helping to identify subtypes relevant for treatment of the disease. TCGA researchers have integrated molecular data from 295 stomach tumors and have discovered four subtypes of gastric cancer. Stratification of patients into these four subtypes paves the way for the development of new personalized therapies. By Theo Knijnenburg Gastric cancer is among the…

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Cancer stratification: Using a systems approach to figure out cancer subtypes.

Cancer Stratification: A Systems Approach

By Theo Knijnenburg ISB Editorial Board Member When a patient receives a diagnosis of breast cancer, it’s a specific subtype of breast cancer, such as invasive ductal carcinoma. Each subtype is characterized by the shape and location of the tumor, its growth progression, prognosis and treatment. The ability to stratify, or group, cancer patients based on the specific characteristics of their cancer type, is the first step toward personalized cancer…

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