PhD, Biomediical Informatics

Oregon Health & Science University

Portland, OR

2014 - 2009

• Dissertation: Connecting Genotypes to Drug Sensitivities in HER2 Positive Cancer Cell Lines

M.S., Biomedical Informatics

Oregon Health & Science University

Portland, OR

2004 - 2002

• Thesis: Developing and validating a tool for microarray cluster analysis

B.A., Chemistry

Reed College

Portland, OR

1998 - 1994

• Thesis: Resonance-Raman Spectroscopy, Chromium Hexacarbonyl, and Me: A Tale of Intrigue

Teaching Statement

N/A

N/A

N/A

I believe in democratizing data science. To this end, I have been involved with several national educational efforts: Big Data to Knowledge, National Library of Medicine’s efforts with data science. My workshops, lectures and lessons have been utilized at multiple schools, and by multiple audiences, including clinicians, bioinformaticians, undergraduates.

I utilize evidence-based pedagogical techniques in my teaching, specifically active learning and psychological safety. I am a firm believer in making students feel psychologically safe and giving them space to be curious. Many of my students have become collaborators in my teaching materials, improving them with their ideas and their questions. As a result, my work has been recognized as being accessible to a wide audience.

I believe that we must give graduate students more transferrable skills, and so I have co-founded BioData Club, a community of practice at OHSU and beyond that focuses on teaching and learning data science skills. I am dedicated to my students, and courses and workshops show consistently high ratings and evaluations. I am also a certified instructor for both The Carpentries and RStudio.

In my educational work, I have focused on Exploratory Data Analysis (EDA) as a way to be curious and to not be afraid of your data, Predictive Modeling and Data Analytics, interactive visualization,Open Science, Team Science, and the importance of interdisciplinary collaboration. I am dedicated to making my work accessible and reproducible by others.

BSTA504: R Programming

Biostatistics Program, OHSU-PSU School of Public Health

Portland, OR

Current - 2021

• Course Director. Basics of effective analysis using the tidyverse, Rmarkdown, and statistical modeling.

BMI569: Data Analytics

Biomedical Informatics, Oregon Health & Science University

Portland, OR

Current - 2015

• Course co-director. Hybrid course co-taught with Kaiser Permanente Insight group.
• Winner of the Sakai Torchbearer Award 2020. Multiple nominations from students.

HIP 523 Computerized Data Management

Human Investigations Program, Oregon Health & Science University

Portland, OR

Current - 2020

• Course instructor. Taught two active lab sessions in exploratory data analysis and predictive modeling.

BMI535/635: Management and Processing of Large Scale Data

Biomedical Informatics, Oregon Health & Science University

Portland, OR

Current - 2020

• Course co-director. A course that focuses on UNIX scripting, parallel computing, and large scale databases.
• With Michael Mooney.

BMI507: Ready for R

Biomedical Informatics, Oregon Health & Science University

Portland, OR

Current - 2020

• Course director. A gentle introduction to visualization, data transformation, and statistics using R and the tidyverse.

NEUS643: Stats for Neuroscientists

Neuroscience Graduate Program, Oregon Health & Science University

Portland, OR

Current - 2020

• Course director. An introduction to image processing, statistics, and machine learning focusing on confocal microscopy data.
• Lecture/Active Learning Labs using RStudio.cloud.

BMI551/651 Bioinformatics and Computational Biology II: Statistical Methods

Biomedical Informatics, Oregon Health & Science University

Portland, OR

2019 - 2015

• Course co-instructor. Provided drop-in sessions for R/Bioconductor programming and general tutoring.

HMSP410/PHE427: Introduction to Health Informatics

Health Systems Management/Public Health Education, Portland State University

Portland, OR

2018 - 2017

• Course co-director. A gentle introduction to relevant data science and informatics concepts for undergraduate students.
• Includes sections on data literacy, genomics, and metadata

NEUS642: Python Bootcamp for Neuroscientists

Neuroscience Graduate Program, Oregon Health & Science University

Portland, OR

2018

• Course director. Week long introduction to Python for non-computational neuroscientists.
• With Daniela Saderi, Lucille Moore, Brad Buran,Charles Heller, Zack Swartz, Lisa Karstens, Stephen David, Michael Mooney.

RBootcamp

Online Course

International

Current - 2015

• Online Interactive Introduction to the Tidyverse. Currently available as a free course to everyone.
• Written with Jessica Minnier. Taken by incoming Bioinformatics and School of Public Health students. Over 2000 external users. Used interationally. Used for training at T-Mobile, OHSU, and multiple institutions
• Over 2000 external users. Used interationally. Used for training at T-Mobile, OHSU, and multiple institutions

burro

R Package

International

Current - 2018

• R Package for exploring data using a Shiny interface. Provides guided exploration of variable association.
• Software is used in multiple courses to teach exploratory data analysis.

BioData Club

Oregon Health & Science University

National

Current - 2015

• Co-founder. Data Science focused community of practice. We are students, postdocs, staff, and faculty focused on learning Data Science skills together
• Developed partnerships with various OHSU groups, including the OHSU Library. Contributed to Data Science Competencies.
• Currently at over 340 members spanning OHSU and beyond.

A gRadual Introduction to Shiny

Workshop

National

2021 - 2017

• Workshop introducing basic interactive visualization and dashboard building using the Shiny framework for R
• Written with Jessica Minnier, Pierrette Lo, and Dar’ya Pozhidayeva
• Given for PDX R User Group, WNAR 2019, and BioData Club 2019. Used by multiple colleges, including Reed College and Lehmann College.

Lowering Psychological Burdens for Students

OHSU Faculty Development Workshop

N/A

10/2020

• Faculty development discussion at OHSU on improving psychological safety in classroom.
• Material is based on Carpentries Instructor Training.

The MD in .Rmd: Teaching Clinicians Data Analytics with R

R/Medicine Conference

Online conference

9/2020

• Talk on our BMI569 Data Analytics course with Kaiser Permanente.

Data Carpentry: R for Social Scientists

N/A

Georgia Gwinnett College (online)

9/2020

• Co-instructor. Taught faculty best practices with spreadsheets, OpenRefine, and R

Open Science Tools Panel

Medical Library Association Conference

National

08/2020

• Invited Panel Member with Kristi Holmes and Vicky Steeves.

How to make a reproducible paper

BioData Club Workshop https://doi.org/10.6084/m9.figshare.12413195.v1

Regional

12/2019

• Workshop introducing best practices in data management and code management to make an analysis reproducible. Written with Aurora Blucher. Given for BioData Club.

My Experience with RStudio Instructor Training

RStudio Education Blog

N/A

11/2019

• Story about becoming an RStudio Certified Instructor in the Tidyverse and Shiny

Data Storytelling Workshop

BioData Club Workshop

Regional

10/2019

• You are making a figure for your paper and want it to be the best it can be. Come and learn techniques for communicating your findings clearly. Learn about the role of color, annotations, and simplifying your figures to communicate effectively.
• Workshop given for BioData Club. RStudio materials can be freely accessed online.

Clincal Data Wrangling: Active/Didactic Learning.

Symposium on Data Science and Statistics

National

7/2019

• Ted Laderas, Nicole Weiskopf, and Eilis Boudreau. Talk given for Symposium on Data Science and Statistics.

Data Scavenger Hunts: Learning about datasets together

CSV Conference https://doi.org/10.6084/m9.figshare.12654140.v1

International

7/2019

• Talk given for CSV Conference

Engaging Students in Statistics & Data Science

Symposium on Data Science and Statistics

N/A

7/2019

• Session Chair. Part of Symposium on Data Science and Statistics 2019.

Conversations about Sleep: Clinical Data Wrangling

AMIA Informatics Educators Conference

National

6/2019

• Ted Laderas, Nicole Weiskopf, and Eilis Boudreau. Talk given for American Medical Informatics Association’s Informatics Educator’s Conference

decampr

R Package

National

5/2019

• R Package for editing interactive lessons using the course-R-starter framework by Ines Montani
• Written with Jessica Minnier

Teaching Bioinformatics Students about Clinical Data

OSU Center for Genome Research and Computing Spring Conference https://doi.org/10.6084/m9.figshare.12654152.v1

Regional

5/2019

• Invited talk.

NHANES Data Scavenger Hunt

BioData Club Workshop

Regional

2/2019

• An introduction to Exploratory Data Analysis using the burro app to explore outcomes using the NHANES (National Health and Nutrition Examination Survey) dataset.
• Written with Jessica Minnier and Thomas Frohwein

Clinical Data Wrangling

NLM T15 Data Science Workshop

OHSU

2019 - 2017

• Multi-day workshop on understanding clinical data quality issues through both didactic lecturing and active data exploration.
• Written with Eilis Boudreau and Nicole Weiskopf.
• Given as an intro to both our incoming clinical and bioinformatics students.

Introduction to iGraph

Interactive Lecture

OHSU

2019 - 2015

• Workshop introducing the basics of network analysis using the igraph package.
• Given for the last 4 years in Guanming Wu’s Network Analysis course

BioDataClub Kit

Guidance and website

National

2019 - 2018

• With Robin Champieux. Website and kit for establishing a BioData Club and your local institution
• Adopted by Northwestern.

Democratizing Data Science Using LearnR and Shiny

RStudio Conference

National

1/2019

• Poster on interactive visualization and pedagogy.
• Written with Jessica Minnier

Software Carpentry

N/A

International

2019

• Contributor to instructor training materials.
• Training materials have been used to train over 100 instructors.

A gRadual introduction to Shiny

Western North American Region (WNAR) of the International Biometric Society conference

National

2019

• Workshop instructor with Jessica Minnier. 15 attendees

Data Exploration to Enable Cross Disciplinary Collaboration.

Cancer Informatics for Cancer Centers (CI4CC) Fall Symposium

National

10/2018

• Invited Speaker. Building Capacity: Leveraging National Efforts on Data Science Training in Cancer Center Context

Open Resources for Teaching Data Science Skills

From Evidence to Scholarship Conference

Reed College, Portland, OR

5/2018

cvdRiskData Prediction Workshop

Big Data to Knowledge (BD2K) workshop

Regional

2018

• A workshop given for Portland State University students exploring the difficulties of predicting cardiovascular risk using shiny for exploratory data analysis and caret for machine learning. Part 1 and Part 2.
• Written with David Dorr
• Altmetric score of 47

Data Literacy Tutorial

Interactive Tutorial

Portland State University

2018 - 2017

• Interactive tutorial introducing the basic concepts of visualization and data literacy
• Used in both HMSP410 and PHE427 courses.

Academic Site Workshop Using GitHub Pages

BioData Club Workshop

Regional

2018

• Workshop for setting up a personal academic website using GitHub Pages
• 115 students, faculty, and staff have used this workshop, many at external institutions

How are Data Science and Systems Science Connected?

Systems Science Program, Portland State University

Regional

2018

• Talk given about the relationship between machine learning and systems science

DSIExplore

R Package

Regional

2017

• LearnR interactive tutorial explaining the basic behind exploratory data analysis for categorial and continuous data
• Written with Jessica Minnier
• Given for 65 adult students in 2017.

Training future biocurators through data science trainings and open educational resources.

F1000 Research

N/A

2017

• Nicole Vasilevsky, Ted Laderas, Jackie Wirz, Bjorn Pederson, David A Dorr, William Hersh, Shannon McWeeney, Melissa Haendel.

Data Science for Basic Scientists

OHSU Symposium on Educational Excellence https://doi.org/10.6084/m9.figshare.12654158.v1

OHSU

2017

• Invited talk.

Research Statement

N/A

N/A

N/A

My research interests are complex diseases, precision medicine, applications of systems science (including network analysis and modeling), and applying data integration to difficult and high-impact translational research questions. These questions include immune system profiling in both infectious disease (tuberculosis) and Acute Myeloid Leukemia, understanding drug sensitivity in the context of multiple cancer types (AML, Colorectal, Breast and Head and Neck Cancer), and quantifying expression differences in alcoholic preference. I have worked with a large number of datatypes (high-throughput immunophenotyping, proteomics, expression, genomic, and functional drug screen data) and have focused on methods and frameworks integrating these datatypes within the biological and clinical context of these translational research questions.

My training in biomedical informatics as a master’s student in Biomedical Informatics, as an NLM Predoctoral Fellow, and as a NLM Postdoctoral fellow has enabled me to communicate with a wide variety of collaborators by giving me a strong background in Cancer Biology, Software Development, and Clinical Systems.

Additionally, I am a strong advocate for Open Science initiatives, most notably the effort for reproducibility in scientific analysis. To this end, I have developed multiple novel software pipelines that transparently process data from raw data to through the final stages of analysis.

flowDashboard

R Package

N/A

Current - 2017

• Visualization framework in R/Shiny and processing pipeline for CyTOF and high dimensionality flow cytometry data.
• Dashboards have been used by 3 research groups at OHSU.

surrogateMutation

R Package

N/A

2014

• R Package for mapping mutations and copy number alterations to networks and associated statistics. http://dx.doi.org/10.5281/zenodo.17303

ExonModelStrain

R Package

N/A

2011

• R Package for detecting alternative exon usage in the Affymetrix Exon Array.

Consense-Cluster

R Package

N/A

2004

• R Package for comparing multiple clustering methods
• 17 citations

Reversible suppression of T cell function in the bone marrow microenvironment of acute myeloid leukemia

PNAS https://doi.org/10.1073/pnas.1916206117

N/A

2020

• Adam J Lamble, Yoko Kosaka, Ted Laderas, Allie Maffit, Andy Kaempf, Lauren K Brady, Weiwei Wang, Nicola Long, Jennifer N Saultz, Motomi Mori, David Soong, Clare V LeFave, Fei Huang, Homer Adams, Marc M Loriaux, Cristina E Tognon, Pierrette Lo, Jeffrey W Tyner, Guang Fan, Shannon K McWeeney, Brian J Druker, Evan F Lind
• OHSU School of Medicine Paper of the Month August 2020.

Illuminating Biological Pathways for Drug Targeting in Head and Neck Squamous Cell Carcinoma

PLOS One https://doi.org/10.1371/journal.pone.0223639

N/A

2019

• Gabrielle Choonoo, Aurora S. Blucher, Samuel Higgins, Mitzi Boardman, Sophia Jeng, Christina Zheng, James Jacobs, Ashley Anderson, Steven Chamberlin,Nathaniel Evans, Myles Vigoda,Benjamin Cordier, Jeffrey W. Tyner, Molly Kulesz-Martin, Shannon K. McWeeney, and Ted Laderas.
• Role: Senior Author. Did code review of entire workflow and published the workflow as an RMarkdown Notebook at mybinder.org

CSF1R inhibitors exhibit anti-tumor activity in acute myeloid leukemia by blocking paracrine signals from support cells

Blood https://doi.org/10.1182/blood-2018-03-838946

N/A

2019

• David K Edwards, Kevin Watanabe-Smith, Angela Rofelty, Alisa Damnernsawad, Ted Laderas, Adam Lamble, Evan F Lind, Andy Kaempf, Motomi Mori, Mara Rosenberg, Amanda d”Almeida, Nicola Long, Anupriya Agarwal, David Tyler Sweeney, Marc Loriaux, Shannon K McWeeney, Jeffrey W Tyner.

Immune checkpoint inhibitors reverse T-cell functional suppression in the bone marrow of a subset of AML patients

The Journal of Immunology

N/A

2019

• Evan F Lind, Adam J Lamble, Yoko Kosaka, Ted Laderas, Lauren Brady, Fei Huang, Brian J Druker, Jeffrey W Tyner, Shannon McWeeney

Immunogenomic Exploration of the Acute Myeloid Leukemia Microenvironment Identifies Determinants of T-Cell Fitness.

Blood https://doi.org/10.1182/blood-2018-99-118424

N/A

2018

• Lauren K Brady, David Soong, Evan F Lind, Yoko Kosaka, Adam J Lamble, Michael Schaffer, Brendan P Hodkinson, Clare Lefave, Ted Laderas, Shannon K McWeeney, Homer Adams, Yann Abraham, Pegah Safabakhsh, Jeffrey W Tyner, Brian J Druker, Fei Huang.

Integrated functional and mass spectrometry-based flow cytometric phenotyping to describe the immune microenvironment in acute myeloid leukemia

Journal of immunological methods https://doi.org/10.1016/j.jim.2017.11.010

N/A

2018

• Adam J Lamble, Matthew Dietz, Ted Laderas, Shannon McWeeney, Evan F Lind
• Role: Developed computational pipeline and dashboard framework for displaying high dimensional flow and cytometry data.

Teaching data science fundamentals through realistic synthetic clinical cardiovascular data

Biorkv

N/A

2017

• Ted Laderas, Nicole Vasilevsky, Bjorn Pederson, Shannon McWeeney, Melissa Haendel, and David Dorr.
• Contribution: First author: helped conceive study, designed bayesian network, developed course material based on dataset.
• Dataset has been used in BMI569, HIP523, and a workshop at PSU.

Comprehensive characterization of VISTA expression in patients with acute myeloid leukemia

Journal of Clinical Oncology https://doi.org/10.1200/JCO.2016.34.15_suppl.e14546

N/A

2016

• Adam Lamble, Yoko Kosaka, Fei Huang, Kate Sasser, Cristina Tognon, Ted Laderas, Shannon McWeeney, Marc Loriaux, Brian J Druker, Jeffrey Tyner, Evan Lind

The Consensus Molecular Subtypes of Colorectal Cancer

Nature Medicine https://doi.org/10.1038/nm.3967

N/A

2015

• Justin Guinney, Rodrigo Dienstmann, Xin Wang, Aurélien de Reyniès, Andreas Schlicker, Charlotte Soneson, Laetitia Marisa, Paul Roepman, Gift Nyamundanda, Paolo Angelino, Brian M. Bot, Jeffrey S. Morris, Iris Simon, Sarah Gerster, Evelyn Fessler, Felipe de Sousa e Melo, Edoardo Missiaglia, Hena Ramay, David Barras, Krisztian Homicsko, Dipen Maru, Ganiraju C. Manyam, Bradley Broom, Valerie Boige, Ted Laderas, Ramon Salazar, Joe W. Gray, Douglas Hanahan, Josep Tabernero, Rene Bernards, Stephen H. Friend, Pierre Laurent-Puig, Jan P. Medema, Anguraj Sadanandam, Lodewyk Wessels, Mauro Delorenzi, Scott Kopetz, Louis Vermeulen, and Sabine Tejpar.
• Contribution: mapped and analyzed OMICs data to consensus cancer subtypes.
• Currently at 1807 citations.

Between Pathways and Networks lies Context

Science Progress https://doi.org/10.3184/003685015x14368898634462

N/A

2015

• Ted Laderas, Guanming Wu, and Shannon McWeeney.

A network-based model of oncogenic collaboration for prediction of drug sensitivity

Frontiers in Genetics https://dx.doi.org/10.3389%2Ffgene.2015.00341

N/A

2015

• Ted G Laderas, Laura M Heiser, Kemal Sönmez

Computational detection of alternative exon usage

Frontiers in Neuroscience https://doi.org/10.3389/fnins.2011.00069

N/A

2011

• Ted G Laderas, Nicole AR Walter, Michael Mooney, Kristina Vartanian, Priscila Darakjian, Kari Buck, Christina A Harrington, John Belknap, Robert Hitzemann, Shannon K McWeeney

High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs

BMC genomics https://doi.org/10.1186/1471-2164-10-379

N/A

2009

• Nicole AR Walter, Daniel Bottomly, Ted Laderas, Michael A Mooney, Priscila Darakjian, Robert P Searles, Christina A Harrington, Shannon K McWeeney, Robert Hitzemann, Kari J Buck

Consensus framework for exploring microarray data using multiple clustering methods

OMICS https://doi.org/10.1089/omi.2006.0008

N/A

2007

• Ted Laderas and Shannon McWeeney
• Based on master’s Thesis. Currently at 17 citations

TandTRAQ: an open-source tool for integrated protein identification and quantitation

Bioinformatics https://doi.org/10.1093/bioinformatics/btm467

N/A

2007

• Ted Laderas, Cory Bystrom, Debra McMillen, Guang Fan, Shannon McWeeney

Selected Blog Posts

Personal Blog

N/A

N/A

• Package Building: How DESCRIPTION, NAMESPACE, roxygen, and devtools::document work together
• So You’ve Accidentally Checked a Large File Into Git
• Getting LearnR tutorials to run on mybinder.org

Getting LearnR tutorials to run on mybinder.org

N/A

N/A

9/2020

• Short blog post about building your docker container and file structures needed for getting a LearnR package running on mybinder.org

Rebuilding the RBootcamp and Generating R Tutorials

RStudio Education Blog

N/A

3/2020

• Story about building our interactive RBootcamp using Ines Montani’s interactive R/Python Framework.
• Written with Florencia D’Andrea and Jessica Minnier

Package Building: How DESCRIPTION, NAMESPACE, roxygen, and devtools::document work together

Personal Blog

N/A

2/2019

• Package Building: How DESCRIPTION, NAMESPACE, roxygen, and devtools::document work together
• So You’ve Accidentally Checked a Large File Into Git

RStudioConf 2019: Education and Organizations

Personal Blog

N/A

1/2019

• Story about presenting our poster about interactive data science education and educational resources/talks at RStudioConf 2019

Things we learned teaching clinical data wrangling

Personal Blog

N/A

10/2018

• My notes on teaching the clinical data wrangling short course, and intro course introducing students to the critical thinking data process with the Sleep Heart Health Study dataset

What we learned teaching Python to Neuroscience Students

Personal Blog

N/A

1/2018

• Notes on organizing an intro Python course for Neuroscience Students
• 1394 views.

So You’ve Accidentally Checked a Large File Into Git

Personal Blog

N/A

1/2018

• Notes on fixing your Git history using the BFG. 1684 views.

Some Lessons we Learned Running Cascadia R

Personal Blog

N/A

6/2017

• Notes on organizing and running the first NW regional R Conference, Cascadia R
• 531 views.

Service Statement

N/A

N/A

N/A

I am a strong supporter of service at OHSU and beyond. I currently participate in the DMICE BCB (Bioinformatics and Computational Biology) Faculty Division meeting, the DMICE Mentoring committee, and have participated in the BCB Curriculum Retreat in order to plan upcoming coursework at DMICE. As a Pacific Islander, I have a unique viewpoint about diversity and have dedicated myself to making classes and workshops psychologically safe.

Beyond OHSU, I believe that we need to increase public engagement of science and increase outreach and mentoring of next-generation science students, especially from disadvantaged populations will enable these students to succeed in STEM-based careers.

As a former student of Saturday Academy’s scientific mentoring program, I want to contribute back to this community and engage potential STEM students through student outreach and mentoring. I am also involved in outreach through the development of course material for the Biocatalyst training program through Oregon Bioscience Association, which provides bioscience training for unemployed or under-employed professionals.

DMICE Assessment and Planning Committee

N/A

N/A

Current - 2017

DMICE BCB Division Committee

N/A

N/A

Current - 2017

Biomedical Informatics Curriculum Committee

N/A

N/A

Current - 2017

DMICE BCB Admissions Committee

Oregon Health & Science University

N/A

Current - 2017

OHSU Computational Forum

N/A

OHSU

Current - 2019

• Co-organizer

Bioinformatics Trainer

DNAnexus

Mountain View, CA

Current - 2021

Assistant Professor, Division of Bioinformatics and Computational Biomedicine

Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

Portland, OR

2021 - 2017

• Developed R/Rstudio based materials and assignments for analytics course. Analytics course won a Sakai award for innovation.
• Developed and taught exploratory data analysis with the {burro} package. Over 150 students have used this software to discuss data with each other.
• Developed and taught Ready for R course. Course has been taken by 1200 external students.

Postdoctoral Researcher, OHSU Knight Cancer Institute

Oregon Health & Science University

Portland, OR

2017 - 2015

Faculty Instructor

Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

Portland, OR

2017 - 2014

• HPC tutorial has been used by over 40 students and to train computational staff to learn the basics of high performance computing
• R-Bootcamp course has been used internally at OHSU and for training for T-Mobile for 3 years with over 2000 users.
• Administered RStudio/Shiny Server at OHSU, along with MySQL/PostGREs Database, and Genome Analysis Toolkit

NLM Postdoctoral Fellow, Division of Bioinformatics and Computational Biology

Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

Portland, OR

2015 - 2014

Visiting Scientist

Sage Bionetworks

Seattle, WA

2015 - 2014

NLM Predoctoral Fellow, Division of Bioinformatics and Computational Biology

Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

Portland, OR

2014 - 2009

Bioinformatics Developer/Project Manager, OHSU Knight Cancer Institute

Oregon Health & Science University

Portland, OR

2009 - 2003

Teaching Assistant/Computer Programmer/Server Admin, Medical Informatics and Clinical Epidemiology

Oregon Health & Science University

Portland, OR

2002 - 2001

Research Assistant/Computer Programmer, Department of Molecular Medicine

Oregon Health & Science University

Portland, OR

2001 - 1999

• Developed and extended real time image processing pipeline using LabView. Conducted surface tension experiments using lung surfactant components

Research Assistant/Teaching Assistant

Gerrity Lab

Reed College

1998 - 1996

• TA in Instrumentation Lab
• Conducted research using resonance raman spectroscopy/
• Programmed in LabView/Igor

Tumor intrinsic and microenvironmental mechanisms driving drug combination efficacy and resistance in AML (Current)

Tyner (PI) U54CA224019

National Cancer Institute

10/01/2022 - 10/01/2017

• Most patients with acute myeloid leukemia (AML) eventually die when their disease becomes resistant to conventional or even newer treatments. Our proposed studies will shed light on the mechanisms of drug resistance, both within the tumor and in the surrounding environment. This knowledge will help identify more effective therapies — involving combinations of two drugs — that will avoid drug resistance and provide better outcomes for patients with AML.
• Role: Computational Biologist

The Gut Microbiome and HLA B27-associated Acute Anterior Uveitis (Current)

Rosenbaum (PI) 5R01EY029266-02

National Eye Institute

5/31/2022 - 09/01/2018

• Uveitis is a leading cause of blindness and acute anterior uveitis is the most common form of uveitis. Although a cell surface molecule known as HLA B27 markedly increases the risk to develop acute anterior uveitis, the mechanism is unknown. We have made novel observations about the effect of HLA B27 on the microbiome in the gut and in the joint in rats, and propose to extrapolate these studies to patients with acute anterior uveitis.
• Role: Coinvestigator

Biomedical Informatics Research Training at Oregon Health & Science University

Hersh (PI) 3T15LM007088026S1

National Library of Medicine

06/01/2019 - 07/01/2017

• Supplement to develop data science materials for T15 training grant.
• Role: Educational Developer and Instructor

A National Center for Digital Health Informatics Innovation (Completed)

Haendel (PI) U24TR002306

National Center for Advancing Translational Sciences

6/30/2022 - 09/01/2017

• To create a national network for enabling digital health research, innovation, and continuous improvement. The goal is to use information science to impact the way that health care functions and the lives of those it serves.
• Role: education, software development, and data management advocate (2017-2019)

Targeting MAIT cells for TB vaccines (completed)

Lewinsohn (PI) OPP1131709

Bill and Melinda Gates Foundation

10/31/2018 - 10/26/2015

• This proposal is designed to establish whether or not a vaccine targeting Mucosal Associated Invariant (MAIT) can be used to prevent tuberculosis (TB).
• Role: Computational Biologist

Biomedical Informatics Research Training at Oregon Health & Science University

Hersh (PI) T15LM007088

National Library of Medicine

6/30/2022 - 07/01/1992

• Predoctoral and postdoctoral training in biomedical informatics
• Role: Predoctoral Fellow (2019-2014), Postdoctoral Fellow (2014-2015)

Beat AML: Precision Medicine for AML Based on Functional Genomics

Druker (PI) (No # Assigned)

Leukemia and Lymphoma Society

5/31/2017 - 5/1/2013

• The major goals of this project is to transform our approach to AML treatment through a deeper understanding of the diversity of the underlying molecular causes of disease and to bring targeted therapies to AML patients through 1) understanding the spectrum of genetic lesions and molecular drivers, 2) functionally annotating drug sensitivity, and 3) Initiating clinical trials with combinations of drugs in refractory patients.
• Role: Computational Biologist