Teaching and Mentoring Interests

Current Courses I teach at OHSU and PSU

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).

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 am also course co-director for HSMP/PHE410 Introduction to Health Informatics. at Portland State University. Spring Quarter, 2018.

DataCamp

I have a free online introductory course at DataCamp called the RBootcamp. In this course, we cover the basics of visualization, data munging, and basic statistics using the tidyverse in R. It is freely available to everyone, but registration is required.

Training Materials/Workshops

I have developed a number of self-directed training materials for learning R and specific packages that I’ve found useful. Most of these are available from my github page and may be used freely by students.

  • Clinical Data Wrangling Workshop - DOI
  • R-Bootcamp (tidyverse) - The new version of RBootcamp, that covers the tidyverse for manipulating data in R. You will need to register on DataCamp. This interactive course was written with both Jessica Minnier and Chester Ismay. DOI
  • R-Bootcamp (Base R) - an MOOC (Massively Open Online Course) for teaching the basics of data manipulation in R (Coursesites registration required). Note that I do not support this course anymore at this point.
  • We taught an introductory bootcamp in Python called NEU640 Python Bootcamp for Neuroscientists.. 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. Winter Quarter, 2018.

Standalone Tutorials

Many of these tutorials have been given through the student club at OHSU that I mentor, called BioData Club. They are all freely available to be reused by other instructors.

  • The Magic of Markdown - An introduction to the many uses of Markdown, including RMarkdown for reproducible scripting.
  • GitHub Pages - A pain free introduction to getting a personal website started using GitHub pages. With Robin Champieux and Eric Leung.

R Tutorials

As a developer and programmer of R, I enjoy teaching others about the basics of data wrangling and analysis. Here are a few of the tutorials I’ve put together.

Big Data to Knowledge

As an instructor under OHSU’s Big Data To Knowledge (BD2K) Training Grant, I have also developed the following short workshops to encourage students to explore data and learn the basics of data-wrangling.

Other Teaching Interests

  • BioData Club - A student and postdoc driven discussion group at OHSU that focuses on practical skills (documentation, software engineering and visualization) necessary for success in data science and bioinformatics.
  • I participate in the PDX R User Group and I was one of the organizers of the first Cascadia R conference
  • I have also started to contribute lesson material to Software Carpentry.

Shiny Apps

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.

Flow Dashboard Demo

A Sample App built with the flowDashboard Shiny Modules package. Meant for visualization of high throughput flow cytometry data. Repo

NHANES explorer

A Depression focused shiny app for the NHANES (National Health and Nutrition Examination Survey) dataset. Built with burro.

Introduction to Interactive Visualization

RMarkdown/Shiny slides introducion for our BMI 569669 Data Analytics course to interactive visualizations.

Introduction to Data Literacy

LearnR Tutorial introducing our HSMP Health Informatics Class to data literacy concepts. Based on a great LearnR tutorial from Mikhail Popov. Repo

Decision Tree Explorer

Simple Shiny App to explore decision tree building with the party paackage. Repo

Introduction to Categorical Data Analysis

LearnR tutorial for the OHSU Data Science Institute introducing students to concepts of categorical data analysis. Part of the DSIExplore package authored with Jessica Minnier.

A Visual Introduction to Clustering Algorithms

Interactive slides with apps to explore properties of clustering algorithms. Built with RMarkdown/Shiny

Surrogate Oncogene Explorer

One of my first shiny apps. Heatmap interface to explore the network effect of gene alterations on networked oncogene signatures. Repo

Recent Posts

More Posts

At some point in your life in Data Science, you will probably struggle with impostor syndrome. We all do - in fact, even though I have used R and have done bioinformatics and data science for more than 15 years, I still struggle with this feeling. As a beginner, the mountain you must climb to master skills in data science seems like a long and impossible one. Caitlin Hudon, in her post about dealing with impostor syndrome has this to say about countering impostor syndrome:

CONTINUE READING

Well, we just finished our clinical data wrangling workshop. This was a 12 hour workshop (spread over 4 days) where students got to work with a real research dataset (the Sleep Heart Health Study data). This is a workshop that we developed as part of an National Library of Medicine T15 training supplement in Data Science. The following is a short report describing the workshop and its outcomes. Intended Audience We designed the workshop for our incoming informatics students (both clinical and biological majors) in order to introduce them to the difficulties of working with clinical data.

CONTINUE READING

I’m still in the process of recovering from my current bout of depression and anxiety. I’d like to talk about what is currently helping me moderate my anxiety. I have been practicing mindfulness and meditation for the past three years and I’m beginning to realize how necessary it is in our information dense age. Many of my symptoms of anxiety are really from an information overglut. I’m currently on way too many projects and am teaching as well.

CONTINUE READING

I just gave a workshop teaching the basics of Shiny (the interactive web visualization framework) for a group of PDX R users. We had 10 people attend, and most of the attendees managed to get through the material and had lots of good questions. I really enjoyed talking with everyone and I hope everyone learned something. We’re planning to give the workshop again to the larger PDX R user community, and some of the attendees last night have volunteered to be TAs.

CONTINUE READING

Well, the week of teaching our Python Bootcamp for Neuroscientists is over. I had the pleasure of working with a great group of students, professors and instructors in developing the material, and had a great time teaching complete beginners to programming and Python. We had the overall goal of introducting 21 Neuroscience Graduate Program students at OHSU to the basics of programming in Python using data that they were interested in: electrophysiology data, and confocal microscopy data.

CONTINUE READING

Software

  • burro. R Package for building data exploration apps for Data Scavenger hunts. With Jessica Minnier and Gabrielle Choonoo. DOI
  • flowDashboard. Shiny modules for building interactive and comparative dashboards for flow cytometry data. See a demo here: https://tladeras.shinyapps.io/sampleFlowDashboard/ DOI
  • DSIExplore. Interactive learnr package for teaching beginning exploratory data analysis and statistics. Jessica Minnier and Ted Laderas. Role: author.
  • infer. Tidy statistical inference package. Andrew Bray, Chester Ismay, Ben Baumer, Mine Cetinkaya-Rundel, Ted Laderas and Nick Solomon. Role: Contributor.
  • surrogateMutation - a package for detecting oncogenic collaboration in somatic mutation and copy number data. DOI
  • surrogateShiny - an R/Shiny Framework for exploring oncogenic collaboration in breast cancer cell lines. See a demo here: https://tladeras.shinyapps.io/surrogateShiny/ DOI
  • Consense - a package for comparing clustering methods. DOI
  • ExonModelStrain - a package for detecting alternative exon usage in the Affymetrix Exon Array. DOI
  • TandTRAQ - Perl Script for merging iTRAQ and XTandem Results.

Recent Publications

More Publications

. CSF1R inhibitors exhibit anti-tumor activity in acute myeloid leukemia by blocking paracrine signals from support cells. Blood, 2018.

PDF

. Immunogenomic Exploration of the Acute Myeloid Leukemia Microenvironment Identifies Determinants of T-Cell Fitness. Blood, 2018.

. Integrated functional and mass spectrometry-based flow cytometric phenotyping to describe the immune microenvironment in acute myeloid leukemia. Journal of immunological methods, 2018.

Code

. Teaching data science fundamentals through realistic synthetic clinical cardiovascular data. bioRxiv, 2018.

Preprint Code Dataset

. Comprehensive characterization of VISTA expression in patients with acute myeloid leukemia.. Journal of Clinical Oncology, 2016.

. Enhanced VISTA expression in a subset of patients with acute myeloid leukemia. Blood, 2016.

. Mass cytometry as a modality to identify candidates for immune checkpoint inhibitor therapy within acute myeloid leukemia. Blood, 2016.

. A network-based model of oncogenic collaboration for prediction of drug sensitivity. Frontiers in genetics, 2015.

PDF Code Poster

. Between pathways and networks lies context: implications for precision medicine. Science progress, 2015.

PDF

. Consensus molecular subtyping through a community of experts advances unsupervised gene expression-based disease classification and facilitates clinical translation. Cancer Research, 2015.

Contact

Other Interests

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.