Training Opportunities
Courses, workshops, and training programs in genomic epidemiology and related fields
Whole Genome Sequencing Curriculum
Organization: New York Food Safety Center of Excellence/ Cornell University
This curriculum aims to provide (i) foundational knowledge needed to understand the genetics and genomics of microbial organisms, as well as the WGS data, how it is acquired and processed; (ii) intermediary knowledge regarding how WGS data is used to generate outputs, such as allele codes, phylogenetic trees and single nucleotide polymorphism (SNP) distance matrices, data visualization using SEDRIC, epi-lab communication; and (iii) advanced knowledge on specific topics (e.g., allele X codes, REP strains) that may present additional challenges to surveillance and outbreak investigation.
Posted: 12/31/2023
Whole genome sequencing for epidemiologists
Organization: New York Food Safety Center of Excellence/ Cornell University
After completion of the module, attendees will know: Why WGS represents a superior molecular epidemiology tool over other methods How WGS has already been used to facilitate improved surveillance and trackback of infectious disease outbreaks.
Posted: 3/9/2017
WGS data analysis methodology – what epidemiologists need to know
Organization: New York Food Safety Center of Excellence/ Cornell University
After completion of the module, learners will know: - How NGS data are analyzed from raw data to sequence contigs
Posted: 4/20/2017
hqSNP, wgMLST and the WGS alphabet soup: what epidemiologists need to know
Organization: New York Food Safety Center of Excellence/ Cornell University
After completion of the module, learners will know: - The advantages of wgMLST and hqSNP trees - Why and how the same raw data can yield different trees - How to interpret trees
Posted: 5/23/2017
Case studies on use of WGS in foodborne disease surveillance and outbreak investigations
Organization: New York Food Safety Center of Excellence/ Cornell University
After completion of the module learners will know: - How WGS is used in foodborne disease surveillance and outbreak investigations - Challenges and best practices for communications of WGS data between epidemiologists and laboratorians
Posted: 6/28/2017
ATG, GAC, What can sequencing do for me?
Organization: Washington Integrated Food Safety Center of Excellence
Whole genome sequencing of enteric organisms has enhanced the ability of public health professionals to detect, investigate, and confirm outbreaks. Understanding how sequence data is generated, analyzed, and visualized makes interpreting sequence data more accessible to users outside the laboratory. This webinar will provide a high-level overview of the topic, taking learners through the sequencing process from test tube to phylogenetic trees, with a focus on why this data matters to foodborne outbreak investigators.
Posted: 11/18/2020
Bioinformatics in Public Health Genomics: A Gentle Introduction
Organization: Washington Integrated Food Safety Center of Excellence
This presentation will provide a general, high-level introduction to the current state of the analysis of genomic data in public health labs in the US.
Posted: 8/15/2022
Using Next Generation Sequencing for Real Time Impact on Disease Control Options
Organization: Washington Integrated Food Safety Center of Excellence
This talk describes instances where routine, rapid sequencing informed disease control work, rather than confirming it.
Posted: 8/15/2022
Using MicrobeTrace to Integrate and Visualize Sequence and Epidemiologic Data
Organization: Washington Integrated Food Safety Center of Excellence
Join us for an overview and live demonstration of MicrobeTrace: a free, intuitive, web-based, standalone tool that can be used to integrate and explore genetic and epidemiologic data. We will provide a live overview of MicrobeTrace and demonstrate how MicrobeTrace was used in Washington state to investigate a multi-county outbreak of E. coli linked to pasteurized yogurt in 2021.
Posted: 8/15/2022
Incorporating NCBI’s Pathogen Detection Portal into Epi Workflows
Organization: Association of Public Health Laboratories
This three-part presentation includes an overview of NCBI PDP from the Centers for Disease Control and Prevention, and two live demos on using PDP for enteric investigations from Washington State Department of Health and New York State Department of Health.
Posted: 5/12/2019
Introduction to Pathogen Genomics in Public Health
Organization: Council of State and Territorial Epidemiologists
Learning objectives: 1. Define genomic epidemiology and how it relates to infectious disease epidemiology more broadly 2. List at least two disciplines outside of epidemiology that are foundational to genomic epidemiology 3. Explain at least one real-word scenario where pathogen genomics can inform response or policy decisions in public health practice 4. Describe at least two challenges that hinder the onboarding and routine application of pathogen genomics in public health practice
Posted: 9/28/2022
Leveraging Wastewater and Clinical Sequencing for COVID Variant Surveillance in a Post-Public Health Emergency Landscape
Organization: Council of State and Territorial Epidemiologists
Spatial-Temporal Distributions of SARS-Cov-2 Sub-Variants in Urban and Rural Counties in North Carolina
Posted: 11/14/2023
Bridging Information Technology and NGS in Public Health
Organization: Association of Public Health Laboratories
This webinar will discuss the IT challenges laboratories face as they build their sequencing and bioinformatics capacity. Participants will have the opportunity to hear from an IT solutions architect and a bioinformatician from different state public health laboratories. The speakers will share how the public health laboratories have built their bioinformatics capacity while considering IT security requirements.
Posted: 2/27/2023
MicrobeTrace: A Data Visualization and Analysis Tool for Outbreak Investigations
Organization: Association of Public Health Laboratories
MicrobeTrace is currently used to visualize contact tracing and sequence data by the CDC, state health departments and academic research groups in the US and internationally. This webinar will provide an overview of MicrobeTrace and how it can be used for an array of bacteria and viruses, including HIV, SARS-CoV-2, viral hepatitis and tuberculosis.
Posted: 9/12/2022
Routine Arbovirus Sequencing for Integration in Public Health
Organization: Association of Public Health Laboratories
This webinar will explore how genomic sequencing approaches for arboviral pathogens can improve our diagnostics, advance our understanding of the epidemiology and ecology of arboviruses and provide insights for transmission and vector control. We will provide an overview of genomic surveillance for different arboviral pathogens and describe high-throughput wet and dry lab approaches that can be employed. Additionally, the speakers will discuss how arboviral genomic data can impact routine public health activities.
Posted: 3/5/2024
NCBI Pathogen Detection Part 1: Introduction to the resource
Organization: Association of Public Health Laboratories
In this webinar, we will provide an overview of the National Center for Biotechnology Information (NCBI) Pathogen Detection system which integrates sequence and associated metadata for foodborne and other pathogen surveillance activities.
Posted: 2/13/2024
Genomic Epidemiology and Public Health Bioinformatics
Organization: European Centre for Disease Prevention and Control
The programme is launched in parallel to the WGS infrastructure support and should facilitate the use of genomic data in EU level surveillance and outbreak response. Details of the training activities including training material can be found on ECDC’s virtual academy (EVA).
Posted: 10/19/2023
PMGR: Using Genomic Epidemiology to Advance Public Health Action
Organization: Centers for Disease Control and Prevention
In this grand rounds presentation, CAPT Ellie Click will describe how applications in genome science can be combined with epidemiology approaches to prevent, control, and respond to pathogens that threaten public health. Rapid advances in genomic technologies, such as genomic sequencing, are transforming how we respond to public health threats. Scientists use genomic sequencing to identify and prevent a wide variety of pathogens, including those that cause foodborne illness, tuberculosis, and COVID-19. Combining genomics and epidemiology—coined “genomic epidemiology”—provides a powerful tool for surveillance, outbreak detection, as well as response, and indicates a future where the human genome can direct public health action.
Posted: 3/13/2022
Introduction to SARS-CoV-2 wastewater analysis
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to introduce participants to theoretical and practical aspects of analysing SARS-CoV-2 in wastewater. Participants will get insights into the laboratory work, the interpretation of SARS-CoV-2 levels in wastewater and the variant analysis with examples from the Danish SARS-CoV-2 wastewater surveillance.
Posted: 1/9/2024
Bacterial genome assembly and quality control
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training workshop is to introduce the participants to theoretical and practical aspects of generating bacterial genome assemblies, and the common tools for how to assess assembly quality.
Posted: 12/3/2023
Introduction to avian influenza outbreak investigation using NGS data
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to introduce public health participants to theoretical and practical aspects of analysing avian influenza sequence data from single samples in a one health approach. Participants will get insights on NGS data analysis (including data quality control) and genotyping, and their use in the context of avian influenza outbreak investigations.
Posted: 11/19/2023
Whole-genome sequencing-based (WGS) detection of antimicrobial resistance (AMR) in bacteria
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to introduce participants to theoretical and practical aspects of detection of antimicrobial resistance (AMR) in bacteria using whole-genome sequence (WGS) data.
Posted: 9/3/2023
From sequencer to polished reads for bacteria
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to introduce participants to the software tools commonly used for assessing quality of and polishing Illumina and Nanopore bacterial sequencing data. The participants will gain insights into interpreting quality control (QC) parameters as well as how to handle bad quality reads and contaminated data.
Posted: 9/11/2023
Introduction to bioinformatic analysis of SARS-CoV-2 amplicon sequencing data
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to introduce participants to theoretical and practical aspects of detection of antimicrobial resistance (AMR) in bacteria using whole-genome sequence (WGS) data.
Posted: 9/24/2023
SARS CoV-2 Bioinformatics
Organization: AFRICA CDC PGI TRAINING
This course was designed to allow you to analyze SARS Cov-2 sequence data
Whole Genome Sequencing - Funginet training toolkit
Organization: TEPHINET
This goal of this course is to describe the basic epidemiology of C. auris and how WGS has helped public health officials learn more about its molecular epidemiology. Additionally, it provides an overview of the laboratory and analytic methods for C. auris WGS when using the data for epidemiologic purposes.
Posted: 7/31/2022
Review of Pathogen Genomics Part 1
Organization: American Society for Microbiology
Speaker: Frederic D. Bushman This course will focus on the fundamentals of pathogen genomics including defining key terms and discussing components of the genome. The impact of mutations on phenotypes and protein expressions will also be discussed.
Posted: 12/31/2022
Review of Pathogen Genomics Part 2
Organization: American Society for Microbiology
Speaker: Frederic D. Bushman Part 2 of this course, focuses on the fundamentals of pathogen genomics, including defining key terms and discussing components of the genome. The impact of mutations on phenotypes and protein expressions will also be discussed.
Posted: 12/31/2022
Connecting the Genome to Molecular Diagnostics
Organization: American Society for Microbiology
Speaker: Rosemary She An overview of molecular methods, from principle to clinical application, will be provided in detail. Strengths and limitations of various approaches will be discussed.
Posted: 12/31/2022
The Evolution of NGS Technologies Part 1
Organization: American Society for Microbiology
Speaker: Mendy Poulter Part 1 of this training—With the advent of NGS, it is crucial to understand the evolution of molecular diagnostics, starting from Sanger sequencing through NGS. Additional topics include the appropriate use of long and short reads, as well as understanding commonly used NGS technologies and platforms.
Posted: 12/31/2022
The Evolution of NGS Technologies Part 2
Organization: American Society for Microbiology
Speaker: Mendy Poulter Part 2 of this training—With the advent of NGS, it is crucial to understand the evolution of molecular diagnostics, starting from Sanger sequencing through NGS. Additional topics include the appropriate use of long and short reads, as well as understanding commonly used NGS technologies and platforms.
Posted: 12/31/2022
Overview of Whole Genome Sequencing
Organization: American Society for Microbiology
Speaker: Nick Moore Whole genome sequencing (WGS) is more frequently being used in outbreak scenarios and for the prediction of antibiotic resistance. This section discusses the history of WGS, including its predecessors and the methodology behind WGS.
Posted: 12/31/2022
Overview of Amplicon Based NGS
Organization: American Society for Microbiology
Speaker: Paige Larkin Amplicon-based NGS is one of the more commonly used types of NGS in the clinical microbiology lab. In this section, participants will learn the principles of amplicon-based NGS and its applications, limitations and impact on patient care.
Posted: 12/31/2022
Overview of Shotgun Metagenomic Sequencing
Organization: American Society for Microbiology
Speaker: Robin Patel As targeted and shotgun metagenomic sequencing increase in popularity, their advantages and limitations are being defined. Real clinical cases and impact will be shared.
Posted: 12/31/2022
Application of Genomic Epidemiology for Surveillance and Infection Prevention in Healthcare Settings—Part 1
Organization: American Society for Microbiology
Speaker: Marie-Claire Rowlinson Part 1 of this training—After learning about the principles and limitations of NGS, participants will discover how NGS is used in epidemiology studies and infection control in hospital settings. Participants will be walked through different clinical scenarios where NGS can be used.
Posted: 12/31/2022
Application of Genomic Epidemiology for Surveillance and Infection Prevention in Healthcare Settings—Part 2
Organization: American Society for Microbiology
Speaker: Marie-Claire Rowlinson Part 2 of this training—After learning about the principles and limitations of NGS, participants will discover how NGS is used in epidemiology studies and infection control in hospital settings. Participants will be walked through different clinical scenarios where NGS can be used.
Posted: 12/31/2022
NGS Data Collection and Storage
Organization: American Society for Microbiology
Speaker: Xiaowu Gai Data collection and storage are crucial components of NGS. Important considerations, including amount of data, storage options, instrumentation needs and security concerns will be addressed.
Posted: 12/31/2022
NGS Sequence Analysis
Organization: American Society for Microbiology
Speaker: Julie Hirschborn Participants will be given an overview of sequence analysis and bioinformatics. Essential terminology will be defined and limitations and challenges discussed. Various approaches and their strengths and weaknesses will be explored.
Posted: 12/31/2022
From Start to Finish: Hands-on Design of NGS and Bioinformatics Practice—Part 1
Organization: American Society for Microbiology
Speaker: Stephanie Goya Part 1 of this training—These hands-on sessions are a practical recapitulation on how to design a NGS experiment and the bioinformatic analysis in different scenarios, with special emphasis on the limitations and benefits of each development. These sessions are a debate space where attendees accompanied by a NGS expert will be able to reaffirm concepts seen in the previous webinars, solve doubts and ask questions of specific interest for their projects.
Posted: 12/31/2022
From Start to Finish: Hands-on Design of NGS and Bioinformatics Practice—Part 2
Organization: American Society for Microbiology
Speaker: Stephanie Goya Part 2 of this training—These hands-on sessions are a practical recapitulation on how to design a NGS experiment and the bioinformatic analysis in different scenarios, with special emphasis on the limitations and benefits of each development. These sessions are a debate space where attendees accompanied by an NGS expert will be able to reaffirm concepts seen in the previous webinars, solve doubts and ask questions of specific interest for their projects.
Posted: 12/31/2022
Introduction to NGS Infrastructure
Organization: American Society for Microbiology
Speaker: Amy Mathers Overview course providing information on the recommended laboratory components and computing requirements recommended to begin NGS applications. Recommendations on what to upgrade based on specific applications (graphics processing units [GPUs], central processing units [CPUs], memory, hard drives, etc.) will be provided, along with a discussion on local vs. high-performance computing (HPC) vs. cloud computing platforms.
Posted: 12/31/2022
Define Different Sequencing Techniques and Platforms
Organization: American Society for Microbiology
Speaker: Winston Timp A practical and detail-oriented course exploring the 3 generations of nucleic acid sequencing technologies. The course will explore the strengths and weakness of the sequencing platforms, provide examples to guide choosing a sequencing approach for different biological questions and the expected data and file types that will be generated.
Posted: 12/31/2022
Next-Generation Sequencing in Microbiology: Pathogen and AMR Detection- Part 1
Organization: American Society for Microbiology
Speaker: Charles Chiu Part 1 of this course—Introduction to targeted NGS and metagenomic approaches to classify pathogens.
Posted: 12/31/2022
Next-Generation Sequencing in Microbiology: Pathogen and AMR Detection- Part 2
Organization: American Society for Microbiology
Speaker: Charles Chiu Part 2 of this course—Introduction to targeted NGS and metagenomic approaches to classify pathogens.
Posted: 12/31/2022
Maintaining Order in the Sequence Tsunami: Sequence Data Management for Clinical Microbiologists and Bioinformaticians
Organization: American Society for Microbiology
Speaker: Andrew Warren Introduction into NGS data management.
Posted: 12/31/2022
Whole Genome Sequencing
Organization: American Society for Microbiology
Speaker: John Dekker Detailed course into whole genome sequencing, including specific steps to generate the sequence data, how third generation sequencing impacts whole genome sequencing (WGS) projects and common challenges in analyzing/understanding WGS.
Posted: 12/31/2022
Accessing, Exploring and Using the Publicly Available Databases and National Sequence Archives for Clinical Microbiologists—Part 1
Organization: American Society for Microbiology
Speakers: Michael Feldgarden and Arjun Prasad Part 1 of this training—Dive into accessing, exploring and using the publicly available databases and national sequence archives for clinical microbiologists, e.g., National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing All Influenza Data (GISAID).
Posted: 12/31/2022
Accessing, Exploring and Using the Publicly Available Databases and National Sequence Archives for Clinical Microbiologists—Part 2
Organization: American Society for Microbiology
Speakers: Michael Feldgarden and Arjun Prasad Part 2 of this training—Dive into accessing, exploring and using the publicly available databases and national sequence archives for clinical microbiologists, e.g., NCBI and GISAID.
Posted: 12/31/2022
Assessing Data Quality and Metrics—Part 1
Organization: American Society for Microbiology
Speaker: David Gaston Advanced level practical course into sequence quality assurance/quality control (QA/QC), recommended cut offs and what to do when you need to work with lower quality sequence data.
Posted: 12/31/2022
Assessing Data Quality and Metrics—Part 2
Organization: American Society for Microbiology
Speaker: David Gaston Advanced level practical course into sequence QA/QC, recommended cut offs and what to do when you need to work with lower quality sequence data.
Posted: 12/31/2022
Quality Control Requirements
Organization: American Society for Microbiology
Speaker: Emily Snavely Follow-up course to "Assessing Data Quality and Metrics—Parts 1 and 2," including error rates between sequencing technologies and introduction into assessing genome quality.
Posted: 12/31/2022
Assay Design, Optimization and Validation—Part 1
Organization: American Society for Microbiology
Speaker: Trish Simner Overview course on steps required to design and implement novel assays for clinical microbiologists. Will include a discussion on recommended sample sizes, troubleshooting steps and regulatory guidelines that can be useful/critical resources.
Posted: 12/31/2022
Assay Design, Optimization and Validation—Part 2
Organization: American Society for Microbiology
Speaker: Trish Simner Overview course on steps required to design and implement novel assays for clinical microbiologists. Will include a discussion on recommended sample sizes, troubleshooting steps and regulatory guidelines that can be useful/critical resources.
Posted: 12/31/2022
NGS Library Creation Approaches, Methods and Design
Organization: American Society for Microbiology
Speaker: Heather Blankenship Advanced course into the practical applications of NGS approaches, including targeted, amplicon and whole genome sequencing. This course will highlight differences in sequencing (wet-lab) components between the approaches.
Posted: 12/31/2022
Sequence Comparison and Phylogeny
Organization: American Society for Microbiology
Speaker: Kelly Oakeson Practical-oriented course on the principles of pathogen identification and sequence comparison. Bioinformatics tools and approaches commonly used for these analyses, along with their benefits and limitations, will be discussed.
Posted: 12/31/2022
NGS of Cultured Fungal Pathogens
Organization: American Society for Microbiology
Speaker: Christina Cuomo Advanced course into whole genome sequencing (WGS) approaches which leverage cultured fungal isolates, highlighting both wet-lab considerations and available bioinformatic tools/workflows.
Posted: 12/31/2022
Introduction to NGS Data Analysis Workflows
Organization: American Society for Microbiology
Speaker: Kelsey Florek Practical course into reproducible workflows and recommended tools for NGS applications.
Posted: 12/31/2022
Metagenomic NGS Methods
Organization: American Society for Microbiology
Speaker: Kevin Chau Advanced course on metagenomic approaches to analyze mixed communities without the need for isolation.
Posted: 12/31/2022
All About Trees: Sequence Comparison and Phylogeny
Organization: American Society for Microbiology
Speaker: Kelly Oakeson Workshop participants will learn how to generate and interpret phylogenetic trees using open-source bioinformatic tools. Multiple real-world examples will be used to highlight benefits and limitations of phylogenetic tree interpretation.
Posted: 12/31/2022
Building NGS Data Analysis Workflows
Organization: American Society for Microbiology
Speaker: Robert Petit In this hands-on activity, participants will learn how to use workflow management tools.
Posted: 12/31/2022
NGS of Cultured Bacterial and Mycobacterial Pathogens
Organization: American Society for Microbiology
Speaker: Emily Snavely Advanced course into WGS approaches which leverage cultured bacterial and mycobacterial isolates. Wet-lab considerations, influence of pathogen characteristics on sequencing and common challenges to data analysis will be covered.
Posted: 12/31/2022
Specifics of Bacterial Genomics
Organization: American Society for Microbiology
Speaker: Shaun Yang Deeper overview in bacterial genome structure, mobile elements, genetic exchange mechanisms (horizontal gene transfer), recombination, etc.
Posted: 12/31/2022
Introduction to Clinical Virology and Viral Genomics
Organization: American Society for Microbiology
Speaker: P Hemarajata Deeper discussion into viral genomes, challenges in ribonucleic acid (RNA) vs. deoxyribonucleic acid (DNA) and single stranded vs. double stranded genomes, range of mutation rates (and why) and how different sequencing technologies and library preps relate to characterizing viral sequences.
Posted: 12/31/2022
Specifics of Eukaryotic Genomics
Organization: American Society for Microbiology
Speaker: Bridget Barker Deeper overview into eukaryotic genomes, including the range in sizes, gene arrangements and transcriptional complexity, repetitive elements and challenges in whole genome sequencing.
Posted: 12/31/2022
Antimicrobial Resistance and NGS—Part 1
Organization: American Society for Microbiology
Speaker: Hannah Gray Advanced course on identifying and characterizing antimicrobial resistance markers. Part 1 focuses on multi-drug resistant organisms (MDRO), e.g. carbapenem-resistant Enterobacterales (CRE).
Posted: 12/31/2022
Antimicrobial Resistance and NGS—Part 2
Organization: American Society for Microbiology
Speaker: Kimberlee A. Musser Advanced course on identifying and characterizing antimicrobial resistance markers. Part 2 focuses on tuberculosis (TB).
Posted: 12/31/2022
Bacterial or Fungal WGS Bioinformatics
Organization: American Society for Microbiology
Speaker: Robert Petit Practical course for assembling whole genomes from data generated by different NGS platforms.
Posted: 12/31/2022
Hospital Infection Control
Organization: American Society for Microbiology
Speaker: Shaun Yang Advanced practical course into using NGS data to identify, characterize and track healthcare-associated infections (HAIs). Lean on case studies to flush out real-world examples.
Posted: 12/31/2022
Bioinformatics with Terra.Bio: Direct-from-Specimen Approaches for Viral Genomic Characterization
Organization: American Society for Microbiology
Speaker: Frank Ambrosio Advanced course into direct-from-specimen sequencing including pros/cons vs. isolation and sequencing. Focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and monkeypox virus (MPXV).
Posted: 12/31/2022
Molecular Evolution and Community Outbreak
Organization: American Society for Microbiology
Speaker: Allison Black Advanced, practical course on NGS methods to provide contract tracing data and include a hands-on activity that reconstructs an outbreak scenario.
Posted: 12/31/2022
Foundations of genomic epidemiology 1: Mutations, substitutions, and genetic divergence trees.
Organization: Chan Zuckerberg Initiative
Today we discussed the overlapping timescales of pathogen evolution and infectious disease transmission, and how to build phylogenetic trees that visualize genetic divergence.
Posted: 3/11/2021
Foundations of genomic epidemiology 2: Molecular clocks and temporally-resolved trees.
Organization: Chan Zuckerberg Initiative
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.
Posted: 3/11/2021
Foundations of genomic epidemiology 3: Phylogeography and trait reconstruction on trees.
Organization: Chan Zuckerberg Initiative
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.
Posted: 3/17/2021
Foundations of genomic epidemiology 4: Under the hood with Nextstrain.
Organization: Chan Zuckerberg Initiative
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.
Posted: 3/25/2021
Foundations of genomic epidemiology 5: Consensus genome quality control.
Organization: Chan Zuckerberg Initiative
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.
Posted: 3/31/2021
Foundations of genomic epidemiology 6: Genomic surveillance data management.
Organization: Chan Zuckerberg Initiative
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.
Posted: 4/8/2021
Foundations of genomic epidemiology 7: Phylogenetic nomenclature systems.
Organization: Chan Zuckerberg Initiative
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.
Posted: 4/14/2021
Foundations of genomic epidemiology 8: Sampling design in genomic epidemiology.
Organization: Chan Zuckerberg Initiative
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.
Posted: 4/28/2021
Foundations of genomic epidemiology 9: Phylodynamic analysis
Organization: Chan Zuckerberg Initiative
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.
Posted: 5/12/2021
Aspen demo + phylogenetic placements
Organization: Chan Zuckerberg Initiative
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.]
Posted: 6/6/2021
Foundations of genomic epidemiology 11: Antigenic evolution
Organization: Chan Zuckerberg Initiative
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.
Posted: 6/13/2021
Foundations of genomic epidemiology 12: Phylogenetic placements versus phylogenetic trees.
Organization: Chan Zuckerberg Initiative
This week I compared and contrasted phylogenetic placements versus phylogenetic trees, and described the different situations when I prefer one over the other.
Posted: 8/3/2021
Foundations of genomic epidemiology 13: Introduction to genomic epi of TB
Organization: Chan Zuckerberg Initiative
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.
Posted: 7/7/2021
Foundations of genomic epidemiology 14: Local cases studies in using genomic epidemiology.
Organization: Chan Zuckerberg Initiative
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.
Posted: 8/4/2021
Foundations of genomic epidemiology 15: Genomic epidemiology of mumps virus.
Organization: Chan Zuckerberg Initiative
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.
Posted: 9/15/2021
Welcome to Season 2 of CZ Genomic Epi Seminar + Updates to Nextclade quality control metrics.
Organization: Chan Zuckerberg Initiative
In this second year of the CZ Genomic Epi seminar series, we kick things off with a discussion of some recent changes to Nextclade that offer improved sequence quality control in response to data quality issues that became apparent with the rise of Omicron infections.
Posted: 7/24/2022
S2 CZ Genomic Epi Seminar: Contamination, Coinfection, and Recombination
Organization: Chan Zuckerberg Initiative
This week we talked about three important processes that can make samples appear to have mixed strains: coinfection, contamination, and recombination. We discussed what these signals can look like, and how you can start to differentiate between these processes by looking at your sequencing read data.
Posted: 7/24/2022
S2 CZ Genomic Epi Seminar: Why sequence whole genomes?
Organization: Chan Zuckerberg Initiative
This week we discuss why within genomic epidemiology we emphasize sequencing whole genomes rather than specific genes or partial fragments of the genome. Today’s material comes from Dudas and Bedford’s 2019 paper, “The ability of single genes vs full genomes to resolve time and space in outbreak analysis”
Posted: 7/24/2022
S2 CZ Genomic Epi Seminar: Monkeypox
Organization: Chan Zuckerberg Initiative
Given the emergence of a new Monkeypox epidemic in non-endemic countries, in this week’s seminar we discuss the potential for, and challenges with, performing genomic surveillance and genomic epidemiology of Monkeypox.
Posted: 6/1/2022
S2 CZ Genomic Epi Seminar: Developing a new amplicon-based WGS protocol - Part 1
Organization: Chan Zuckerberg Initiative
Today’s seminar is Part 1 of the two part series discussing how to develop a new amplicon-based sequencing protocol. In Part 1, we focus on using a tool called PrimalScheme to design multiplex amplicon schemes for sequencing.
Posted: 6/15/2022
S2 CZ Genomic Epi Seminar: Developing a new amplicon-based WGS protocol - Part 2
Organization: Chan Zuckerberg Initiative
Today’s seminar is Part 2 of the two part series discussing how to develop a new amplicon-based sequencing protocol. In Part 2, we focus on how to test and troubleshoot the candidate primers generated from PrimalScheme.
Posted: 7/27/2022
S2 CZ Genomic Epi Seminar: Sample size calculations for variant detection and prevalence.
Organization: Chan Zuckerberg Initiative
In today's seminar, Dr. Shirlee Wohl joined us to discuss her work in developing a framework for estimating how many samples you should sequence to detect a variant at a particular frequency or accurately estimate variant prevalence.
Posted: 8/14/2022
Session 1 - Introduction to Genomic Epidemiology
Organization: WHO / PAHO
[Concepts and Methods of Genomic Epidemiology](https://www.paho.org/en/documents/concepts-and-methods-genomic-epidemiology) - Dr. Pimlapas Leekitcharoenphon, Researcher, Research Group for Genomic Epidemiology National Food Institute (DTU Food), Denmark. [Applications of Bioinformatics in the Real-Time Molecular Surveillance of Viral Pathogens](https://www.paho.org/en/documents/applications-bioinformatics-real-time-molecular-surveillance-viral-pathogens) - Dr. Niema Moshiri, Assistant Teaching Professor Computer Science & Engineering University of California, San Diego [Field deployment of sequencing technology -practical considerations and solutions](https://www.paho.org/en/documents/field-deployment-sequencing-technology-practical-considerations-and-solutions) - Dr. Ian Goodfellow, Department of Pathology, Cambridge University, United Kingdom.
Session 2 - Operationalization and Integration of Genomic Data Into National Surveillance
Organization: WHO / PAHO
[Objectives of genomic data in enhancing surveillance activities](https://www.paho.org/en/documents/genomic-epidemiology-objectives-genomic-data-enhancing-surveillance-activities) - Dr. Jairo Mendez, Advisor, Infectious Hazard Management Unit at PAHO/WHO. [Genomic surveillance of antimicrobial resistance in Shigella sonnei in Belgium 2013-2019](https://www.paho.org/en/documents/genomic-surveillance-antimicrobial-resistance-shigella-sonnei-belgium-2013-2019) - Dr. Natalie Fischer, Scienso, National Public Health Institute, Belgium [Large scale genomic surveillance of SARS-CoV-2 in the UK: challenges and lessons learned ](https://www.paho.org/en/documents/large-scale-genomic-surveillance-sars-cov-2-uk-challenges-and-lessons-learned)- Dr. Cristina Ariani, Wellcome Sanger Institute, England, UK
Genomic Epi Toolkit: Welcome and Overview
Organization: Centers for Disease Control and Prevention
CDC’s Dr. Greg Armstrong gives an introduction to the COVID-19 Genomic Epidemiology Toolkit and describes the role for genome sequencing in public health.
Posted: 1/7/2021
Genomic Epi Toolkit: Module 1.1 – What is Genomic Epidemiology?
Organization: Centers for Disease Control and Prevention
This module provides an introduction to genomic epidemiology, with specific reference to SARS-CoV-2 sequencing for epidemiologic investigations.
Posted: 1/7/2021
Genomic Epi Toolkit: Module 1.2 – The SARS-CoV-2 Genome
Organization: Centers for Disease Control and Prevention
This module describes the basics of microbial genomes, with specific refence to the SARS-CoV-2 genome.
Posted: 1/7/2021
Genomic Epi Toolkit: Module 1.3 – How to read a phylogenetic tree
Organization: Centers for Disease Control and Prevention
This module describes the anatomy of phylogenetic trees and how to interpret them in the context of transmission.
Posted: 1/7/2021
Genomic Epi Toolkit: Module 1.4 – Emerging variants of SARS-CoV-2
Organization: Centers for Disease Control and Prevention
This module introduces basic concepts relevant to the emergence of new SARS-CoV-2 variants and the role of sequencing in their detection and definition.
Posted: 4/20/2021
Genomic Epi Toolkit: Module 2.1 – SARS-CoV-2 sequencing in Arizona
Organization: Centers for Disease Control and Prevention
This module provides insight into how SARS-CoV-2 sequencing is used to describe the genomic epidemiology of a state and as an investigative tool in COVID-19 outbreak settings. You can read more about this work: [An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona](http://mbio.asm.org/content/11/5/e02107-20) [external icon](http://mbio.asm.org/content/11/5/e02107-20)
Posted: 1/7/2021
Genomic Epi Toolkit: Module: Module 2.2 – Healthcare cluster transmission
Organization: Centers for Disease Control and Prevention
This module provides insight into two separate outbreaks at long-term care settings, and how sequencing helped clarify the pattern of transmission in these settings. You can read more about this work: [Serial testing for SARS-CoV-2 and virus whole-genome sequencing](https://www.cdc.gov/mmwr/volumes/69/wr/mm6937a3.htm)
Posted: 1/7/2021
Genomic Epi Toolkit: Module 2.3 – Investigating workplace-community transmission
Organization: Centers for Disease Control and Prevention
This module investigates an outbreak at a meat processing plant using sequencing to differentiate workplace and community transmission. You can read more about this work: Utilization of whole genome sequencing to understand SARS-CoV-2 transmission dynamics in long-term care facilities, correctional facilities and meat processing plants in Minnesota, March – June 2020external icon
Posted: 3/4/2021
Genomic Epi Toolkit: Module 2.4 – Superspreading event in a pre-symptomatic population
Organization: Centers for Disease Control and Prevention
This module reviews how genomic epidemiology was used to investigate a COVID-19 superspreading event in a congregate care setting. You can read more about this work: [Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events](https://science.sciencemag.org/content/early/2020/12/09/science.abe3261) [external icon](https://science.sciencemag.org/content/early/2020/12/09/science.abe3261)
Posted: 4/15/2021
Genomic Epi Toolkit: Module 2.5 – Confirming SARS-CoV-2 reinfection with whole genome sequencing
Organization: Centers for Disease Control and Prevention
This module investigates a case study that demonstrates how whole genome sequencing can be used as an investigative tool to identify cases of true reinfection.
Posted: 8/6/2021
Genomic Epi Toolkit: Module 2.6 – Detecting and prioritizing SARS-CoV-2 variants
Organization: Centers for Disease Control and Prevention
This module describes the detection and genome sequencing of SARS-CoV-2 variants to prioritize COVID-19 investigation and contact tracing activities.
Posted: 10/21/2021
Genomic Epi Toolkit: Module 2.7 – Wastewater-based variant tracking for SARS-CoV-2
Organization: Centers for Disease Control and Prevention
This module describes the detection of SARS-CoV-2 RNA in municipal wastewater to provide early warning of increased community transmission and to inform clinical specimen selection for viral whole genome sequencing.
Posted: 11/16/2021
Genomic Epi Toolkit: Module 3.1 – Getting started with Nextstrain
Organization: Centers for Disease Control and Prevention
This module gives an introduction to [Nextstrain](https://nextstrain.org/), a powerful tool for interactive tree visualization.
Posted: 1/7/2021
Genomic Epi Toolkit: Module 3.2 – Getting started with MicrobeTrace
Organization: Centers for Disease Control and Prevention
This module introduces [MicrobeTrace](https://microbetrace.cdc.gov/MicrobeTrace/) for transmission network analysis using SARS-CoV-2 sequencing and contact tracing data.
Posted: 3/4/2021
Genomic Epi Toolkit: Module 3.3 – Real-time phylogenetics with UShER
Organization: Centers for Disease Control and Prevention
This module provides an introduction to [UShER](https://genome.ucsc.edu/cgi-bin/hgPhyloPlace), an easy to use web portal for fast phylogenetic tree calculation.
Posted: 3/4/2021
Genomic Epi Toolkit: Module 3.4 – Walking through Nextstrain trees
Organization: Centers for Disease Control and Prevention
This module demonstrates how to navigate through Nextstrain phylogenetic trees using various functionalities such as filtering, zooming, coloring and labeling to further analyze SARS-CoV-2 genomic epidemiological data. Nextstrain provides a list of [SARS-CoV-2 resources](https://nextstrain.org/groups/blab/ncov/tutorial) [external icon](https://nextstrain.org/groups/blab/ncov/tutorial) and publicly available analyses to help explore their tool.
Posted: 3/11/2021
Genomic Epi Toolkit: Module 3.5 – Public genome repositories for SARS-CoV-2
Organization: Centers for Disease Control and Prevention
This module introduces two public repositories for sharing SARS-CoV-2 genome sequence data and basic tips for searching them.
Posted: 4/14/2021
Genomic Epi Toolkit: Module 3.6 – Sequencing strategies for SARS-CoV-2
Organization: Centers for Disease Control and Prevention
This module introduces some strategies to consider when deciding when and how to use genome sequencing to assist with epidemiologic surveillance and investigation of SARS-CoV-2.
Posted: 9/28/2021
Advancing Genomic Epidemiology for Public Health: Novel Clustering Techniques and Serial Interval Estimation for SARS-CoV-2 Sequences
Organization: PHA4GE
Welcome to Episode 9 of the PHA4GE Genomic Horizons webinar series! In this episode, Prof. Caroline Colijn from Simon Fraser University shares her expertise on advancing genomic epidemiology for public health.
Posted: 3/2/2023
PHA4GE Webinar Series: SARS-CoV-2 Data Management
Organization: PHA4GE
CanCOGen VirusSeq Data Portal Christina K. Yung, PhD, Ontario Institute for Cancer Research MAJORA Sam Nichols, PhD, University of Birmingham
Posted: 6/1/2021
Pathogen genomic surveillance in Asia: Findings from a 13 country assessment
Organization: PHA4GE
We are thrilled to announce Episode 11 of the PHA4GE Genomic Horizons Webinar Series, featuring a talk by **Assistant Professor Ruklanthi de Alwis** from **Duke-NUS Medical School Centre for Outbreak Preparedness**. Ruklanthi shares her expertise and insights on “Pathogen genomic surveillance in Asia: Findings from a 13 country assessment”.
Posted: 3/22/2023
Our feature presentation: Different strategies to predict antimicrobial resistance in Enterococcus
Organization: PHA4GE
We are thrilled to announce the highly anticipated Episode 10 of the PHA4GE Genomic Horizons Webinar Series, featuring a talk by** Dr. Robert Beiko** from **Dalhousie University**. Join us as we delve into the fascinating topic of “**Different strategies to predict antimicrobial resistance in Enterococcus**“.
Posted: 6/13/2023
Metagenomics In The Future Of Genomic Surveillance
Organization: PHA4GE
This episode will be presented by Dr Victoria Carr from the Wellcome Sanger Institute and will explore the exciting potential of metagenomics in the context of genomic surveillance.
Posted: 4/4/2023
One-health microbial genomics approach for epidemiological tracking of bacterial pathogens along the farm-to-form continuum
Organization: PHA4GE
In episode 7 we have a guest presentation from Prof. Mohamed Elhadidy, who is a professor of Biomedical Sciences at Zewail City of science and technology, Egypt. Dr. Elhadidy research program aims to develop a better understanding of the pathogenesis, ecology, evolution, and transmission of bacterial foodborne and zoonotic diseases through the implementation of different population genetics and comparative genomic studies of these bacterial pathogens.
Posted: 8/22/2022
Containerized Workflows, Cloud Compute Infrastructure, and GUI Web Applications: a Model for Distributed Public Health Bioinformatics
Organization: PHA4GE
In episode 6 we have a guest presentation from Kevin Libuit, M.S., who is the Chief Technology Officer of Theiagen Genomics.
Posted: 3/8/2022
Ethical, Legal, And Social Considerations For Real-World Data In Public And Private Domains
Organization: PHA4GE
In episode 5 we have a guest presentation from Dr. Rachele Hendricks-Sturrup who is the Research Director of Real World Evidence at the Duke-Margolis Center for Health Policy. Prior to this role, she served as Health Policy Counsel and Lead at the Future of Privacy Forum and Research Fellow at Harvard Pilgrim Health Care Institute. As a researcher, bioethicist, and policy practitioner, her work centers on addressing implementation and ethical, legal, and social implications issues at the intersection of health policy and innovation.
Posted: 2/21/2022
Raising Skills And Lowering Bars: Software Development And Capacity Building To Support SARS-CoV-2 Genomic Epidemiology In California
Organization: PHA4GE
Dr. Alli Black, Chan Zuckerberg Initiative Dr. Patrick Ayscue, Chan Zuckerberg Biohub The Public Health Alliance for Genomic Epidemiology, invites you to a webinar on **Global Genomics** This webinar is organized by the PHA4GE Secretariat in partnership with the Chan Zuckerberg Initiative and Chan Zuckerberg Biohub.
Posted: 11/22/2021
Global Genomics
Organization: PHA4GE
**Malaria Genomics and Bioinformatics for Public Health in Ghana** Dr. Anita Ghansah, University of Ghana **Overview of SARS-CoV-2 Genome Sequencing: Where Does Pakistan Stand?** Dr. Waqasuddin Khan, AGA Khan University The Public Health Alliance for Genomic Epidemiology, invites you to a webinar on **Global Genomics** This webinar is organized by the PHA4GE Secretariat in partnership with the University of Ghana and the Aga Khan University
Posted: 10/15/2021
Whole genome sequencing to strengthen foodborne disease surveillance – WHO's webinar
Organization: WHO
Whole genome sequencing (WGS) is a laboratory technique which is revolutionizing public health and more specifically the control and prevention of foodborne diseases. WGS is useful for understanding foodborne diseases through enhancing routine surveillance, outbreak detection, outbreak response and for source identification using a One Health approach, given its potential to change how we detect and monitor microbial hazards in the food chain, as well as how we assess, investigate and manage food safety risks.
Posted: 6/29/2023
Real-time Whole Genome Sequencing Surveillance for Healthcare Outbreak Detection and Investigation
Organization: Labroots
Webinar Abstract: Traditional methods of infection prevention to detect healthcare-associated outbreaks have remained unchanged for many years. Investigators often rely on examining infection trends for increased incidence and then use reactive whole genome sequencing (WGS) to confirm or refute its presence. This method frequently misidentifies transmission and misses transmission where it has occurred. More recently, WGS surveillance has emerged as an alternative approach for infection prevention. By sequencing pathogens regardless of the suspicion of an outbreak, investigators can ideally detect transmission early and implement interventions before pathogens spread further. This webinar will discuss the background and emergence of WGS surveillance as well as infection prevention considerations for healthcare facilities. Moreover, the webinar will discuss recent cost-benefit analyses of WGS surveillance and potential barriers to implementation. Dr. Alexander Sundermann is an Assistant Professor at the University of Pittsburgh, Division of Infectious Diseases, Center for Genomic Epidemiology.
Posted: 2/27/2023
Introduction to Genomic Epidemiology part 1
Organization: Washington State Department of Health
In this three-part series, Dr. Alli Black introduces common situations where pathogen genomic data analysis can support public health investigations, the foundational theory of genomic epidemiology, and the basics of building, reading, and using phylogenetic trees.
Posted: 1/7/2023
Introduction to Genomic Epidemiology part 2
Organization: Washington State Department of Health
In this three-part series, Dr. Alli Black introduces common situations where pathogen genomic data analysis can support public health investigations, the foundational theory of genomic epidemiology, and the basics of building, reading, and using phylogenetic trees.
Posted: 1/31/2023
Introduction to Genomic Epidemiology part 3
Organization: Washington State Department of Health
In this three-part series, Dr. Alli Black introduces common situations where pathogen genomic data analysis can support public health investigations, the foundational theory of genomic epidemiology, and the basics of building, reading, and using phylogenetic trees.
Posted: 1/31/2023
Fundamentals of Bacterial Genomics part 1
Organization: Washington State Department of Health
**Description** In this three part short course, Stephanie Lunn introduces the molecular microbiology and genomics of bacterial pathogens, including: - What encompasses a bacterial genome, and how is it organized? - What are the important assumptions and principles of bacterial genomes when performing bioinformatic analysis and using them for genomic epidemiology? - An introduction to the core, accessory, and pan genome. - A discussion of horizontal gene transfer, including impacts to the genome and implications for genomic epidemiological inference. **Learning Objectives** Part I 1. List some assumptions of bacterial genomes 2. Explain the association between bacterial genome size and number of ORFs 3. Explain the minimal genome concept in relation to bacterial lifestyles 4. Give examples of content found in the genome 5. Explain the functional category of genes as a percentage of the genome
Posted: 12/30/2023
Fundamentals of Bacterial Genomics part 2
Organization: Washington State Department of Health
**Description** In this three part short course, Stephanie Lunn introduces the molecular microbiology and genomics of bacterial pathogens, including: - What encompasses a bacterial genome, and how is it organized? - What are the important assumptions and principles of bacterial genomes when performing bioinformatic analysis and using them for genomic epidemiology? - An introduction to the core, accessory, and pan genome. - A discussion of horizontal gene transfer, including impacts to the genome and implications for genomic epidemiological inference. **Learning Objectives** Part II 1. What are some additional assumptions of bacterial genomes? 2. Be able to explain the difference between core genome, pan genome, and accessory genome 3. Understand different considerations when deciding on core genome and pan genome approaches
Posted: 12/30/2023
Fundamentals of Bacterial Genomics part 3
Organization: Washington State Department of Health
**Description** In this three part short course, Stephanie Lunn introduces the molecular microbiology and genomics of bacterial pathogens, including: - What encompasses a bacterial genome, and how is it organized? - What are the important assumptions and principles of bacterial genomes when performing bioinformatic analysis and using them for genomic epidemiology? - An introduction to the core, accessory, and pan genome. - A discussion of horizontal gene transfer, including impacts to the genome and implications for genomic epidemiological inference. **Learning Objectives** Part III 1. Briefly describe the fate of DNA that enters the cell through horizontal gene transfer 2. Define recombination; briefly describe the difference between nonhomologous recombination and homologous recombination 3. Briefly describe the three mechanisms of horizontal gene transfer in bacteria: transformation, transduction, and conjugation 4. Briefly explain how these mechanisms can influence the core genome, accessory genome, and pan-genome
Posted: 12/30/2023
Accelerating the Use of Pathogen Genomics and Metagenomics in Public Health: A Workshop
Organization: The National Academies
Welcome Remarks, Workshop Overview, and Goals David Blazes, Bill & Melinda Gates Foundation, in person Chair, Workshop Planning Committee
Posted: 7/28/2024
Current State of Pathogen Genomics Metagenomics in the U.S. Public Health Enterprise
Organization: The National Academies
Session 1: Current State of Pathogen Genomics/Metagenomics in the U.S. Public Health Enterprise Moderator: David Blazes, Bill & Melinda Gates Foundation - Current State of Pathogen Genomics in the U.S. Public Health System Greg Armstrong, Ridgway Consulting, LLC, - Applications of Pathogen Genomics in Public Health – National Level Duncan MacCannell, U.S. Centers for Disease Control and Prevention - Applications of Pathogen Genomics in Public Health – State Level Ruth Lynfield, Minnesota Department of Health, in person
Posted: 7/28/2024
Applications in Early Warning and Preparedness – Panel Discussion
Organization: The National Academies
Panel Discussion Moderator: Wondwossen Gebreyes, The Ohio State University - Genomic Surveillance for Antimicrobial Resistance Yvan Hutin, World Health Organization - Wastewater Surveillance Rob Knight, University of California San Diego - Genomic Sequencing to Inform Therapeutic Usage Lisa Purcell, Third Rock Ventures - Pathogen Genomics for Outbreak Epidemiology Pardis Sabeti, Broad Institute - Applications of Pathogen Genomics in H5N1 Outbreak Tavis Anderson, U.S. Department of Agriculture
Posted: 7/28/2024
Data Infrastructure, Interoperability, Classification, and Stewardship
Organization: The National Academies
Moderator: Ana Bento, Cornell University - Current State of Infrastructure and Interoperability of Pathogen Genomics Data in the U.S. Steve Sherry, National Institutes of Health - Integration of Data Streams to Augment Genomic Data Melissa Haendel, University of North Carolina, National COVID Cohort Collaborative - PHA4GE Data Standards System and Structure – Application in South Africa Alan Christoffels, Public Health Alliance for Genomic Epidemiology - Data Processing Structures and Determining the Value of Sequenced Data Kristian Andersen, Scripps Research, virtual
Posted: 7/28/2024
Privacy, Ownership, and Democratization Considerations in the U.S. – Panel Discussion
Organization: The National Academies
Moderator: Dick Wilder, Georgetown University - Considerations for Sovereignty and Governance of Pathogen Genomics Data on an International Scale Alexandra Phelan, Johns Hopkins University - Personal Privacy – Risk Mitigation Related to Human Genome Sequences in Data Sets Claudia Emerson, McMaster University - Data Policy and the Development of a Universal IRB Ben Berkman, National Institutes of Health - Democratization Efforts and Integration of Alternate Data Systems Bronwyn MacInnis, Broad Institute
Posted: 7/28/2024
National Academies Day 1 Synthesis
Organization: The National Academies
Day 1 overview
Posted: 7/28/2024
Welcome Remarks, Review of Day 1
Organization: The National Academies
David Blazes, Bill & Melinda Gates Foundation
Posted: 7/28/2024
Identifying Gaps in Current Applications, Funding, and Research
Organization: The National Academies
Moderator: Liliana Brown, National Institutes of Health - Applications for New Pathogen Detection and Limitations of Genomics Data Charles Chiu, University of California San Francisco - Workforce Training Alli Black, Washington State Department of Health - Gaps and Opportunities for Priority Investments Heather Carleton, U.S. Centers for Disease Control and Prevention
Posted: 7/28/2024
Envisioning the Future of Pathogen Genomics – Presentation and Panel Discussion
Organization: The National Academies
Moderator: Larry Madoff, Massachusetts Department of Public Health; University of Massachusetts Chan Medical School, Pathogen Genomics in the Future of Public Health: Chikwe Ihekweazu WHO - Mike Worobey, University of Arizona - Courtney Lias, US Food and Drug Administration - Sharon Peacock, University of Cambridge - Barney Graham, Morehouse School of Medicine
Posted: 7/28/2024
National Academies Synthesis and Close
Organization: The National Academies
Final synthesis of the July 2024 workshop
Posted: 7/28/2024
Terra.bio Genomic Characterization
Organization: Association of Public Health Laboratories
The goal of this course is to evaluate quality control metrics during characterization of SARS-CoV-2 genomes using the Terra platform.
Posted: 8/25/2024
Terra.bio Genomic Epidemiology
Organization: Association of Public Health Laboratories
The goal of this course is to utilize genomics to understand the epidemiology of SARS-CoV-2 using the Terra platform.
Posted: 8/25/2024
StaPH-B Recordings
Organization: StaPH-B
Recordings from the State Public Health Bioinformatics Group
Phyloseminar Recordings
Organization: Phyloseminar
phyloseminar.org is organized by [Frederick "Erick" Matsen](http://matsen.fhcrc.org/) and Erick would like to thank the following individuals for their help: David Bryant, Brian Claywell, Aaron Darling, Alexei Drummond, Stephane Guindon, Tracy Heath, Robin Kodner, Chris Nasrallah, Thomas Sharpton, and Tanja Stadler. Please [contact Erick](mailto:matsen@fhcrc.org) with any comments or questions.
WNV Seminar Part 1
Organization: Massachusetts Department of Public Health
NE BRR Seminar: WNV Part 1 of 2, presented by Theigaen Genomics and the Massachusetts Department of Public Health Bioinformatics Regional Resource.
WNV Seminar Part 2
Organization: Massachusetts Department of Public Health
WNV Seminar Part 2 of 2, presented by Theigen Genomics and Massachusetts Department of Public Health Bioinformatics Regional Resource.
Influenza Seminar Part 1
Organization: Massachusetts Department of Public Health
Influenza Seminar Part 1 of 2, presented by Theiagen Genomics and Massachusetts Department of Public Health Bioinformatics Regional Resource.
Influenza Seminar Part 2
Organization: Massachusetts Department of Public Health
Influenza Seminar Part 1 of 2, presented by Theiagen Genomics and Massachusetts Department of Public Health Bioinformatics Regional Resource.
TB Seminar Part 1
Organization: Massachusetts Department of Public Health
TB Seminar Part 1 of 2, presented by Theiagen Genomics and Massachusetts Department of Public Health Bioinformatics Regional Resource.
TB Seminar Part 2
Organization: Massachusetts Department of Public Health
Influenza Seminar Part 1 of 2, presented by Theiagen Genomics and Massachusetts Department of Public Health Bioinformatics Regional Resource.
Advanced Bioinformatics - Dev Practices and Git Fundamentals Part 1
Organization: Massachusetts Department of Public Health
Dev Practices and Git Fundamentals Part 1 of 2, presented by Theiagen Genomics and Massachusetts Department of Public Health Bioinformatics Regional Resource.
Advanced Bioinformatics - Dev Practices and Git Fundamentals Part 2
Organization: Massachusetts Department of Public Health
Dev Practices and Git Fundamentals Part 2 of 2, presented by Theiagen Genomics and Massachusetts Department of Public Health Bioinformatics Regional Resource.
MGETS: Session 1 – Molecular Microbiology
Organization: Michigan Department of Health and Human Services
The Midwest Genomic Epidemiology Training Series (MGETS) is a 4-part series—led by genomic epidemiology expert, Dr. Arianna Miles-Jay—designed to provide basic training on the fundamental topics that underly genomic epidemiology while tying these topics to real-world applications. This session introduces genomic epidemiology and covers key topics in molecular microbiology such as defining a genome, understanding why microbial genomes shed light on microbial spread, how features of a genome can influence their connection to spread, and how genomes are used to help identify concerning infections.
Posted: 9/13/2024
MGETS: Session 2 – Sequencing
Organization: Michigan Department of Health and Human Services
The Midwest Genomic Epidemiology Training Series (MGETS) is a 4-part series—led by genomic epidemiology expert, Dr. Arianna Miles-Jay—designed to provide basic training on the fundamental topics that underly genomic epidemiology while tying these topics to real-world applications. This session covers key topics in sequencing including the definition and history of sequencing, the sequencing process, different approaches to sequencing, as well as common challenges with sequencing.
Posted: 9/13/2024
MGETS Session 3 Bioinformatics
Organization: Michigan Department of Health and Human Services
The Midwest Genomic Epidemiology Training Series (MGETS) is a 4-part series—led by genomic epidemiology expert, Dr. Arianna Miles-Jay—designed to provide basic training on the fundamental topics that underly genomic epidemiology while tying these topics to real-world applications. This session covers key topics in bioinformatics including the definition of bioinformatics, the basics of bioinformatics in the contexts of sequence assembly, annotation, and comparison, as well as the implementation of bioinformatic tools.
Posted: 10/31/2024
MGETS Session 4 Infectious Disease Epidemiology
Organization: Michigan Department of Health and Human Services
The Midwest Genomic Epidemiology Training Series (MGETS) is a 4-part series—led by genomic epidemiology expert, Dr. Arianna Miles-Jay—designed to provide basic training on the fundamental topics that underly genomic epidemiology while tying these topics to real-world applications. This final session revisits the interdisciplinary nature of genomic epidemiology and covers key infectious disease epidemiology topics in the context of genomic epi including applications of pathogen classification and genomic data to address epidemiological questions, aid in transmission detection and estimation of epidemic dynamics, and inform prevention and response efforts.
Posted: 12/15/2024
Empowering AMR Research through R: Analysis and Visualisation
Organization: European Centre for Disease Prevention and Control
**This training will introduce participants to advanced visualization techniques for antimicrobial resistance (AMR) and whole genome sequencing (WGS) data. The focus is on practical, hands-on applications using real-world datasets, including heatmaps and integrated analysis of phenotypic and genotypic resistance. **
Posted: 6/17/2025
Molecular Epidemiology and Global Transmission of Cholera
Organization: European Centre for Disease Prevention and Control
**This two-half-day training explores the use of genomic tools in outbreak investigations, using the 2010 Haitian cholera outbreak as a case study (DOI: [10.1128/mBio.00157-11](https://doi.org/10.1128/mbio.00157-11)). ** **Through guided analysis of molecular and genomic data, participants will compare traditional typing methods (e.g., Pulsed-field gel electrophoresis-PFGE) with modern approaches like Whole-Genome Sequencing-Based Typing (WGST), and develop skills in interpreting phylogenetic relationships, antimicrobial resistance (AMR), and virulence profiles, and genomic epidemiology in a real-world context. The course includes a simulation exercise to reinforce practical understanding.**
Posted: 9/2/2025
Phylogenetics and Alignments
Organization: European Centre for Disease Prevention and Control
_The aim of this virtual training is to introduce participants to theoretical and practical aspects of alignments and phylogenetics. Participants will gain a basic understanding of what a phylogeny is, and how it can be generated and assessed for quality and trustworthiness_
Posted: 3/19/2025
Waterborne disease and Water Surveillance
Organization: European Centre for Disease Prevention and Control
_The aim of this virtual training is** **to introduce participants to the theoretical and practical aspects of waterborne disease surveillance, using Leptospirosis as an example. Participants will gain insight into surveillance tools and the state of the art in human Leptospirosis. They will also gain knowledge on Leptospirosis surveillance from an animal perspective. Additionally, in a second session, microbiological assessment of water quality will be covered. Participants will be first introduced to water monitoring before delving into the design of molecular tools and bathing water monitoring._
Posted: 7/23/2024
Pathogens and Health Risks in Seafood Products
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to provide participants with comprehensive knowledge on the health risks associated with seafood products. The focus will be on understanding norovirus in shellfish, exploring the genomic and epidemiological surveillance for seafood products, examining the French REMI network for shellfish production areas surveillance, and engaging in a practical session to address outbreak scenarios. Additionally, participants will gain insights into the specific risks posed by marine pathogens (Vibrio, Hepatitis A, Phytotoxin (Paralytic Shellfish Poisoning - PSP), the challenges in quantitative microbial risk assessment, and the epidemiology and detection of parasites in seafood, with practical case studies to enhance understanding.
Posted: 9/11/2024
Focus on the Agents of Whooping Cough
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to provide participants with an in-depth understanding of whooping cough (pertussis) epidemiology, surveillance, and vaccination strategies. Participants will learn how genomic tools are used for surveillance, examine the epidemiology of recent outbreaks, and explore the public health impacts of vaccination, particularly in the context of pregnancy and early infancy. Additionally, practical sessions will provide hands-on experience in the rapid genotyping of Bordetella pertussis.
Posted: 11/4/2024
RSV Insights: Genomic Evolution, Treatments, and Public Health Strategies
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to provide participants with in-depth knowledge of RSV (Respiratory Syncytial Virus), including its genomic diversity, evolution, available treatments, and emerging vaccine strategies. The focus will be on how genomic data informs public health responses, the impact of RSV on vulnerable populations, and ongoing advancements in treatment and prevention. The training will also explore regulatory frameworks and public health strategies for managing RSV outbreaks.
Posted: 12/12/2024
Focus on the agents of diphtheria
Organization: European Centre for Disease Prevention and Control
**The aim of this virtual training is to provide participants with in-depth knowledge of the agents causing diphtheria, and their diagnosis, clinical definition, antibiotic resistance and taxonomy. Diphtheria surveillance, vaccination strategies, and treatment protocols will also be covered. This webinar will also allow participants to gain practical bioinformatics skills for genotyping _C. diphtheriae_ and _C. ulcerans_ strains.**
Posted: 3/6/2025
Building bioinformatics workflows
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to provide learners with skills to create and maintain workflows for automating routine bioinformatics tasks.
Posted: 3/20/2025
Nanopore Sequencing Technology
Organization: European Centre for Disease Prevention and Control
**The aim of this virtual training workshop is to provide participants with a comprehensive understanding of Nanopore sequencing technology, from its underlying principles to its practical applications in epidemiological surveillance of infectious diseases. The webinar will enable participants to explore the latest advancements in Nanopore technology, develop key bioinformatics skills for analysing Nanopore sequencing data, and understand its diverse applications in fields such as virology, bacteriology, and mycology. In this virtual training, a focus will be given on applications to the surveillance and outbreak investigation of pathogens.**
Posted: 4/10/2025
Klebsiella pneumoniae genomic epidemiology and antimicrobial resistance
Organization: European Centre for Disease Prevention and Control
**The aim of this virtual training workshop is to provide participants with an in-depth understanding of the population biology, genomics, capsular diversity and antimicrobial resistance of _Klebsiella pneumoniae_, and how their study informs public health action against this prominent ESKAPE pathogen, including vaccine-based strategies. The virtual training will also introduce the use of LIN codes for strain-level classification, studies in the One Health context, and highlight international initiatives such as KlebNet.**
Posted: 9/10/2025
Unix for beginners & Introduction to the Conda ecosystem
Organization: European Centre for Disease Prevention and Control
The aim of this virtual training is to introduce participants to working in Unix and creating Conda environments for running simple bioinformatics tasks. The training is divided into three sessions. In the first session, participants will be introduced to the Unix ecosystem and basic Unix commands useful for inspecting various files. In the second session, participants will focus on file manipulation and consolidate their understanding of the command line interface. The third session aims to enhance participants’ ability to perform bioinformatics tasks in the command line by setting up and using Conda environments.
Posted: 8/21/2024
R data analysis and visualisation for beginners
Organization: European Centre for Disease Prevention and Control
_ _R is an open source software, a widely used programming language for statistical data analysis and a powerful tool for visualisation. The **aim **of this virtual training is to introduce participants to data analysis and plotting in R.
Posted: 2/24/2025
Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Organization: Wellcome Connecting Science
Get familiar with Linux and its command line in order to access the full range of bioinformatics tools available to researchers.
Bioinformatics for Biologists: Analysing and Interpreting Genomics Datasets
Organization: Wellcome Connecting Science
Boost your career by gaining the skills to install and modify the elements of a bioinformatics workflow to suit your needs.
Eukaryotic Genome Assembly: How to Use BlobToolKit for Quality Assessment
Organization: Wellcome Connecting Science
The BlobToolKit software is an essential tool for the quality assessment of novel genomes. It is being used to support the ambitious EarthBioGenome project to sequence the genomes of all 1.5 million eukaryotic species on the planet, not just humans or model organisms.
Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis
Organization: Wellcome Connecting Science
Predict antimicrobial resistance, master data-sharing, and enhance your expertise in AMR genomics using cutting-edge databases.
Selecting the method and data for building transmission networks: a Mtb case study
Organization: PHA4GE
We're excited to announce episode 14 of the PHA4GE Genomic Horizons webinar series, featuring a talk by Conor Meehan PhD, FHEA, FRSB, Associate Professor of Microbial Bioinformatics at Nottingham Trent University! PHA4GE has started a Phylogenetics sub-working group that will be working on a Phylogenetics for Public Health Guidance Document. Prof Meehan will be giving a talk on multiple approaches on approaches (parsimony, distance, maximum likelihood) with a focus on Mtb.
Posted: 5/7/2025
Introduction to Public Health Phylogenetics
Organization: PHA4GE
PHA4GE has launched a **Phylogenetics Sub-Working Group** focused on developing a Phylogenetics for Public Health Guidance Document. To kick things off, Dr. Dyson will be leading an introductory session on: **Introduction to Public Health Phylogenetics Using Case Studies**. This session is a great opportunity to learn about the role of phylogenetics in public health and engage with the ongoing work of the Phylogenetics Sub-Working Group. We hope you’ll join us to get involved and help shape this important initiative!
Posted: 3/19/2025
Democratising Bioinformatics: Breaking the Bioinformatics Barrier in AMR Genome Analysis with AMRColab
Organization: PHA4GE
Dr. Su Datt earned his Ph.D. in Structural and Molecular Biology from University College London and now leads a research team specializing in structural bioinformatics. His work explores how mutations impact protein structures with applications in host-virus interactions, antimicrobial resistance (AMR), and crop breeding. AMRColab, his latest initiative, aims to make advanced bioinformatics tools accessible to researchers worldwide, with a focus on low-resource settings.
Posted: 11/25/2024
Best Practices for Public Health Bioinformatics Pipelines
Organization: PHA4GE
We are thrilled to announce a PHA4GE **Bioinformatics Pipelines and Visualizations Working Group** Webinar, featuring a talk by** Kevin Libuit** from _Theiagen Genomics_. Kevin shares the progress made by the working group on “**Best Practices for Public Health Bioinformatics Pipelines**“. The field of public health bioinformatics relies heavily on the development and sustainability of high-quality software to support efforts in disease surveillance, outbreak investigation and genomic research. However, the lack of standardized guidelines and best practice for the development of software in this domain inhibited progress towards easily-accessible, reproducible, interoperable, and secure bioinformatics for pathogen genomics.
Posted: 3/3/2024
Part I: Molcular Biology of Viral Genomics Fundamentals
Organization: Washington State Department of Health
Part I: Molecular Biology of Viral Genomics - Briefly explain why molecule biology concepts are relevant to understanding viral genomics - Define the dogma of molecular biology as it relates to the flow of genetic information - Connect the concepts of replication, transcription, and translation as it relates to virus biology and the changes that we could see in the genome - Describe features of DNA - Discuss directionality and explain its importance and relevance to viral genomics - Briefly summarize the processes of replication, transcription, and translation
Posted: 8/31/2024
Part II: Viral Genome Overview
Organization: Washington State Department of Health
Part II: Viral Genome Overview - Discuss the type of genetic material viruses can be made of - Give some examples of viral genome structures - Explain how classifying viruses by replication strategies can be beneficial to understanding viral genomes - Discuss what makes viral genomes compact and efficient - Discuss how viral genomes are a biological parts list - Provide some examples of information that is encoded in a viral genome and what information is not encoded in a viral genome
Posted: 8/31/2024
Part III: Viral Genome Evolution
Organization: Washington State Department of Health
Part III: Viral Genome Evolution - Discuss how genetic variation can occur in viruses - Discuss the impact of reassortment on analyses - Define mutation rate and why it’s difficult to quantify - Discuss how genome sequences can allow us to infer an estimate of the substitution rate - Briefly explain how evolution can change viral populations, and how viral genomes evolve in response to selective pressure - Give examples of how viral genomes can adapt to host interactions
Posted: 9/30/2024
Part IV: Viral Genome Diversity
Organization: Washington State Department of Health
Part IV: Viral Genome Diversity - Explain how viruses can be diverse, and why understanding the biology of the viral pathogen you’re working with impacts how you think about and use the data - Explain how “sense” relates to viral genomes - Distinguish between positive-sense RNA and negative-sense RNA - Discuss some genomic elements of viral genomes - Discuss how families of viral groups can be similar and different in genome organization - Describe how the reproductive life cycle of a virus impact the changes we see in the genome - Discuss how whole genome sequencing only manages to capture a fraction of viral diversity
Posted: 10/21/2024
CSTE AMD Webinar Series: SARS-CoV-2 Variant Modeling in a Post-Pandemic World
Organization: Council of State and Territorial Epidemiologists
Program Area: AMD Speaker: Nicholas G. Reich, PhD | Professor of Biostatistics – University of Massachusetts, Amherst **Moderators**: Meagan Burns, MPH | Senior Informatics Epidemiologist – Massachusetts Department of Public Health Arianna Miles-Jay, PhD | Manager, Genomic Analysis Unit – Michigan Department of Health and Human Services
Posted: 3/17/2025
HIV Cluster Detection and Response
Organization: Council of State and Territorial Epidemiologists
**Speakers:** Arianna Miles-Jay, PhD | Manager, Bioinformatics & Genomic Epidemiology Unit, – Michigan Department of Health and Human Services. Speakers: Anne Marie France, PhD, MPH | Epidemiologist & Lead of the Cluster Detection and Molecular Epidemiology Team in the Detection and Response Branch of CDC’s Division of HIV Prevention. Lauren Ostrenga, MPH | HIV Surveillance Coordinator at the Louisiana Office of Public Health. **Objectives:** Join us for two wonderful presentations on HIV Cluster Detection and Response. Anne Marie France, PhD, MPH, from the Detection and Response Branch of CDC’s Division of HIV Prevention will present on Implementation of HIV Cluster Detection and Response in the United States. Lauren Ostrenga, MPH, from Louisiana Office of Public Health’s STD/HIV/Hepatitis Program will speak to HIV Cluster Detection & Data Dissemination Activities in Louisiana.
Posted: 4/23/2024
Applications of Web-Based Tools for Genomic Epidemiology
Organization: Council of State and Territorial Epidemiologists
**Speakers:** Krisandra Allen **Objectives:** Join the Centre for Genomic Pathogen Surveillance (CGPS) to walk through examples of how to answer real world epidemiology questions using web-based tools including dynamic data visualizations. Learning Objectives: Understand two types of epidemiologic questions that genomic data can be used to answer. Demonstrate how to import metadata into web-based tools for co-visualization with genomic data. Explain the importance of communication and integration of lab and epi data sources to accomplish genomic epidemiology.
Posted: 8/22/2023
Intuitive and Powerful Tools for the Molecular Epidemiology Space- Nextstrain and MicrobeTrace
Organization: Council of State and Territorial Epidemiologists
**Speakers:** Anupama Shankar, MSc, MS | Biologist – Division of HIV/AIDS Prevention, Intervention and Support Centers for Disease Control and Prevention Alli Black, PhD |Senior Epidemiologist – Washington State Department of Health
Posted: 4/25/2023
CSTE AMD Webinar Series: Combating Healthcare-associated Infections with AMD: Local and National Perspectives
Organization: Council of State and Territorial Epidemiologists
**Speakers:** Alison Halpin, Mary Hayden **Objectives:** Learning objectives: 1\. Describe how NGS is used as a tool for healthcare epidemiology. 2\. Review which types of NGS analyses can be used for in healthcare epi. 3\. Describe how molecular subtyping is used in healthcare epidemiology. 4\. Examine how the Regional Innovative Public Health Laboratory provides actionable data for public health use.
Posted: 3/7/2023
HantaNet: Uniting genetic and epidemiological data
Organization: Council of State and Territorial Epidemiologists
**Speakers:** Shannon Whitmer, PhD | Microbiologist – Viral Special Pathogens Branch, Diagnostics and Capacity Building Team, US CDC **Objectives:** Please join the Shannon Whitmer from the Centers for Disease Control and Prevention Viral Special Pathogens Branch explore how HantaNet can integrate epi and sequence data into a dashboard for data integration, visualization, and sharing. **Title**: HantaNet: Uniting genetic and epidemiological data **Moderators**: Meagan Burns, MPH | Senior Informatics Epidemiologist – Massachusetts Department of Public Health Arianna Miles-Jay, PhD | Manager, Bioinformatics & Genomic Epidemiology Unit, – Michigan Department of Health and Human Services
Posted: 3/21/2024
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