ISB News

Genetic Switch May Help Marine Microalgae Respond to Higher CO2 Levels

3 Bullets Rapid climate change, including ocean acidification caused by increasing carbon dioxide (CO2) levels, is predicted to affect the oceans, sea life, and the global carbon cycle. Marine microalgae, including diatoms, are responsible for converting CO2 into oxygen and biologically usable carbon through photosynthesis. How these organisms will respond over the short and long term to rising CO2 is unknown. Growth experiments and transcriptomic analyses performed by UW and…

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New $500K OSPI Award Aids ISB’s Work with Marysville School District

Above: Dr. Dana Riley Black, Director for ISB’s Logan Center for Education, speaks to educators about how her team and other ISB researchers work with school districts. FOR IMMEDIATE RELEASE Marysville School District Scores $500,000 OSPI Funding for Science & Engineering Workshops for Teachers 3-Year Award Supports Partnership with ISB & UW Engineering to Provide Professional Development for District SEATTLE, May 1, 2015 – The Office of Superintendent of Public…

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Lucas Myers is a biology instructor at Lower Columbia College.

ISB’s Impact on College Science Courses

By Dana Riley Black Director for Logan Center for Education Recognizing that systems biology has fostered a paradigm shift in the practice of biology, ISB has interest in supporting educators in advancing science-related course offerings to better reflect contemporary practices of biology. With leadership from ISB’s Logan Center for Education, ISB educators and scientists have collaborated with Washington’s State Board for Community and Technical Colleges to offer faculty development for…

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From left to right: High school teachers Tami Caraballo and Jennifer Duncan-Taylor work with ISB’s Claudia Ludwig, Baliga Lab Education Program Manager, to learn about ocean acidification, cancer cells, and biofuel.

ISB Q&A: High School Science Teachers

From left to right: High school teachers Tami Caraballo and Jennifer Duncan-Taylor work with ISB’s Claudia Ludwig, Baliga Lab Education Program Manager, to learn about ocean acidification, cancer cells, and biofuel. Through the MJ Murdock Charitable Trust’s Partners in Science program, ISB has been able to host two high school science teachers in the Baliga Lab to participate in active research projects. The experience offers teachers valuable insight that textbooks…

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The Most Powerful Tool for Reconstructing a Gene Network

Scanning EM of bacteria being eaten by white blood cell Photo Credit: Adrian Ozinsky 3 Bullets: Nearly a decade ago, ISB’s Baliga Lab published a landmark paper describing cMonkey, an innovative method to accurately map gene networks within any organism from microbes to humans. Two new papers describe the benchmark results of cMonkey and also the release of cMonkey2, which performs with higher accuracy. Using this approach, genetic and molecular…

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Baliga Lab: A Global Map To Fight Tuberculosis

3 Bullets: The disease progression of tuberculosis is extremely complex and it’s poorly understood. ISB and Seattle BioMed researchers have made an important step by developing a comprehensive map of gene regulation in tuberculosis. A resulting open-access web portal offers any scientist the ability to mine the collected data. By ISBUSA Tuberculosis (TB) remains a top global health threat due to its remarkable complexity in disease progression. To help understand…

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Baliga Lab: ‘The Universe Under a Microscope’

This is an excerpt from Environmental Microbiology Reports, 2015, authored by Arjun Raman, a postdoc in the Baliga Lab here at Institute for Systems Biology. The beauty of a living thing is not the atoms that go into it, but the way those atoms are put together. Information distilled over four billion years of biological evolution. Incidentally, all the organisms on the Earth are made essentially of that stuff. An…

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A breakthrough in understanding the genetic ‘architecture’ of bipolar disorder

3 Bullets: Bipolar disorder (BD) is a common, severe and recurrent psychiatric disorder with no known cure and substantial morbidity and mortality. Heritable causes contribute up to 80 percent of lifetime risk for BD. Scientists hope that identifying the specific genes involved in risk for bipolar disorder will lead to new ways to treat the disease. ISB researchers identified contributions of rare variants to BD by sequencing the genomes of…

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ISB Releases Kaviar, World’s Largest Public Catalog of Human Genomic Variation

3 Bullets: Kaviar is ISB’s comprehensive catalog of human genomic variation Kaviar combines 31 data sources for a total of 151 million single nucleotide variants (SNVs), covering 5% of all the positions in the human genome A researcher studying possible disease-causing variants can use Kaviar to answer the question, “Have these variants been observed before, and if so, how often?” By Terry Farrah A typical pair of human genomes are…

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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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Infographic showing types of data

‘Integrating big data and actionable health coaching to optimize wellness’

The journal BioMed Central Medicine published a commentary by Dr. Lee Hood, Dr. Jennifer Lovejoy, and Dr. Nathan Price on the Hundred Person Wellness Project – phase 1 of the 100K Wellness Project. The article was published on Jan. 9, 2015. ABSTRACT: “The Hundred Person Wellness Project (HPWP) is a 10-month pilot study of 100 ‘well’ individuals where integrated data from whole-genome sequencing, gut microbiome, clinical laboratory tests and quantified…

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Pushing the Molecular Switches of Tuberculosis Into Overdrive to Map Interactions

3 Bullets: Mycobacterium tuberculosis (MTB) infects more than 1.5 billion people worldwide partly due to its ability to sense and adapt to the broad range of hostile environments that exist within hosts. To study how MTB controls its responses at a molecular level, ISB researchers and their collaborators at Seattle Biomed perturbed almost all MTB transcription factor regulators and identified the affected genes. This comprehensive map of molecular switches in…

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ISB’s 100K Project A Top Story on GenomeWeb

By ISBUSA GenomeWeb announces 2014’s top-10 most-read articles on personalized medicine and the article on ISB’s 100K Wellness Project was No. 1. Here’s an excerpt from GenomeWeb’s Jan. 5 story: NEW YORK (GenomeWeb) – GenomeWeb readers in 2014 were most interested in a story about a large study investigating why some people remain healthy while others get sick. The top article was about healthcare entrepreneur Leroy Hood’s efforts to advance…

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How One Family of Microbial Genes Rewires Itself for New Niches

3 Bullets: When an organism duplicates its genes, it increases its ability to adapt and colonize new environments. ISB researchers used the systems approach to study how one family of microbial genes evolved to bring functions that were adaptive to specific environments. This new understanding of how gene regulatory networks rewire themselves has many potential applications, including how to wire new functions into an organism for biofuel production, bio-remediation or…

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What’s the Secret to ‘Extreme Longevity’?

3 Bullets: ISB researchers and their collaborators studied a group of supercentenarians (110 years or older) to explore the genetics of ‘extreme longevity.’ The group performed whole-genome sequencing on 17 supercentenarians in order to look for any rare protein-altering variants associated with extreme longevity. While the researchers did not find a single cause for extreme longevity within this sample size, the genomic data is now available for future studies. By…

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ISB Recieves $6.5M NIH Contract to Create Cancer Genomics Cloud with Google and SRA International (Image credit: MIT Tech Review)

Cancer Genomics Cloud: ISB and Google Featured in MIT Tech Review

(Above illustration from MIT Technology Review.) MIT Technology Review published an article about the launch of Google Genomics and included a mention of ISB’s new Cancer Genomics Cloud project. ISB received an up-to $6.5 million, two-year NIH contract in collaboration with Google and SRA International. From the MIT Technology Review article: The idea is to create “cancer genome clouds” where scientists can share information and quickly run virtual experiments as…

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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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A New Approach to Identifying How the Deadly Dengue Virus Multiplies

3 Bullets: Dengue virus is the most prevalent mosquito-borne virus worldwide, infecting an estimated 400 million people per year and causing about 25,000 deaths. It’s necessary to understand the molecular mechanisms of dengue replication in order to develop an effective treatment. Researchers at ISB and Seattle BioMed developed a novel approach for identifying host proteins that associate with dengue replication machinery. By Thurston Herricks Dengue virus (DENV) infects approximately 400…

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