ISB News

William Poole, 2013 undergrad intern

Former Undergrad Intern Publishes Algorithm in PLOS Computational Biology

Posted March 1, 2017 In a study published in PLoS Computational Biology, researchers at Institute for Systems Biology (ISB) have developed a multiscale mutation clustering algorithm (M2C) that identifies variable length regions with high mutation density in cancer genes. The M2C algorithm was developed by William Poole (first author on the paper), who started as a summer intern in 2013 as part of ISB’s Center for Systems Biology internship program….

New Paper on Huntington’s Disease

Feb. 27, 2017 ISB researchers and colleagues from several institutes published a new study today in Human Molecular Genetics. The key points of the study “High resolution time-course mapping of early transcriptomic, molecular and cellular phenotypes in Huntington’s disease CAG knock-in mice across multiple genetic backgrounds” are: A multi-institute collaboration mapped in high resolution the earliest effects of the Huntington’s disease mutation in mice. The study included four different genetic…

Lena Joesch-Cohen

ISB Undergrad Intern Publishes Paper in Journal

Congratulations to Lena Joesch-Cohen (pictured above), who was one of ISB’s 2016 summer undergrad interns, just published a paper on the project she completed with Gustavo Glusman (Principal Scientist, Hood Lab). “Differences between the genomes of lymphoblastoid cell lines and blood-derived samples” was published on Feb. 23, 2017, in Dove Press. In a recommendation letter that Gustavo wrote to support Lena, he said this: “Lena is an outstanding scholar. Despite…

New Study: Using Single-Cell Technology to Predict Cell Behavior

In a study published in PLOS BIOLOGY, researchers at Institute for Systems Biology (ISB) explain how they developed a new theory for predicting cell-fate decisions and demonstrate, for the first time, that cells indeed undergo a critical transition – or tipping point – when they commit to a particular lineage. Jan. 9, 2017 3 Bullets: ISB researchers developed a new theory that uses state-of-the-art single-cell technology to make predictions about…

Comprehensive study of esophageal cancer reveals several molecular subtypes, provides new insight into increasingly prevalent disease

The Cancer Genome Atlas Research Network recommends clinical trials organizers and drug manufacturers focus on newly discovered molecular subtypes GRAND RAPIDS, Mich., Jan. 4, 2017 –– A comprehensive analysis of 559 esophageal and gastric cancer samples, collected from patients around the world, suggests the two main types of esophageal cancer differ markedly in their molecular characteristics and should be considered separate diseases. The study, published today in Nature from The…

New Study Identifies Organ-Specific Biomarkers for Acute Liver Injury

ISB scientists recently published a study in the Journal of Proteome Research that presents results from a study on identifying organ-specific blood biomarkers for acute liver injury due to over-exposure to acetaminophen. From the summary: 3 Bullets: Finding organ-specific blood biomarkers for disease that are clinically useful is challenging. New study identifies organ-specific blood biomarkers for acute liver injury caused by over-exposure to acetaminophen. ISB researchers use the powerful, targeted…

New Baliga Lab Publication in Cell Systems

The Baliga Lab’s Dr. Christopher Plaisier was the lead author of the study “Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis” which published online in Cell Systems on July 14. Dr. Plaisier wrote a summary of the research: 3 Bullets: Using data from TCGA and ENCODE, ISB researchers developed integrative database and analysis platforms that provide insight about the underpinnings of glioblastoma multiforme. Researchers developed a…

A Landscape of Pharmacogenomic Interactions in Cancer

The journal Cell published a study today (July 7) about the integrated analysis of drug response in 1,001 cancer cell lines. This study was undertaken by a large international group of researchers including ISB Senior Research Scientist Theo Knijnenburg. The researchers integrated heterogeneous molecular data of 11,215 tumors and 1,001 cell lines in order to study the drug response of these cell lines to 265 anti-cancer drugs. They uncovered numerous…

NIH Research Matters Features ISB’s MTB Paper

NIH Research Matters published an article on our tuberculosis paper. “The incredibly large number of possible drug combinations taken together with the difficulty of growing Mtb in the laboratory make discovery of effective combination therapy extremely challenging,” Dr. Nitin Baliga says. “We hope that our systems-based strategy will accelerate TB drug discovery by helping researchers prioritize combinations that are more likely to be effective.” READ THE ARTICLE

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….