I am an Assistant Professor in the Division of Bioinformatics and Computational Biology in the Department of Medical Informatics and Clinical Epidemiology at OHSU (BCB/DMICE) and a member of the OHSU Knight Cancer Institute. My research focus is on the Systems Biology of Complex Diseases. I use integrative modeling approaches across OMICs types to achieve this.
With over sixteen years of bioinformatics experience, I have developed methods for low-level preprocessing and high-level analysis of many OMICs types, including expression (especially alternative splicing), phosphoproteomics, proteomics, and genomics. My experience in functional genomics has led me to use models such as Graphical Models and Networks to integrate these many OMICs types into building a unified picture of integrated systems-level dysregulation in complex diseases such as alcoholism and cancer.
I am also actively involved in teaching and utilizing interactive visualization, especially in the analysis of high-dimensional mass cytometry data.
PhD in Biomedical Informatics, 2014
Oregon Health & Science University
MS in Biomedical Informatics, 2004
Oregon Health & Science University
BA in Chemistry, 1998
Teaching and education is one of my passions. I spend a lot of time developing coursework/workshops in a variety of Data Science Topics. Most of my material is freely available to be reused by other instructors.
I teach in the summer hybrid BMI569/669 Data Analytics course at OHSU (Hybrid course co-taught with Kaiser Permanente Data & Information Management Enhancement (DIME) group). This is a super fun course for me to teach and it focuses on both organizational behavior and communicating analytic results. It is a great blend of practical soft skills in communication and hard analytic skills.
I am a co-instructor for our Clinical Data Wrangling short course along with Eilis Boudreau and Nicole Weiskopf. This is an optional workshop for our students (more info at the link), developed as part of our NLM T15 Data Science Supplement.
I am a co-instructor for *BMI535/635 Management and Processing of Large Scale Data *, Winter quarter 2019.
I am also a co-instructor for BMI551/651 Bioinformatics and Computational Biology II: Statistical Methods, providing drop-in sessions for R programming and general tutoring.
I was course co-director for HSMP410/PHE427 Introduction to Health Informatics at Portland State University. Spring Quarter, 2017-2018.
Click the titles to see the teaching materials. Feel free to reuse, fork, and contribute! There are more teaching materials available on my CV page.*
A workshop that I’ve given on the basics of building Shiny apps. Given multiple times for PDX R User Group.
Practical coursework in R/SQL for our hybrid Data Analytics Course taught with Kaiser Permanente. This course has been taught from 2013 to the present during summer quarter for students in the Biomedical Informatics program at OHSU..
Self paced tutorial for learning about cluster computing using exacloud, the exascale computing cluster at OHSU. Covers simple jobs, batch jobs, and interactive jobs using SLURM.
Course material I have been developing for PHE427, Health Informatics. This is a course that is co-taught with Bill Hersh for the OHSU/PSU School of Public Health. They are intended for students with very little math and programming background. Where possible, I’ve tried to have hands-on activities for each of the subjects.
A pain free introduction to getting a personal academic website started using GitHub pages. With Robin Champieux, Eric Earl, and Eric Leung.
This is a week-long course meant to introduce neuroscience students to the basics of python with data types familiar to them, including imaging and electrophysiology data. Taught with Stephen David, Brad Buran, Daniela Sadieri, Lucille Moore, Charlie Heller, Zack Schwartz.
I love using the shiny app framework for both data exploration in research and teaching. Click any of these links to go to the app.
Interactive slides with apps to explore properties of clustering algorithms. Built with RMarkdown/Shiny
I have a parallel career as a composer and performing musician. I started taking cello lessons when I turned 30. I’m a lifelong learner and I love to play with and accompany other musicians. For more information, please see my artist webpage.
In order, they are:
I am clinically depressed and have anxiety, but I am high-functioning. I do my best to meet deadlines, but sometimes there is a lot on my plate and I need to manage my anxiety and depression.
The number one thing to know is that last minute deadlines are a significant stress on my anxiety and affect me very negatively. I realize that this is the more often the case than not with grant deadlines, but the sooner you can ask for something before its deadline, the better.
These are hard deadlines for collaborating with me:
If you don’t like these deadlines, there are other people out there who will probably work with you.
I do best when there is mutual respect between me and my collaborators. Good collaborations take time and I have to learn to trust working with you.
Email me and we’ll set up an appointment to talk. If you are interested in what I’m interested in (see above), I will see if we can set up some sort of internship.
Email me and we’ll set up a time to talk. Note that I have been burned pretty badly in the past, so our goals have to align or we might have to negotiate a contract and scope of work.
You get one of these a year. I’ll print you a coupon. You cannot get more. I value my own mental health more than responding on the weekends. Be respectful.
Please do not try to send me an appointment for the current time and expect to talk. I’m not going to respond. I feel this is disrespectful, and I don’t have the patience or energy to do so.