ISB News

CRI iAtlas

CRI iAtlas Expands to Interactive Analysis of Data on Immunotherapy Treatments

CRI iAtlas is a comprehensive web-based resource that allows oncologists and researchers to study and analyze interactions between tumors and the immune microenvironment. The iAtlas team released immuno-oncology modules that allow investigators to access and work with genomics data from trials of treatment with immune-checkpoint inhibitors.


ISB Researchers Among Recipients of AACR Team Science Award

The American Association for Cancer Research (AACR) has recognized The Cancer Genome Atlas (TCGA) project with the 2020 AACR Team Science Awards. Award recipients include Dr. Ilya Shmulevich, ISB professor and head of the Shmulevich Lab; ISB senior research scientist Dr. Vésteinn Þórsson; and former Shmulevich Lab members Drs. Brady Bernard and Theo Knijnenburg.

ISB researchers

Unveiling the Guerrilla Warfare Tactics of Mycobacterium Tuberculosis

ISB researchers have unveiled new insights on how Mycobacterium tuberculosis, the pathogen that causes tuberculosis, enters and exits a dormant state in human hosts. About a quarter of the world’s population has latent TB, so these important findings will enable and accelerate the discovery of more effective TB drugs.

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…

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….

ISB-CGC banner image

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…

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 Excerpt from the official White House press release: Official White House press release Full Cancer Moonshot Report Puget Sound Business Journal article

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,…

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…

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…

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)…

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…

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…

Now researchers can explore genomic data across space and time

The figure above is part of a four-step procedure for the multiscale segmentation of genomic signals. 3 Bullets: Understanding systems from a multiscale perspective gives us a more detailed and holistic view of how features or functions from each scale connect and interact in a given system. The challenge is integrating the different types of information that come from each scale in an efficient way that yields the most insight….