Courses, present and past

Johns Hopkins University, 2011-present

  • Spring 2025: EN 580.492 Critical Thinking in Science. How do we know if a scientific claim is true? This course will explore ways of thinking critically and skeptically about scientific and medical claims, through close readings of scientific papers and the evidence within them.
  • Spring 2020-2024: EN 601.350 Genomic Data Science. This course has a new name, but it is very similar to the course with the same number (350/340) that was taught in 2016-2018. Note that this is co-listed as a BME course and is part of the new Genomics concentration in BME.
  • Spring 2016, 2017 & 2018: EN 601.350 (formerly 600.340). Introduction to Genomic Research. Cross-listed in both the CS and BME Departments, this undergraduate course counts towards the required coursework for both majors. Tues-Thurs 3:00-4:15pm.
  • Spring 2015: BME 580.689. Computational Personal Genomics. Cross-listed in both the BME and CS Departments. Tues-Thurs 9:00-10:15am. Official catalog listing.
  • I give a lecture each year in 330.600 Pharmacology in the School of Medicine
  • SUMMER INTERNSHIPS. We’ve been taking summer interns every summer for 16 years. Since 2018, my lab accepts applications only through the BDP Summer Undergraduate Research Program at Hopkins. Interns are usually mentored by a postdoc, advanced graduate student, or staff scientist in the lab. For information on how to apply, see https://research.jhu.edu/hour/internal/.

Genomic Data Science specialization on Coursera

Our Coursera Specialization on Genomic Data Science launched in June 2015 and is still going strong in 2025, with over 100,000 attendees to date. You can find links to the courses, most of the videos, and extra materials on the JHU Data Science Lab site. Some details:

  • The specialization includes seven courses
  • Every class runs every month and lasts for one month
  • All classes are free (although Coursera tries hard to get everyone to pay)

Introduction to Genomic Technologies, the overview for the specialization, is taught by Steven Salzberg and Jeff Leek (formerly at JHU and now at the Fred Hutchinson Cancer Center).

Python for Genomic Data Science, a very gentle (and very basic) introduction to programming in Python, is taught by Mihaela (Ela) Pertea and Steven Salzberg

University of Maryland, 2005-2011

CMSC 828H, Computational Gene Finding and Genome Assembly, Fall 2010. .

CMSC 828G, Fall 2009: Bioinformatics for Metagenomics. Fall 2009.

CMSC 828N, “Computational Gene Finding and Genome Assembly”, Spring 2006, Spring 2007, Fall 2007, Fall 2008.

CMSC 838K, “How to do research,” Fall 2008.

TIGR, 1997-2005, and earlier

Advances in Genome Technology and Bioinformatics, offered by TIGR and the Marine Biology Laboratory at Woods Hole, October 2004.

CS 439 Computational Biology, Fall 1999 and earlier years at Johns Hopkins University (long out of date)