Instructional Materials and Workshop Reports

Interactive Review

A long time can pass between learning an analysis and finally getting to apply it to real data. Interactive workflows allow researchers to quickly review and further familiarize themselves with common analyses.

Example

Short Courses

Most scientists do not have time to commit to a full course. Creating targeted short courses helps researchers fit new skills into their research schedule.

ML for Biologists

R for Biologists

Evaluation

It is hard to improve what you don't track. Course design is an iterative process that includes surveying outcomes, soliciting input, and evaluating inefficiencies.

Example Report

More Products

Sanders, S. Tutorials, Genomic Resources Clogmia. Github, 2026, https://github.com/kallistaconsulting/genomic_resources_clogmia/blob/main/tutorials

Sanders, S. Introduction to R for Biologists. E-book, National Center for Genome Analysis Support, Second Edition, 2020. PDF

Intro to R for Biologists. National Center for Genome Analysis Support. UITS IT Training. Retrieved March 8, 2022, from https://ittraining.iu.edu/explore-topics/titles/rinto/index.html

IU PTI. (2020). Intro to R for Biologists [YouTube Playlist]. Retrieved March 8,2022, from https://www.youtube.com/playlist?list=PLqi-7yMgvZy-1vFDC7dlQB7hfTrcH5Qh7

Transcriptome Assembly, Annotation, and Analysis. National Center for Genome Analysis Support. UITS IT Training. Retrieved March 8, 2022, from https://ittraining.iu.edu/explore-topics/titles/denovo/index.html.

IU PTI. (2020). De novo Assembly of Transcriptomes [YouTube Playlist]. Retrieved March 8,2022, from https://www.youtube.com/playlist?list=PLqi-7yMgvZy_IaAiPG89AX2cQH2JY4Ifo

HPC Onboarding for Biologists. National Center for Genome Analysis Support. UITS IT Training. Retrieved March 8, 2022, from https://ittraining.iu.edu/explore-topics/titles/bionboard/index.html.

IU PTI. (2020). HPC Onboarding for Biologists [YouTube Playlist]. Retrieved March 8,2022, from https://www.youtube.com/watch?v=eQ660XXG9MI&list=PLqi-7yMgvZy8WeQD1euRu51tRZJRbmyCs

Metagenomics Analysis. National Center for Genome Analysis Support. UITS IT Training. Retrieved March 8, 2022, from https://ittraining.iu.edu/explore-topics/titles/ncgas-meta/index.html

Mining the Sequence Read Archive (SRA). National Center for Genome Analysis Support. UITS IT Training. Retrieved March 8, 2022, from https://ittraining.iu.edu/explore-topics/titles/ncgas-sra/index.html

Workshop Reports

Sanders, S., C. Ganote, B. Papudeshi, C. Stewart. T. Doak. (2019) "Summary Report on Scaling the Introduction to R for Biologists Workshop by National Center for Genome Analysis Support (NCGAS) to a Massive Open Online Course (MOOC)", Indiana University, Bloomington, IN. PTI Technical Report. Retrieved from http://hdl.handle.net/2022/24888

Sanders, S., C. Ganote, B. Papudeshi, C. Stewart. T. Doak. (2019) “Summary of the National Center for Genome Analysis Support (NCGAS) 2018-2019 de Novo Transcriptome Workflow and Workshops”, Indiana University, Bloomington, IN. PTI Technical Report. Retrieved from http://hdl.handle.net/2022/24887

Course Instruction

To teach is to learn. I convert my notes while learning into educational content, allowing me to identify gaps and explore concepts with others. I have taught 23 semester-long courses and countless workshops and short courses over two decades.

Courses Taught

* indicates full semester course

Department of Biology, University of Notre Dame, Notre Dame, IN

2025

*Professor, Courses in Undergratate Research Education (CURE) Biology Lab, Notre Dame IN

2024

*Professor, Topics In Bioinformatics – Single Cell Technologies, Notre Dame IN
*Professor, Topics in Bioinformatics – Machine Learning and AI, Notre Dame IN
*Professor, Applied Bioinformatics, Notre Dame IN
*Professor, Courses in Undergraduate Research Education (CURE) Biology Lab, Notre Dame IN

2023

*Professor, Topics In Bioinformatics – Single Cell RNAseq, Notre Dame IN
*Professor, Topics in Bioinformatics – Machine Learning, Notre Dame IN
*Professor, Applied Bioinformatics, Notre Dame IN
*Professor, Courses in Undergratate Research Education (CURE) Biology Lab, Notre Dame IN

National Center for Genome Analysis Support at Indiana University, Bloomington, IN

2021

*Lead Instructor, Microbial Genome Assembly and Analysis, GEMS at Indiana University and University of Illinois Urbana-Champaign, online
Lead Organizer and Instructor, Transcriptomes Assembly, Annotation and Analysis Workshop, NCGAS at Indiana University, online
Lead Organizer and Instructor, HPC On-boarding for Biologists, NCGAS at Indiana University, online
*Capstone Mentor, Senior Capstone, Luddy School of Informatics, Computing, and Engineering at Indiana University, Bloomington, IN
*REU Mentor, Emerging Scholars Research Experience for Undergraduate Women, Center for Women in Computing at Indiana University, Bloomington, IN

2020

Organizer, NCGAS-Supported Research Webinar, online
Organizer, NCBI Tools in the Cloud, NCGAS and NCBI, online
Lead Organizer and Instructor, Introduction to R for Biologists, NCGAS at Indiana University, online

2019

Lead Organizer and Instructor, de Novo Assembly and Annotation of Transcriptomes , NCGAS at Indiana University, Bloomington, IN
Lead Organizer and Instructor, Introduction to R for Biologists, NCGAS at Indiana University, Bloomington, IN
Lead Organizer and Instructor, HPC On-boarding for Biologists, NCGAS at Indiana University, Bloomington, IN
Instructor, Metagenomic Analysis, NCGAS at Indiana University, Bloomington, IN
*REU Mentor, Emerging Scholars Research Experience for Undergraduate Women, Center for Women in Computing at Indiana University, Bloomington, IN

2018

Instructor, Environmental Genomics Workshop, MDIBL, Mount Desert Island, ME
Lead Organizer and Instructor, de Novo Assembly of Transcriptomes using HPC Resources Workshop, NCGAS at Indiana University, Bloomington, IN
Lead Instructor, Introduction to R for Biologists, NCGAS at Indiana University, online
Lead Instructor, Introduction to R for Biologists, NCGAS at Indiana University, Bloomington, IN
*REU Mentor, Emerging Scholars Research Experience for Undergraduate Women, Center for Women in Computing at Indiana University, Bloomington, IN

2017

Lead Instructor, Introduction to R: Mapping, Indiana University Center for Women in Information Technologies, Bloomington, IN
Instructor, Environmental Genomics Workshop, MDIBL, Mount Desert Island, ME
Guest Lecturer, Advance Computing for Biologists, Bethune-Cookman University, Daytona, FL

2016

Instructor, Environmental Genomics Workshop, MDIBL, Mount Desert Island, ME
Guest Lecturer, Advance Computing for Biologists, Bethune Cookman University, Daytona, FL

University of Notre Dame, Notre Dame, IN

2016

*Course Instructor, Basic Computing for Biologists

2015

*Course Instructor, Basic Computing for Biologists

2014

Guest Lecturer, General Biology I on Mutations and Gene Therapy

2012

*Teaching Assistant, Physiology Laboratory I, Department of Biological Sciences

2011

*Teaching Assistant, Physiology Laboratory I, Department of Biological Sciences

University of Texas at Tyler, Tyler, TX

2010

*Teaching Assistant, Anatomy and Physiology Laboratory II, Department of Biology

2009

*Teaching Assistant, General Biology Laboratory II, Department of Biology

2008

*Teaching Assistant, General Biology Laboratory I and II, Department of Biology

Michigan State University, East Lansing, MI

2007

*Instructor,Vetward Bound Enrichment Summer Program, College of Veterinary Medicine.

2004-2007

Supplemental Instructor, General Biology, Organic Chemistry, and Introductory Physics, Vetward Bound, College of Veterinary Medicine Research

Seaholm High School, Birmingham, MI

2003

*Teaching Assistant, AP Computer Science, Seaholm High School

Research Supervision

Graduate

Elizabeth Brooks – Mentee, Employee, recent PhD (2026)
Brett Coggins – Project Collaboration, recent PhD (2026)
Kate Mortensen - Graduate Research Assistant (2yrs), current PhD student
Layla Freeborn - Mentee, Employee (4 yrs), Research Computing Facilitator and Team Lead
Ezra Amiri - Project Mentee (1yr), PhD

Undergraduate

Eliza Foran - Research Undergraduate, Intern (3yrs), currently in industry position
Lyric Cooper - Research Undergraduate (1 yr), completing B.S. in Biology
Christine Campbell - Research Undergraduate, Intern, Employee (3 yrs), completing B.S. in Informatics
Tenecious Underwood - Research Undergraduate (2 yrs), current PhD student