The Data Science Garage

Using Data Science to Fight Cancer

The Lab

Our lab works on the intersection of computer engineering, statistical analysis and biology science. Based out of the OHSU Knight Cancer Institute we study systems biology, cancer, computational systems and integrative analysis. We work on projects funded by the Nation Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI).

If you are interested, we are looking for:

• PhD Students
• Post Docs
• Engineering Staff
• Scientific Research Staff

Projects

Jan 27, 2019

GDAN

The NCI’s Genomic Data Analysis Network (GDAN) was launched in 2016 to continue the work started by the TCGA in the analysis of large cancer cohorts.

Jan 27, 2019

AnVIL

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Space (AnVIL) is a project to build a data commons to allow researchers to efficiently analyze and visualize genomics data on the cloud.

Aug 22, 2018

GA4GH G2P

Aug 22, 2018

SMC Het

Aug 19, 2018

Grip

GRaph Integration Platform

Apr 27, 2016

BMEG

BioMedical Evidence Graph

Apr 27, 2016

DREAM-SMC

Somatic Mutation Calling

Apr 27, 2016

DREAM-SMC-RNA

RNA Fusion Calling and Isoform Quantification

Apr 27, 2016

Funnel

Funnel Task Execution Server

Apr 27, 2016

MC3

Multi-Center Mutation Calling in Multiple Cancers

People

Researchers

Brian Walsh

Senior Research Software Engineer

Graph Databases, Machine Learning, Pan Cancer, Cross Project Data Harmonization

Jordan Lee

Computational Biologist

Machine Learning, Precision Medicine, Computational Biology, Cancer Systems Biology

Liam Beckman

Research Software Engineer

Software Development, Computational Biology

Matthew Peterkort

Research Software Engineer

Machine Learning, Precision Medicine, Computational Biology, Cancer Systems Biology

Grad Students

Brian Karlberg

PhD student

Computational Biology, Precision Oncology

Principal Investigators

Kyle Ellrott

Assistant Professor

Computational Biology, Data Science, Machine Learning, Precision Medicine, Cancer Early Detection

Alumni

Malisa Smith

Student Intern

Jeena Lee

Student Intern

Ryan Spangler

Research Software Engineer

Allison Creason

Alex Buchanan

Adam Struck

Research Software Engineer

Graph Databases, Machine Learning, Data Science

Recent Posts

Bridge2AI

Kyle Ellrott

Oct 1, 2022 0 min read

Starting work on the AnVIL

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) project will provide a platform for researchers to study Genomic data in the cloud. As part of this project, we will be providing methods to enable analysis APIs.

Nov 25, 2018 1 min read

Debugging Network Failures

Handling Failures from OpenStack Swift in Funnel When building distributed services, handling failures from other services is a fact of life. We use OpenStack Swift as our object storage service, and we use Funnel to transfer thousands of objects to and from Swift.

Alex Buchanan

Aug 25, 2018 4 min read

G2P Whitepaper

In 2014, Dr. Margolin, Dr. Stuart and Dr. Ellrott wrote a draft white paper outlining the need for a computational model to efficiently communicate known Genotype/Phenotype association. This working group would eventually evolve into Variant Interpretation for Cancer Consortium VICC.

Adam Margolin, Josh Stuart, Kyle Ellrott

Jan 1, 2017 17 min read

Reproducible Science: Cancer Researchers Embrace Containers in the Cloud

We’ve posted an article on the Google AI Blog about reproducibility in DREAM Challenges.

Kyle Ellrott

Sep 6, 2016 1 min read

Recent Publications

Michael C Schatz, Anthony A Philippakis, Enis Afgan, Eric Banks, Vincent J Carey, Robert J Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L Grossman, others

January, 2022 Cell genomics

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

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Sean K Maden, Brian Walsh, Kyle Ellrott, Kasper D Hansen, Reid Thompson, Abhinav Nellore

January, 2022 bioRxiv

recountmethylation enables flexible analysis of public blood DNA methylation array data

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Allison Creason, David Haan, Kristen Dang, Kami E Chiotti, Matthew Inkman, Andrew Lamb, Thomas Yu, Yin Hu, Thea C Norman, Alex Buchanan, others

January, 2021 Cell systems

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

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Heidi L Rehm, Angela JH Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, Lawrence J Babb, Maxmillian P Barkley, Michael Baudis, Michael JS Beauvais, Tim Beck, others

January, 2021 Cell genomics

GA4GH: International policies and standards for data sharing across genomic research and healthcare

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Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G Espiritu, Amit G Deshwar, Matei David, Nathan M Wilson, Stefan Dentro, Jeff A Wintersinger, Lydia Y Liu, Minjeong Ko, others

January, 2020 Nature biotechnology

A community effort to create standards for evaluating tumor subclonal reconstruction

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Alex H Wagner, Brian Walsh, Georgia Mayfield, David Tamborero, Dmitriy Sonkin, Kilannin Krysiak, Jordi Deu-Pons, Ryan P Duren, Jianjiong Gao, Julie McMurry, others

January, 2020 Nature genetics

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

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Sergei Yakneen, Sebastian M Waszak, Michael Gertz, Jan O Korbel

January, 2020 Nature biotechnology

Butler enables rapid cloud-based analysis of thousands of human genomes

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Adam Struck, Brian Walsh, Alexander Buchanan, Jordan A Lee, Ryan Spangler, Joshua M Stuart, Kyle Ellrott

January, 2020 JCO clinical cancer informatics

Exploring integrative analysis using the BioMedical evidence graph

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Mary A Wood, Austin Nguyen, Adam J Struck, Kyle Ellrott, Abhinav Nellore, Reid F Thompson

January, 2020 Bioinformatics

Neoepiscope improves neoepitope prediction with multivariant phasing

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Satoshi Hirano, Lixing Yang, Malene Juul, Colin A Purdie, Brian Patrick O'Neill, Rolf Kabbe, Elli Papaemmanuil, Yu Fan, D Neil Hayes, Benjamin Raeder, others

January, 2020 Nature

Pan-cancer analysis of whole genomes.

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See all publications