ISB News

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…

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…

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…

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…

The Institute for Systems Biology has a mission to make data available to the world. In a paper recently published in the journal Current Protocols in Bioinformatics, proteomics researchers in the lab of Dr. Robert Moritz provide a step-by-step tutorial demonstrating how to take advantage of web-based applications that let researchers share and use proteomics data.

Let Us Tell You Everything We Know About Proteomics – Everything

3 Bullets: Proteomics experiments generate huge amounts of raw data, most of which cannot be easily shared or described in a publication. ISB researchers curate publicly accessible databases that allow researchers to share their data with the world and to use data others have collected. All data are analyzed in a consistent manner and results are presented via searchable, user-friendly web applications. By Dr. Kristian Swearingen Institute for Systems Biology…

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…

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…

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…

Baliga Lab: Uncovering the Genetic Adaptability of Tuberculosis

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…

Analyzing Family Genomics Reveals New Culprit in Rare Disease

3 Bullets: Adams-Oliver syndrome (AOS) is a rare congenital disease characterized by scalp lesions and limb defects. Additional vascular abnormalities and heart defects can lead to early death in some patients. By analyzing twelve families affected with the disease, we identified causal mutations in a new disease gene, NOTCH1, in five families. NOTCH1 is likely to be the major cause of AOS. NOTCH1 codes for a transcription factor that governs…

New Structural Map Helps To Understand Aggressive Tumors

3 Bullets: Aggressive tumor growth is linked to high activity of a macromolecular assembly called RNA polymerase I. ISB and FHCRC researchers collaborate to map the architecture of the assembly using a powerful crosslinking-mass spectrometry (CXMS) technology. Structural maps provide important insights into therapeutic targets for cancer treatment. By Mark Gillespie Rapidly growing tumor cells require large amounts of protein for their survival. This increased protein synthesis, or translation, can…

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…

ISB Researchers Identify New Protein Modification Critical to Growth of Tuberculosis Pathogen

3 Bullets: Institute for Systems Biology and Seattle BioMed researchers collaborated and discovered a new protein post-translational modification in the human pathogen Mycobacterium tuberculosis. Post-translational modifications are essential mechanisms used by cells to diversify protein functions and ISB scientists identified the rare phosphorylated tyrosine post translational modification on Mycobacterium tuberculosis proteins using mass spectrometry. Inhibiting phosphotyrosine modified amino acids in Mycobacterium tuberculosis severely limits the growth of this widespread deadly…

ISB's Ilya Shmulevich describes his lab's work in The Cancer Genome Atlas project and how ISB and FHCRC could collaborate.

Melding ISB and FHCRC Brain Power for Cancer Research

(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….

It's National Cancer Research Month. Please visit aacr.org to learn more. Or please support Institute for Systems Biology directly at https://www.isbscience.org/support.

It’s National Cancer Research Month: How To Help

May has been designated "National Cancer Research Month" and we'd like to share a little about how ISB is using the systems biology approach to tackle some of the complexities of researching cancers. You can read our four-part series on how ISB's pioneering systems biology has made an impact and continues to clear new pathways for the cancer research field. Please visit aacr.org to learn more about NCRM. Support ISB's…

Data Visualization from Largest Genetics Catalog of Deadliest Brain Tumor

In Cancer Research, It’s HOW That Matters

By Martin Shelton, Theo Knijnenburg and Joseph Zhou ISB Editorial Board Members The oldest existing record of cancer occurs in a 4000-year-old Egyptian papyrus. It describes, in detail, a woman with symptoms eerily similar to those of modern breast cancer patients. As for the prescribed treatment, there was simply this statement: “No cure.” Sadly, this short and assertive conclusion remains true. According to the American Cancer Society’s annual cancer statistics…

Cancer Detection requires a cross-disciplinary, systems biology approach.

Cancer Detection: A Systems Biology Approach

By Martin Shelton ISB Editorial Board Member With the exception of cancers of the skin, mouth, and blood, it is difficult to detect cancer by sight or with a routine health screen. The natural variety that exists at the cellular level — even within cells of the same type — challenges our ability to differentiate healthy tissue from diseased. This variety, what biologists call heterogeneity, means that equally healthy cells…