News

Dr. Nyasha Chambwe, a postdoctoral fellow in the Shmulevich Lab at Institute for Systems Biology, discusses some data analysis with colleague Summer Elasady.

In the News: Basketball and Biology

Congratulations to Dr. Nyasha Chambwe on being featured in the May 20 issue of Puget Sound Business Journal’s “People in Research” column. The profile reveals Dr. Chambwe’s path to ISB, starting with a full-ride scholarship to Jackson State University. She has been working on a study on pre-term birth and soon will be moving to projects related to glioblastoma and leukemia. Read the PSBJ article… Photo above: Dr. Nyasha Chambwe,…

New TCGA publication on adrenocortical carcinoma

Our group has contributed to a recent paper published by the TCGA Research Network on a study about adrenocortical carcinoma (ACC) in Cancer Cell. The study describes the comprehensive analysis of 91 ACC specimens from four continents using state of the art genomic technologies and computational methods. In addition to identification of novel ACC driver genes, pathways and refined subtypes, the AWG analysis revealed whole genome doubling (WGD) as a…

Bio-IT features Sheila Reynolds

Congrats to Sheila Reynolds on being featured on the Bio-IT World Conference site for her presentation on ISB’s Cancer Genomics Cloud project. Read the Q&A here.

Ilya Shmulevich at GCPNext

Using Google Cloud Platform to Give Researchers Easier Access to Cancer Data

ISB’s Dr. Ilya Shmulevich attended Google Cloud Platform’s GCPNext conference in San Francisco and presented on ISB’s Cancer Genomics Cloud project. He explains how his team used GCP to create better access for a broad range of researchers to cancer genomics data (from The Cancer Genomics Atlas) and the tools with which to explore that data. Watch Dr. Shmulevich’s talk below.

ISB Spotlight: Lisa Iype

Dr. Lisa Iype (Ilya Shmulevich group) has been promoted to Senior Bioinformatics Scientist. She has experience in biochemistry, software and website development, and data analysis. She works with high-dimensional cancer data sets and looks for significant patterns which may provide insight into cancer development and progression. Dr. Shmulevich commented: “Lisa has made major contributions to The Cancer Genome Atlas project through her participation in tumor working groups, including thyroid carcinoma…

Event: Cancer Think Tank

Cure First is hosting the forum “Cancer Think Tank.” Speakers include ISB’s Dr. Ilya Shmulevich and Dr. Brady Bernard. Date: January 21, 2016 Time: 1-5:30 p.m. MED talks, breakout sessions, and panel discussion; 6-8 p.m. networking with wine and dinner Why: To jump start innovative collaborations in cancer research with the goal to submit proposals for funding to accelerate the discovery of new, less toxic and targeted therapies. Who: This…

ISB’s Cancer Genomics Cloud Team Launches BigQuery Platform

Genomeweb published an article on the Cancer Genomics Cloud pilots. Learn more about ISB’s CGC project. PDF: Cancer Genomics Cloud Pilot Developers Provide Update, Open Up Platforms for Early Testing | GenomeWeb NEW YORK (GenomeWeb) – The developers of the three proposals selected by the National Cancer Institute for the Cancer Genomics Cloud pilots — an effort to build sustainable computing infrastructure for analyzing omics data from the Cancer Genome…

Prostate Cancer Study Identifies Numerous Subtypes of the Disease

Prostate cancer is the second most common cancer in men worldwide. Integrative analysis led to the identification of 7 subtypes of prostate cancer. Changes in signaling pathways and DNA repair genes may suggest new opportunities for therapy. By Lisa Iype Prostate cancer is the second most common cancer in men worldwide. The clinical behavior of prostate cancer is variable with some men exhibiting indolent prostate cancer which can be monitored…

New TCGA Publications on Melanoma and Lower-Grade Gliomas

Our group has contributed to two recent papers published by The Cancer Genome Atlas on Genomic Classification of Cutaneous Melanoma, published in Cell, and Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas, published in The New England Journal of Medicine. Our group’s contributions were led by Sheila Reynolds (melanoma) and Brady Bernard (lower-grade glioma).

The Women of ISB: Phyliss Lee, Software Engineer

Name: Phyliss Lee Lab: Shmulevich Research: I help create websites and pages for the Cancer Genomics Cloud Pilot Project. The tools that I’m building will not only help scientists gather petabytes of cancer genomic data faster, but will also help them run analyses and visualize the data graphically. What I’m building has the potential to reach millions of people. Working at ISB: What I like about being in science is…

Mouse Hair Cycle Expression Dynamics Modeled as Coupled Mesenchymal and Epithelial Oscillators

Congratulations to Ryan Tasseff, Research Scientist, et. al., on their new paper “Mouse Hair Cycle Expression Dynamics Modeled as Coupled Mesenchymal and Epithelial Oscillators” in PLOS Computational Biology!

Announcing our new NCI-funded project with Google and SRA International: The Cancer Genomics Cloud

We are very excited to start on an a new, NCI-funded project with partners Google and SRA International, to develop a cloud based platform — the Cancer Genomics Cloud (CGC) — to enable cancer genomics research at unprecedented scale. Read More http://www.genomeweb.com/informatics/nci-contracts-isb-google-sra-team-develop-infrastructure-cancer-genomics-cloud-p http://www.fiercebiotechit.com/story/isb-teams-google-nci-cancer-genomics-cloud-project/2014-10-13 http://www.nbcnews.com/tech/innovation/google-teams-put-cancer-genome-research-cloud-n226681

New TCGA Publication on Thyroid Carcinoma

Our group participated in the paper “Integrated Genomic Characterization of Papillary Thyroid Carcinoma” published by The Cancer Genome Atlas. Lisa Iype, Bioinformatics Scientist, led our group’s contributions. Learn More

New TCGA Publication on Gastric Adenocarcinoma

Our group participated in the paper “Comprehensive molecular characterization of gastric adenocarcinoma” published by The Cancer Genome Atlas. Vesteinn Thorsson, Senior Research Scientist, played a key role as a data coordinator and analysis coordinator. This involved the integration of multiple data types generated by DNA sequencing, RNA sequencing, protein arrays, and clinical information from 295 patients with stomach cancer. Learn More

Multiscale Representation of Genomic Signals

A new paper entitled “Multiscale representation of genomic signals,” is published in Nature Methods. The approach, inspired by multiscale methods in image processing, allows researchers to integrate, analyze and visualize information across multiple resolutions (scales) of the human genome. Learn More