Need Help In Data Analysis?

DIEPS staff collaborate globally to help researchers conduct phylogenetic analysis, time-series analysis, and/or mathematical modeling and publish co-authored studies in peer-reviewed journals. To begin a discussion about how DIEPS might be able to provide assistance in an analysis, please provide detailed information about the proposed project in the fields below.

Please note that DIEPS has limited staff and may not be able to accommodate all requests. We will try to get back to you within one week of your application.

MISMS MinION Workshop – Colombia

Training Workshop for the Implementation of MinION Sequencing for Influenza Viruses 

February 6-8, 2020

Irotama Resort

Santa Marta, Colombia

Workshop Objective

This three-day workshop, held February 6-8th, 2020 in Santa Marta, Colombia, introduced new technologies and advanced informatics approaches that can be used for infectious disease genomic characterization in resource-limited settings. Using the portable, low-cost Oxford Nanopore MinION sequencing platform, we will introduce the essential laboratory and computational skills required to perform extensive genetic characterization of viral pathogens, using influenza A virus as a primary demonstration. Topics will include sample preparation, bioinformatics, and phylogenetic approaches to characterize newly sequenced sampled against publicly available data.

By the completion of the workshop, attendees were provided access and training to all essential bioinformatics tools required to establish real-time genetic characterization capabilities in their primary laboratories or at field sites using the low-cost Oxford Nanopore MinION sequencing platform. Best practices for implementing these new technologies in research, clinical, and public health laboratories were emphasized.

 

Instructors/staff:

Johns Hopkins University: Tom Mehoke, Peter Thielen

Fogarty International Center: Martha Nelson, Nidia Trovao

 

Workshop Agenda

Day 1 (Thursday Feb 6) 

Introduction to Genomics Technologies and Oxford Nanopore Sequencing

 

Time Event Presenter
9:00am Welcome and Introductions

  • Pre-session surveys
Peter Thielen
9:30am Low-Resource Genome Sequencing with Oxford Nanopore: Outbreak response and Influenza Applications  Peter Thielen
10:00am Data Analysis Objectives: Rapid Characterization and Consensus Sequence Generation Peter Thielen
11:00am BREAK
11:15am Rapid Talks: Single Slide Presentations from Attendees Attendees
12:00pm Lunch / Surveillance Meeting Field Trips

 

Day 2 (Friday Feb 7):

Laboratory Considerations and Basic Bioinformatics

 

Time Event Presenter
9:00am Practical Considerations: Establishing a Genomics Wet Laboratory

  • Efficient isolation of nucleic acids (DNA/RNA)
  • Targeted and untargeted sequencing approaches
  • Accurate quantification of DNA
  • Minimizing contamination
Peter Thielen
9:30am Concepts: Optimized Influenza A Virus Sample Preparation with Ligation reagents

  • Time- and reagent-optimizing considerations
  • Sequencing of influenza multi-segment PCR amplicons
Peter Thielen
10:00am BREAK
10:15am Hands on: Sequencing with the MinION Peter Thielen
11:45pm Data Manipulation and Exploratory Data Analysis

  • Complete consensus generation on generated data
Tom Mehoke
12:15pm Lunch
1:15pm Introduction to Phylogenetics Concepts

  • 101 talks on principles of phylogenetics
  • Common mistakes
Martha Nelson
2:15pm Using data produced by the MinION

  • Outline of general analysis workflow
  • Initial processing vs. in depth analysis
Tom Mehoke
2:45pm BREAK
3:00pm Hands-on: Processing data produced so far

  • Visualization of processed data
  • Introduction to folder hierarchy
  • Consensus sequence generation
Tom Mehoke
5:00pm Day 2 Review

Revisit data from the earlier sequencing run

Recap of topics

Post-session evaluations

 

Day 3 (Saturday Feb 8):

Phylogenetics

 

Time Event Presenter
9:00am Identifying Genomes and Building a Genetic Sequence Dataset

  • Genbank
Nídia Trovão
10:00am Multiple Sequence Alignment and Building a Phylogenetic Tree

  • AliView
  • MEGA
Nídia Trovão
11:00am BREAK
11:15am Post-processing of Phylogenetic Trees

  • FigTree
Martha Nelson
12:15pm Lunch
1:15pm How To: Interpret a Phylogenetic Tree Martha Nelson
2:15pm Final Recap

  • Open Discussion: Moving forward with resource development and applied research
  • Post-session evaluations
3:00pm BREAK
3:15pm Time to Work With Your Own Data All instructors available for questions

 

 

 

 

MinION Workshop – Colombia

MISMS Influenza Workshop – Zambia

POSTPONED

New date TBD

 

FIC MISMS workshop 

Influenza epidemiology, digital surveillance and evolutionary dynamics

March 12-13, 2020

ANISE meeting, Livingstone, Zambia

 

Link for Registration

This training workshop is held in conjunction with the March 2020 meeting of the ANISE network in Zambia and follows scientific research sessions and training modules led by the GISAID and WHO teams earlier in the week.

Information on influenza epidemiology and evolutionary dynamics is particularly useful to guide intervention strategies, optimize surveillance, and vaccine design, but such studies remain scare in low-income settings. Digital surveillance uses novel data streams (Google searches, Twitter, data from participatory surveillance systems) to help monitor and forecast influenza activity in settings where traditional surveillance data may be lacking, sparse, or lag by several weeks. Phylogenetic analyses of influenza sequence data are important to shed light on the global, regional and local migration of influenza viruses, their evolution, and the match of circulating strains with available vaccines.

The objective of this two-day MISMS workshop is to train epidemiologists and virologists from Africa (particularly from countries with available data) on the use of the quantitative epidemiological methods for digital surveillance and forecasting, and on phylogenetic analyses for phylodynamics and phylogeography using the BEAST package.

This workshop will include two separate modules devoted to (i) epidemiology and (ii) phylogenetics. Both modules will include theory and practice sessions. Participants will be invited to work with their own data and with publicly available sample datasets.

Participants in the epidemiological module will be taught how to use different R packages for statistical analyses of influenza time series (lab-confirmed cases, ILI or SARI) and develop models using digital surveillance signals (Google, Twitter). They will learn how to use and analyse various Google tools, such as Google searches, Google correlates, and Google Trends. Short-term influenza forecasting models will also be presented. Participants will be walked through examples using sample datasets, and if time allows, a few hours will be devoted to the analysis of the participants’ own data. There will be a live demo of InfluenzaNet, an on-line platform for influenza participatory surveillance.

Participants in the phylogenetic module will learn how to prepare a sequence dataset, explored it using maximum likelihood phylogenies and use the BEAST platform to perform advanced phylogenetic analyses to understand the spatial and evolutionary dynamics of influenza viruses. BEAST is a cross-platform program for Bayesian analysis of molecular sequences using Markov chain Monte Carlo (MCMC) algorithms. Outputs include rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.

Participants will be provided a sample FASTA influenza datasets and walked through an example of BEAST analysis. An overview of the possible uses of BEAST will be discussed. If time allows, a few hours will be devoted to the analysis of the participants’ own data.

 

Faculty:

Trevor Bedford, Fred Hutchinson Cancer Institute, WA, USA (TBC)

Daniela Paolotti, Institute for Scientific Interchange, Italy

Mauricio Santillana, Boston Children Hospital, MA, USA (TBC)

Kaiyuan Sun, NIH-Fogarty, Bethesda, MD, USA

Nídia Sequeira Trovão, NIH-Fogarty, Bethesda, MD, USA

Cécile Viboud, NIH-Fogarty, Bethesda, MD, USA

MISMS Workshop – Zambia

Short-Term Visiting Fellows Program

The Division of International Epidemiology and Population Studies (DIEPS) has a long-standing tradition of hosting visiting international and US researchers for training in methods of analyzing infectious disease data and long-term collaboration and publication. Some of our past visitors are listed below:

Cheryl Cohen

Alice Fusaro

Aba Mahamat

Anthony Newall

Baltazar Nunes

Nesli Saglanmak

 

If you are interested in visiting us for an extended period of time, please complete the application below to describe your research interests. We typically accept 3-4 visiting researchers per year.

 

MISMS Influenza Workshop – South Africa

 

 

 

 

 

Register here (Closed)

Fogarty International Center, NIH – National Institute for Communicable Diseases

Training Workshop on Infectious Diseases Dynamics and Evolution

December 3-5, 2018

Johannesburg, South Africa

 

Workshop outline:

A better understanding of the epidemiology and evolutionary dynamics of infectious diseases is particularly useful to guide intervention strategies, optimize surveillance, and vaccine design, but detailed studies remain scare in low- and middle-income settings.

The objective of this 3-day FIC-NICD workshop is to train epidemiologists, microbiologists, virologists and public health professionals, on the use of the computational methods in infectious diseases. Participants will learn how to use computational methods to characterize seasonality, disease burden, transmission dynamics, molecular analysis and phylodynamics of viral infections, with key focus on influenza and HIV.

Participants will be invited to work with their own data and with publicly available sample datasets. The workshop will include 2 parallel tracks on epidemiology and phylogenetics.

Participants to the epidemiology module will be taught how to use different R packages for statistical and mathematical analyses of epidemiological data, and other tools (such as EpiPoi) to visualize and define influenza seasonality and epidemic periods, estimate excess mortality or excess morbidity, infer time trends, estimate the reproduction number of epidemics, and fit simple mechanistic transmission models to data.

The phylodynamics/phylogeographic module will train participants in the use of the BEAST platform, to perform advanced phylogenetic analyses aimed at deciphering the spatial and evolutionary dynamics of viruses; influenza and HIV will be used as case studies. BEAST is a cross-platform program for Bayesian analysis of molecular sequences using Markov chain Monte Carlo (MCMC) algorithms. Outputs include rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.

Participants will be provided a sample FASTA sequence datasets and walked through an example of BEAST analysis. An overview of the possible uses of BEAST will be discussed. If time allows, a few hours will be devoted to the analysis of the participants’ own data.

 

Faculty:

Philippe Lemey, University of Leuven, Belgium

Martha Nelson, Fogarty International Center, NIH

Amanda Perofsky, Fogarty International Center, NIH

Juliet Pulliam, SACEMA, South Africa

Andrew Rambaut, University of Edinburgh, Scotland

Nidia Trovao, Fogarty International Center, NIH

David Spiro, Fogarty International Center, NIH

Kaiyuan Sun, Fogarty International Center, NIH

Cecile Viboud, Fogarty International Center, NIH

 

Draft Agenda overview

 

Monday, December 3

Morning. Introductions and Research highlights (plenary; will include examples from influenza, HIV, animal-human interface and emerging infectious)

Afternoon: Break into phylogenetics and epidemiology groups

Start of 101 talks on principles of phylogenetics and disease modeling

Late afternoon: Software installation checks.

 

Tuesday December 4: 101 talks and software demonstrations

Epi track:

  • Principles of time series analyses & wavelets.
  • R estimation, SIR and TSIR models, network models
  • Worked out example of time series/seasonality analyses in R**.
  • Demonstration of EpiPoi, free software for visualization and analyses of spatio-temporal datasets
  • Building models with increasing levels of complexity: HIV case study

Phylogenetics track:

  • Principles of phylogenetics.
  • Sequence alignments, maximum likelihood trees, detection of temporal signals.
  • What you need to know before using BEAST + worked-out BEAST example
  • Post-processing of BEAST trees

** For those who need more than a refresher in R, additional examples (and time) are available to become more familiar with R, in break-out groups.

Tuesday evening: Maria Giovani, NIAID programmes

 

Wednesday December 5: Presentations and hands-on practice with own data

Morning: Short presentations by participants (plenary or break-out groups, depending on size)

Remaining analytical topics to be covered

Afternoon: Work with your own data in small groups, facilitated by instructors.

MISMS South Africa 2018 Registration

MISMS Influenza Workshop:

Fogarty International Center, National Institutes of Health

December 3-5, 2018, Johannesburg, South Africa