Gen Epi Resources

Genomic Epidemiology Seminar Series

Seminars occur every second Thursday from 11am to 12pm Pacific time over Zoom.If you would like to be added to the calendar invitation, please email Alli Black at If you have any follow-up questions or would like to chat more about these topics, please feel free to contact Alli to set up a follow-up call!

Seminar Recordings

  • Week 1 - Today we discussed the overlapping timescales of pathogen evolution and infectious disease transmission, and how to build phylogenetic trees that visualize genetic divergence.
  • Week 2 - During this seminar we discussed measuring divergence over time in order to estimate the average rate of evolution of a pathogen. We also discussed how to use that rate to make phylogenetic trees with branch lengths in units of calendar time.
  • Week 3 - This week we discussed phylogeography, the technique in genomic epidemiology of inferring spatial migration patterns of a pathogen across the tree. We discussed the inferential procedure that allows this, as well as caveats and things to be cautious about.
  • Week 4 - In this seminar we discuss Nextstrain, especially how pipelines are specified in Nextstrain Augur, and different ways to navigate the genomic data visualization in Nextstrain Auspice.
  • Week 5 - This week we discussed consensus genome quality control, including different quality metrics, the impact of different quality issues on downstream analyses, and how to look at BAM files to assess support for different sites in the consensus genome.
  • Week 6 - This week we talked all about data types and data organization. We discussed how using data models helps to organize genomic surveillance metadata and specifically mentioned the PHA4GE data specification for SARS-CoV-2. And then Dan Lu walked us through different genomic data structures, what those different structures are useful for, and which repositories each can be submitted to. She finished the talk off with a discussion of handling GISAID rejections and looking at calls in BAM files.
  • Week 7 - In today's seminar we talked about phylogenetic nomenclature systems (why we use them and types of systems). We finished off with a more detailed discussion of the Pango nomenclature system for SARS-CoV-2.
  • Week 8 - This week we tackled the tricky subject of sampling design. While we don't (yet) have formal frameworks for estimating sample size in genomic epidemiology, today we discussed study design, and specifically how to think about sample selection for different types of genomic epidemiological questions/studies.
  • Week 9 - In this week's seminar I introduced "phylodynamic" analysis - a particular area of genomic epidemiology where we infer changes in pathogen population size from the shapes of coalescent phylogenetic trees.
  • Week 10 - This week I gave a demo of CZ Gen Epi, the new piece of software that CZI is developing for managing genomic data, that eventually will allows folks to build Nextstrain trees independently with a GUI interface. Since that capability isn't active quite yet, I also discussed phylogenetic placements in UShER and Nextclade, and how to pull relevant data out of CZ Gen Epi to use in those phylogenetic placements. [Since the recording of this video, CZ Gen Epi has added this capability.]
  • Week 11 - This week Dr. Sidney Bell joined us to discuss antigenic evolution of viruses - that is, how viral surface proteins can change how they "look" to our immune systems, and in some cases eventually escape our immunity.
  • Week 12 - This week I compared and contrasted phylogenetic placements versus phylogenetic trees, and described the different situations when I prefer one over the other.
  • Week 13 - This week we branched out from SARS-CoV-2, and I gave some examples of how you can use genomic epidemiology to investigate the epidemiology of TB.
  • Week 14 - This week the focus was on practical applications of genomic epidemiology, and I walked through some case studies showing different ways in which genomic epidemiology has supported epi investigations in California.
  • Week 15 - This week was another short break from SARS-CoV-2, and we turned our attention towards genomic epidemiology of a different viral pathogen - Mumps virus.
  • CZ Gen Epi Tutorial! - This tutorial introduces self-serve tree building in CZ Gen Epi, and discusses what the different tree types are useful for.


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