ISB News

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…

Decoding the Microbial Gene-Recycling Program: Researchers 'Unzip' Genetic Instruction Manuals

New Open-Access Multiscale Model Captures Dynamic Molecular Processes in Unprecedented Detail

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…

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…

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….

The Rise of Open Proteomics

Researchers at EMBL-EBI, Institute for Systems Biology and other partnering organizations have launched ProteomeXchange, a public portal for exchanging proteomics data generated from mass-spectrometry experiments and other related information. From the EMBL-EBI-issued press release: Eric Deutsch, head of PeptideAtlas at the Institute for Systems Biology in the U.S., says: “I’m certain that the ProteomeXchange system is already leading to greater awareness and reuse of publicly available datasets. I’m regularly contacted…

‘Demystifying Disease, Democratizing Health Care’

In the Feb. 26, 2014, issue of Science Translational Medicine, Dr. Lee Hood and Dr. Nathan Price, of Institute for Systems Biology, deliver an editorial stating the vision of the 100K Wellness Project. The project will track health-related data types for 100K individuals longitudinally over the course of 20-30 or more years. "Unsustainable cost increases threaten the global health care system, and further progress is stymied more by societal than…

Tiniest Malfunctions in a Cell Can Cause Devastating Diseases

3 Bullets: ISB researchers are studying peroxisomes, which are cellular organelles that are linked to a rare syndrome that causes progressive organ complications and infant mortality. Peroxisomes have a role in metabolizing and breaking down cellular waste. Because peroxisomes easily change shape and function according to a cell’s needs, a systems approach is necessary to help decipher that complexity. By Dr. Thurston Herricks Dane Tolmie was a 19-month old boy…

Largest Genetics Catalog of Deadliest Brain Tumor Released

  By Varsha Dhankani Glioblastoma multiforme (GBM) is the most common and deadliest of malignant primary brain tumors in adults. Because of its lethality, GBM was selected as the first brain tumor to be sequenced as part of The Cancer Genome Atlas (TCGA), a comprehensive project funded by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) to map the genomes of more than 25 types…

Publications: A ‘Google Map’ of Human Metabolism

ISB associate professor Nathan Price and Vangelis Simeonidis, a visiting scholar from Luxembourg Centre for Systems Biomedicine (LCSB is a major strategic partner with ISB), contributed to this paper – “A community-driven global reconstruction of human metabolism” – that was published today in Nature Biotechnology. An excerpt describing the collaborative project from a press release is below. An interactive map is forthcoming.   From Medicalxpress.com: “An international consortium of university…