ISB News

Baliga Lab: New Publication in ‘Nature Microbiology’

The Baliga Lab and colleagues at Center for Infectious Disease Research published (online in advance of print) this landmark study today in the journal Nature Microbiology: Seattle researchers created a genetic blueprint of the cunning tuberculosis bacteria, then used it to predict and rank potential drug targets 3 Bullets: Researchers at the Institute for Systems Biology and Center for Infectious Disease Research have deciphered how the human pathogen Mycobacterium tuberculosis…

New Publication in ‘Cancer Cell’

As part of The Cancer Genome Atlas project, the Shmuelvich Lab and colleagues published a paper in the journal Cancer Cell related to the rare cancer adrenocortical carcinoma. Read the summary: 3 Bullets: Adrenocortical carcinoma (ACC) is a rare, under-researched endocrine cancer with limited therapeutic options and overall poor outcome. TCGA researchers performed comprehensive analysis of 91 ACC samples to gain better understanding of potential genetic causes of the cancer….

Dr. Kristian Swearingen, ISB research scientist.

Dissecting Mosquitoes is Hard!

Photo by Hsiao-Ching Chou Dr. Kristian Swearingen is a research scientist in the Moritz Lab at ISB. He and his collaborators just published a paper in PLOS Pathogens that describes potential new targets for malaria vaccines. Read his article about the research. Asked about the challenge of having to dissect thousands of mosquitoes, he commented: When we started this project, my collaborators collected all the parasites and I focused on…

ISB Q&A: Dr. Robert Moritz on Ötzi the Iceman

Ötzi the Iceman: In a study published in the Jan. 8, 2016, issue of the journal Science, researchers from the Moritz group at ISB collaborated with a worldwide consortia headed by Prof. Albert Zink and Dr. Frank Maixner, of the Institute for Mummies and the Iceman at the European Academy of Bozen/Bolzano (EURAC) in Italy; Prof. Thomas Rattei, of the University of Vienna; and Dr. Rudi Grimm, of University of…

New Research on IBD from ISB’s Family Genomics Group

Our Family Genomics group and collaborators analyzed the whole genome sequences of five families with high burden of inflammatory bowel disease (IBD) in order to elucidate the genomic architecture of IBD. Read about the research here… 3 Bullets: In medical genetics it is an unsolved question to what degree complex diseases are influenced by rare variants with potentially large effects in relation to the many common and weak-effect variants that…

The 5300-year-old Helicobacter pylori genome of the Iceman

ISB’s Moritz Group, which specializes in proteomics, collaborated on research related to study pathogens from the stomach content and microbiome of Ötzi, a glacier mummy from the European Copper Age. The results were published in Science. Read the article here. Institute for Systems Biology collaborates with researchers worldwide to study pathogens in the stomach content and microbiome of the 5300 year old European Copper Age glacier mummy “Ötzi” and discovers…

Genetic Disease Breakthrough Published in ‘Nature Communications’

FOR IMMEDIATE RELEASE Genetic Disease Breakthrough Published in Nature Communications SEATTLE, DEC. 18, 2015 – A team of investigators based in Seattle, Amsterdam, and Luxembourg, have established the cause of a rare syndrome consistent with Fanconi Anemia, a chromosome instability disorder which is clinically typified by birth defects, bone marrow failure, leukemia, and susceptibility to solid tumors. The results were reported by researchers from the Institute for Systems Biology (Seattle),…

Researchers determine architecture of a macromolecular complex regulating gene expression and DNA repair

General transcription factor TFIIH plays central roles in gene transcription and DNA repair ISB researchers and collaborators map the architecture of the TFIIH complex using powerful crosslinking-mass spectrometry (CXMS) technology and integrative modeling Structural maps provide critical insights into how mutations in TFIIH subunits lead to disease phenotypes By Jie Luo and Mark Gillespie The expression, or transcription, of genes controls the identity and function of a cell. DNA damage…

A Mixture of Markers from Two Distinct Cell Types Indicates Poor Prognosis in Breast Cancer

3 Bullets: Identifying the most aggressive cells in cancer (cancer stem cells) is essential for designing effective therapy and predicting patient outcomes. Using single-cell analysis techniques, researchers at ISB and Luxembourg Centre for Systems Biomedicine have identified the molecular signatures of two types of malignant breast tissue cells. Researchers found an interesting twist: the two cell types “cooperate” to increase malignancy potential and they promote a third hybrid stem-cell type….

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…

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…

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…

ISB releases open-source software to analyze digital fingerprint of protein data

3 Bullets SWATH mass spectrometry, an emerging protein analysis technique being pioneered by ISB researchers, provides a digital fingerprint of all accessible proteins in a sample. The data generated by the SWATH technique are highly complex and require sophisticated computational tools in order to extract identities from a sea of data. ISB researchers have released a free, open source program that allows users to confidently identify and quantify proteins analyzed…

ISB and P&G researchers identify markers of healthy skin development

3 Bullets: The barrier function of skin is integral to personal well-being and is associated with several widespread diseases such as eczema and psoriasis. ISB and Procter & Gamble researchers used human skin grown in the lab to measure changes in protein levels as the skin matures. The results of this study provide many new markers for healthy skin development. By Dr. Kristian Swearingen and Dr. Jason Winget In a…

Researchers Find Key Protein Tied to Production of ‘Good’ Cholesterol

3 Bullets: Inflammation causes cholesterol buildup and leads to cardiovascular disease, the leading cause of death in the world ISB, Seattle Biomed, and Oregon State University researchers collaborate to identify a compendium of proteins that control expression of a key regulator of cholesterol efflux Targeting cholesterol efflux to HDL is a potentially important therapeutic strategy for preventing and treating cardiovascular disease By Dr. Mark Gillespie Cells of the immune system,…

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…

Tuberculosis Research: A ‘Molecular Road Map’ to Help Understand Gene Regulation

The journal “Trends in Microbiology” recently published a spotlight article on a tuberculosis research collaboration between scientists at Institute for Systems Biology and Seattle BioMed. The paper “The DNA-binding network of Mycobacterium tuberculosis” was published in the journal “Nature Communications” (Jan. 12, 2015): “MTB employs about 200 different molecular switches to sense and respond to the shifting, hostile landscape of the host. To identify and understand the intertwining gene regulatory…

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…