Martha Nelson

Short-Term Visiting Fellows Program

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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

Magnus Gottfredsson

Jong-Won Kang

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.

 

Martha Nelson

Hiring post-doctoral fellows

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Post-doctoral fellowships · Infectious Disease

Fogarty International Center · Bethesda, MD

The Fogarty International Center (FIC), at the National Institutes of Health (NIH) in Bethesda, MD, is seeking post-doctoral fellows to study the epidemiology and evolutionary dynamics of human pathogens on a global scale. The position is within the Division of International Epidemiology and Population Studies (DIEPS), which has a long history of running computational projects and field studies, developing data-rich models, managing international collaborations and training programs, and translating research findings to policy, particularly in the area of influenza (see MISMS project). In addition to conducting primary research, the candidate(s) will have the opportunity to be an instructor at international training workshops. Successful candidates will work in the historic Stone House on the NIH Bethesda campus and enjoy fruitful interactions with the dynamic community of NIH intramural scientists. The candidate will participate in international research networks that generate data, for example NIAID’s Centers of Excellence in Influenza Research and Surveillance (CEIRS) and the RSV DIVERGE project. DIEPS has broad research interests that include disease modeling and forecasting, anti-microbial resistance, and pathogen evolution at the human-animal interface.

Successful candidate(s) will have a doctoral degree (PhD or equivalent) in computational or evolutionary biology, bioinformatics, or related quantitative fields. Strong quantitative and communications skills are required. The ability to critically evaluate data, publish scientific papers, work in interdisciplinary environments, and present at conferences is essential.

Interested candidates should contact Martha Nelson (nelsonma@mail.nih.gov) or Cécile Viboud (viboudc@mail.nih.gov). Applications should include a cover letter, a CV, a brief statement of research interests, and the names (and contact info) of three references. Salary will be commensurate with experience and NIH guidelines. US and non-US citizens are encouraged to apply.

 

Martha Nelson

Developing influenza vaccines for swine in Mexico

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MISMS researchers characterized the high levels of genetic diversity of influenza viruses circulating in swine in Mexico, working closely with veterinarians in Mexico and with funding from a major animal vaccine manufacturer. The study is available online at Emerging Infectious Diseases and will be published in print next month. The study was a collaboration between the NIH, USDA, and University of Minnesota, which performed the genetic sequencing of the viruses. USDA performed antigenic cartography to visualize how the host immune system ‘sees’ virus lineages differently. MISMS staff performed the phylogenetic analysis, which showed that the viral diversity seen in Mexican swine comes primarily from humans (reverse zoonosis) and US exports of live hogs to Mexico. The direction of trade of live hogs between countries is critical in shaping where viruses are found globally.

 

Martha Nelson

Special Issue on 1918 Centennial in AJE

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In commemoration of the centennial of the 1918 influenza pandemic, the American Journal of Epidemiology convened a collection of 12 articles on the epidemiology of the pandemic, led by MISMS staff Cecile Viboud and Justin Lessler. The 12 articles consider a growing body of work on the archeo-epidemiology of past pandemics, the socioeconomic and geographic drivers of influenza mortality and natality impact, and renewed interest in immune imprinting mechanisms and the development of novel influenza vaccines. They also highlight persisting mysteries in the origins and severity of the 1918 pandemic and the need to preserve rapidly decaying information that may provide treasure troves for future generations.

Martha Nelson

MISMS accomplishments highlighted for Fogarty’s 50th birthday

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Fogarty’s team of infectious disease modelers used the occasion of the Center’s 50th birthday to review its achievements, consider lessons learned, and explore possible future directions in an article published by the journal Epidemics and featured in Global Health Matters. The article highlights the exceptional productivity and ROI of the MISMS program, including a cost-per-article published of less than $8,000.

 

 

Martha Nelson

Cities’ population and transportation patterns affect how flu epidemics play out

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MISMS researchers published a study in Science showing that winter flu epidemics in smaller cities tend to have higher flu epidemic intensity than in larger cities highly connected by extensive transportation systems, which have longer, more consistent flu seasons.

The study has important implications for understanding how cities of different sizes should prepare for annual flu epidemics. Smaller cities with more spiked epidemics may need to increase their surge capacity, while larger cities may need to prepare for epidemics that last for many months.

Martha Nelson

Register for the 2018 MISMS training workshop in South Africa

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Just Announced:

  • December 3-5, 2018
  • Training Workshop on Infectious Diseases Dynamics and Evolution
  • Hosted by the National Institute for Communicable Diseases (NICN)
  • Johannesburg, South Africa
  • Registration  (Closed) and more information here
Martha Nelson

MISMS Influenza Workshop – South Africa

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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.

Martha Nelson

MISMS South Africa 2018 Registration

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MISMS Influenza Workshop:

Fogarty International Center, National Institutes of Health

December 3-5, 2018, Johannesburg, South Africa

Martha Nelson

2018 Summer Intern Class

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Congratulations to our 2018 Summer Interns Class!

Five college students joined DIEPS this summer to work on MISMS projects.

MISMS interns Allison Randy-Cofie, Garret Kern, Felix Wu, Anne Lheem, Josh Grubbs (front row, left to right)

Allison Randy-Cofie, Amherst College ’19

Project: Bioinformatics. Generating sub-sampled data sets of influenza A viruses from human, swine, equine, avian and canine hosts for all segments of the viral genome

Anne Lheem, Harvard University ’21

Project: Epidemiology. Identifying associations between influenza virus activity and antibiotic use on a global scale.

Felix Wu, Amherst College ’22

Project: Bibliometrics. Conducting a review of the publications produced by the MISMS and RAPIDD programs to assess their scientific impact and geographical diversity of co-authorship (published in Epidemics).

Garret Kern, Brown University ’22

Project: Bioinformatics. Creating a tool in Python to facilitate the downsampling of large genetic data sets by specified criteria (host, location, time, etc.). Creating R code to visualize pathogen data collected in humans and animal hosts (published in the Journal of Infectious Diseases). 

Josh Grubs, Duke University ’18

Project: Biosafety. Creating protocols for chemical safety for use in Pakistan and other developing countries.