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…
There’s something calming about watching algae grow. What you see in the tubes are two types of algae: Thalassiosira pseudonana or “Thaps” is the brown diatom. Chlamydomonas reinhardtii or “Chlamy” is the green algae. We use Thaps to study ocean acidification and Chlamy is for studying biofuel production.
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…
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…
Photo above: Students participating in PROJECT BIOTECH Summer Camp. Photo credit: Shoreline Community College By Dina Kovarik Project Manager, Baliga Lab The Shoreline Community College (SCC) Biotech Program and the Amgen Biotech Experience (ABE) program partnered with the Institute for Systems Biology (ISB) to develop a one‐week summer camp for high school students called PROJECT BIOTECH. The camp took place at SCC on July 7‐11, 2014. While the Puget Sound…
3 Bullets: Novel systems approach uses high-resolution structures of protein-DNA complexes to predict where transcription factors (genetic switches) bind and regulate the genome. This approach can help researchers better understand and predict binding sites for non-model organisms or ‘exotic’ species. Having such insight and predictive capabilities is critical for reverse- and forward-engineering organisms that could be pivotal for new green biotechnologies. By Jake Valenzuela and Justin Ashworth Researchers at the…
3 Bullets: The Institute for Systems Biology and Seattle BioMed have collaborated to reconstruct the gene regulatory network of the human pathogen Mycobacterium tuberculosis. Finely tuned gene regulation has allowed Mycobacterium tuberculosis to survive unnoticed in an apparently healthy host for decades; understanding those subtleties is critical for advancing treatment. The identification of co-regulated sets of genes and their regulatory influences offers validated predictions that will help guide future research…
3 Bullets: Microbes are efficient because their streamlined genomes allow them to evolve and adapt rapidly to complex environmental changes. Decoding the highly-compressed information within a microbial genome requires sophisticated systems biology tools to map the genetic programs, and understand how they are executed. ISB researchers invented novel algorithms to unzip and decode microbial genomes into the EGRIN 2.0, an open-access multiscale model that captures instructions for executing the dynamic…
(Photo above: ISB’s Dr. Ilya Shmulevich describes his lab’s work in The Cancer Genome Atlas project and how ISB and FHCRC could collaborate.) Big health challenges require big science. Cancers are prime examples of overwhelmingly complex diseases that need the power of a cross-disciplinary, systems biology approach to decipher the underlying dysfunctional gene networks in order to find ways to prevent and manage the diseases and develop more effective therapies….
FREE SUMMER SYSTEMS SCIENCE WORKSHOP AT ISB FOR TEACHERS: Registration for the summer systems science workshop for high school science, math and CTE teachers is now open. The workshop is hosted by Claudia Ludwig and Dina Kovarik, of the Baliga Lab at ISB, and takes place July 21-25. The focus is on how to implement systems science in the classroom. For more information about the workshop, please visit this site….
National: At the beginning of April, Dana Riley Black, ISB’s Director of Education, was invited to participate in one of three Ideas Labs hosted by the National Science Foundation in Washington D.C. The weeklong lab was related to the new NSF program “Improving Undergraduate STEM Education” (IUSE) and was focused on discussing ideas for integrating quantitative literacy into undergraduate biology education. The reason for this particular topic is that while…
NOAA National Marine Sanctuaries and Ocean Acidification Program is holding a webinar series starting March 19 through June on the topic: "Sharing Ocean Acidification Resources for Communicators and Educators." ISB's Claudia Ludwig, the Education Program Manager in the Baliga Lab, will present: Ocean Acidification: A Systems Approach to a Global Problem When: Wed., April 23, 2014, 3 p.m. PST (6 p.m. EST) Primary Audience: Teachers, Formal Educators Project Website: http://baliga.isbscience.net/drupal/education/?q=content/ocean-acidification-systems-approach-global-problem…
NOAA National Marine Sanctuaries and Ocean Acidification Program is holding a webinar series starting March 19 through June on the topic: "Sharing Ocean Acidification Resources for Communicators and Educators." ISB's Claudia Ludwig, the Education Program Manager in the Baliga Lab, will present: Ocean Acidification: A Systems Approach to a Global Problem When: Wed., April 23, 2014, 3 p.m. PST (6 p.m. EST) Primary Audience: Teachers, Formal Educators Project Website: http://baliga.isbscience.net/drupal/education/?q=content/ocean-acidification-systems-approach-global-problem…
Dr. Lee Hood's 75th birthday party took place at ISB on Oct. 10. Here's the photo gallery. As part of the presentations, Dr. Nitin Baliga (ISB's Director and SVP) shared a fun video he made using footage he shot during the faculty retreat. Exactly how many PhDs does it take to find a Prius battery? Watch and find out:
WHAT YOU HEARD IN THE NEWS: NPR aired this story (on Sept. 5) about research just published in the journal Nature Genetics suggesting that tuberculosis may have existed more than 70,000 years ago. Tuberculosis Hitched a Ride When Early Humans Left Africa ‘ “The old, traditional view was that tuberculosis emerged during the Neolithic transition when people started to domesticate animals and develop agriculture, which started about 10,000 years ago,”…
ISB will collaborate with Seattle BioMed and ETH Zurich on a $16.6 million tuberculosis grant from the National Institutes of Health. Seattle BioMed issued this press release today: FOR IMMEDIATE RELEASE SEATTLE, AUG. 15 — Seattle BioMed has been awarded a grant from the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, that will take a comprehensive systems approach to the problem of tuberculosis…
Célya Gruson-Daniel, the founder of HackYourPhD, has been traveling across the United States to make a documentary about open science. She stopped by ISB on Aug. 5, 2013, to interview Dr. Nitin Baliga, who is our senior vice president and director. The short interview is below. Learn more about the Hack Your PhD documentary at this site: http://hackyourphd.org/USA
Just as the Seattle tourist traffic picks up in the summer, the intern and visitor traffic at ISB spikes during July and August. It’s always inspiring to see the fresh faces of high school students in our halls. On Aug. 7, the MESA Math Scholars came to ISB to visit our labs and spend some time with a few of our scientists. MESA stands for Mathematics, Engineering, Science Achievement and…
