Monthly Archives: October 2019

Manging Software Projects with Git and Github, 11/4

Category : News/Events

Join us on Monday November 4th from 12-12:50 to hear from Steve Pittard about Manging Software Projects with Git and Github. Lunch will be provided.


Professional Healthcare Worker – Epidemiology, closes 11/3

The Georgia Department of Public Health is the lead agency entrusted by the people of the state of Georgia with the ultimate responsibility for the health of communities and the entire population.

The agency is seeking one highly qualified candidates for the position of Professional Healthcare Worker within the Epidemiology Section/Office.

The incumbents will be employed for approximately 15-20 hours per week. The pay will be $14 an hour. The schedule is flexible, but the employees must conduct interviews, enter data, and perform other activities at the Department of Public Health offices in downtown Atlanta during normal business hours for more than half of the total weekly work time. Additional interviews and duties can be conducted during weeknight and weekend hours. This job can potentially include more hours during the summer and holiday breaks.

Job Responsibilities
The Georgia Department of Public Health is looking for a current MPH students or an incoming MPH-seeking students to assist in patient interviewing, data entry, data collection, data management, medical chart reviews, and other clerical work. This position include calling cases and controls to conduct interviews related to communicable disease surveillance, special studies, and outbreaks. Data entry and management responsibilities will include using various databases, such as Excel, Access, and the Georgia electronic notifiable disease system. Although the person filling this position will have the opportunity to learn about notifiable disease surveillance in general, the focus will be following up on reportable enteric disease cases and invasive bacterial disease surveillance conducted by the Emerging Infections Program.

This position could fulfill MPH practicum requirements. As part of a practicum experience, the student will:
1. Gain an understanding of how notifiable disease surveillance functions.
2. Understand how outbreak investigations are conducted.
3. Have an opportunity to analyze notifiable disease surveillance, study, and/or outbreak data.

This position are temporary and intended for students enrolled in an accredited public health degree program as the intention of the job duties is to provide applied public health knowledge and skills. This position is also limited to 2 years contingent on availability of funds.

Minimum Qualifications
Bachelor’s degree and one year of work related experience
Four years of work related experience at an executive level

Preferred Qualifications:

Students seeking Master in Public Health or related degree from an accredited degree program
Experience working with databases
Experience conducting interviews

To apply, click HERE.

Health Planner III, Maryland Department of Health

Category : Alumni

Main Purpose Of Job
The main purpose of this position is to assist in the development of plans, monitor grants related activities, including programmatic, fiscal and contractual to ensure compliance with federal, state and Departmental requirements. This position also oversees specific activities related to Health System Preparedness in Maryland as instructed and assists in the development of health systems emergency preparedness, response and recovery plans.

Minimum Qualifications
Education: Possession of a Bachelor’s degree from an accredited college or university in Health Planning, Public Health, Health Science, Hospital Administration, or Health Care Administration.

Experience: Three years of professional experience in health planning.

Notes: 1. Possession of a Master’s degree from an accredited college or university in a field identified above may be substituted for one year of experience.

2. Possession of a Doctorate degree from an accredited college or university in a field identified above may be substituted for three years of experience.

3. Possession of a Bachelor’s degree from an accredited college or university and one year professional experience in health planning may be substituted for the required specialized Bachelor’s degree.

4. Applicants may substitute experience in health or hospital administration for the required experience on a year for year basis, provided the applicant has at least one year of professional experience in health planning.

5. Health Planning experience obtained in a State Health Planning and Development Agency or in a Health System Agency as designated by Public Law 93-641 may be substituted at the rate of three months for four months of the required experience.

6. General Health Planning experience as required above is defined as experience obtained in a professional capacity in an operation established solely for the delivery/evaluation of health services (e.g. Hospitals, H.M.O.’s, Insurance Companies). Such experience must have been the primary purpose of the position during the time in question. Health Planning duties which are performed only incidentally are not considered as qualifying.

The desired candidate should have experience in the development of health systems emergency preparedness, response and recovery plans.

For more information and to apply, click HERE.

2nd Year GLEPI MPH: Rutika Raina

Category : #IamEmoryEPI , GLEPI

For this week’s #IamEmoryEpi spotlight, we met up with Rutika Raina!

Tell us where you went to school:

I did my undergrad in India, where I studied Biotechnology.

What are your primary research interests?

My research interest is in non-communicable diseases; particularly psychiatric illness and neurological disorders. I am doing my thesis on Schizophrenia.

What did you do this past summer?

I was working at the Erasmus Medical Center in the Netherlands at their psychiatric epidemiology department during summer. I loved every bit of my experience in the Netherlands. I actually got to take some time off to roam around and I went to Belgium and Italy for vacation; attended the pride parade in Amsterdam.

How did you find the research that you are currently conducting?

I found my practicum by literally sending an email to the HOD at their Epi Department and things kind of worked smoothly from there. I had an interview and I got in and they actually reimbursed me for my travel expenses.

What is your favorite part about being at Emory?

My favorite part about doing my MPH at Emory is the diversity. The people that I have met and the friends that I have made; the relationships that I have forged, these are the things I am going to be carrying away after I graduate. Oh, also the food that I have had from different cultures and backgrounds. I love it! Obviously, some hard skills too but that’s why we are here, I guess!

Do you have any advice for MPH students?

My advice to the first years would be to take advantage of every opportunity to explore their interests. Graduate school is a lot of work but make sure to breathe once in a while and just broaden your perspective because Rollins provides you with so much that it is overwhelming at times.

What are three fun facts about yourself?

1. I am a trained dancer and I don’t miss an opportunity to dance. I have danced for 6hrs at a stretch.
2. I love music to the extent that I absolutely dislike having music apps. I download physical files of each song that I like!
3. I have been a year early for all my high school years and even during undergrad because I was promoted to 1st grade directly since I had the skills required for it already at the age of 5. I might be one of the youngest in our cohort too (23 years!)


Humanitarian Logistics and Supply Chain Management in Emergencies, 11/8

Category : News/Events

The lecture will be held in the Rollins Auditorium on November 8th from 3-5 pm with a reception to follow. More information can be found in the flier above. 

Medicaid: The Policy and Politics of Health Reform, 11/19

Category : News/Events

RSVP to Nancy Sterk for the Michael M.E. Johns, MD Lecture on Helath Policy being held on Tuesday November 19 at 3pm.

Epi Alumnus Datta Patil, Award of Distinction

Category : News/Events

After completing his MPH at the Rollins School of Public Health, Dattatraya Hari Patil became the lead biostatistician in the Department of Urology, where he has had a tremendous impact on urological research and education.

Patil holds exceptional skills in statistical analysis and data management and has employed them for a number of projects. For example, he successfully instituted a statistics and clinical data repository and provides an analytic perspective to urological investigations ranging from health services research in cancer and reproductive medicine, to the development of biomarkers for guiding clinical decision-making, to interrogating the immune response in cancer.

His work has resulted in multiple peer-reviewed journal articles as well as grants from the National Institutes of Health and the American Cancer Society. He has contributed to more than 100 scientific publications and has given numerous research presentations at institutional, regional and national meetings. His presence also has been pivotal to the recruitment of several faculty who now constitute a vibrant critical mass of investigators.

Patil has contributed to Emory’s educational mission by helping train others in biostatistics and clinical trials. He has impacted urology graduate medical education through his partnership with 11 different urology residents on research projects. Nearly all of his collaborations have led to the learners presenting their work at regional or national meetings and in peer-reviewed publications. He also leads an annual didactics course which has been very well-received by the residents.

Senior Data Scientist, CAMRIS

Category : Alumni

CAMRIS is an international development and research firm that realizes innovative solutions to health and development challenges through high-quality, cost-effective program and research management services. With experience working in more than 80 countries, we combine our proven systems with today’s most effective, evidence-based best practices to improve the lives of people around the world.

The United States Agency for International Development (USAID) has contracted through Social Solutions International partnered with CAMRIS, to recruit and hire qualified individuals for the following position:

Office of Professional Development and Management Support, Bureau for Global Health, United States Agency for International Development

Title: Senior Data Scientist

GS:14 $117,191.00-$152,352.00

Application Deadline:Open until Filled


The U.S. President’s Malaria Initiative is the US Government’s (USG) flagship global malaria initiative led by USAID and implemented together with the Centers for Disease Control and Prevention. The Initiative is results-based, focused, and exhibits a high level of financial and programmatic accountability. In 2015, PMI launched the next six-year strategy, setting forth a new bold vision, and an ambitious goal with specific objectives. The PMI Strategy for 2015-2020 takes into account the progress over the past decade and the new challenges that have arisen, and reflects the U.S. Government’s commitment to work with PMI-supported countries and partners to further reduce malaria deaths and substantially decrease malaria morbidity working toward the long term vision of a world free of malaria.


The Bureau for Global Health (GH) serves as the Agency’s primary source of intellectual capital, technical leadership, and donor coordination for the health sector. GH is vested with the responsibility for advancing field-relevant, state-of-the-art research and the transfer of new technologies and approaches to field programs and in technically and programmatically supporting USAID Mission health program implementation in the field. The Office of Infectious Disease (ID) is one of GH’s eight offices. The Malaria Division is one of four divisions of the ID Office. Leadership, management, and oversight of PMI are carried out from the Malaria Division under the leadership of the US Global Malaria Coordinator as are management of USAID’s malaria research investments (most notably vaccine, drug, and insecticide research programs) and USAID’s global partner engagement including WHO and RBM Partnership to End Malaria.

To succeed in eliminating malaria, countries and their partners need to deploy the right resources at the right place and at the right time. By getting better, more accurate insights from existing data and accelerating the data-to-action cycle, countries and their partners can better respond to changes in on-the-ground conditions. That is why, in 2018, PMI began a major transformation toward greater use of data to inform decisions on resource allocation. As part of this new effort, PMI launched a new quarterly reporting process to ensure operational decision-making is based on timely and granular malaria data. In addition, at the headquarters level, PMI is developing a web-based data platform (“PMI Data Lake”) with analytics tools that will facilitate the triangulation and use of relevant datasets, including visualizations of epidemiological, supply chain, entomological, demographic, programmatic, and financial data. Building on decades of investments in malaria surveillance, monitoring, and evaluation, PMI is also expanding its support for the strengthening of malaria-related data systems and building institutional capacity within ministries of health and national malaria control programs to improve data quality and use.


As a key member of the Data Integration team, the Senior Data Scientist will provide subject matter expertise to support PMI’s increased focus on enhancing data-driven decision-making internally and externally within focus countries.

Specifically, the Senior Advisor will:

Technical Leadership

Carry out rigorous, quantitative analyses and triangulation of data from a variety of sources (e.g. financial, programmatic, epidemiological, entomological, supply chain, demographic) to unearth implementation obstacles and opportunities, and employ cutting edge approaches and tools to generate compelling data visualizations.
Undertake innovative applied statistical and computational methods and application of model-based statistics, addressing issues such as sample bias, spatial dependence, and model validation, to better map malaria related data.
Implement, document, and test relevant computer code (in R, Python, C++, SQL or equivalent) to make the new methods and model features available to the broader team and broader audiences.
Perform data quality checks on existing datasets used in epidemiological and statistical analyses and improve existing tools for automating data validation processes.
Lead discussions and communicate highly technical information to both subject matter expert and non-expert audiences about quantitative analyses in order to interpret, vet, improve, and finalize results, and to formulate sound conclusions.
Actively engage and coordinate efforts with the Malaria Modeling Consortium to integrate methods and results of separate workstreams.

Country Support

Provide technical and programmatic support to one or more PMI focus countries and participate as an integral member of one or more inter-agency country support teams.
Provide guidance and support to Missions and PMI country teams on the development of annual country malaria operational plans and assist in monitoring and tracking overall progress of PMI plans and activities.
Provide advice and technical assistance to Missions involved in malaria efforts, particularly the PMI-targeted countries in sub-Saharan Africa.
Provide support to Missions by participating in country support teams, reviewing mission strategies and annual reports and helping them to meet needs for technical and programmatic support.


Minimum of a Master’s degree (PhD preferred) in applied quantitative discipline such as, but not limited to, statistics, economics, computer science, ecology or epidemiology from a recognized institution.
9 Master’s degree and 9+ years relevant experience or equivalent combination of education and experience or Bachelor’s and 11 years.
Practical experience in statistical inference, space-time mathematical models, or infectious disease modeling. Experience with machine learning and data mining
Extensive experience with data wrangling, analysis and visualization using leading tools (such as at least of the following Tableau, Power BI, R, D3.js, or similar). Data analytics and visualization proficiency will be tested.
Demonstrated ability to securely and efficiently manage large, disparate datasets, and problem-solving skills working on complex projects in a highly sensitive environment.
Experience facilitating data analysis projects through rapid prototyping sprints, iterative design and execution, delivery and on-going support in a dynamic and agile environment with changing requirements and priorities.
Experience with spatial data objects (e.g., shapefiles, rasters), survey data (e.g. DHS, MIS) and/or administrative data (e.g., HMIS, DHIS2) from health facilities is preferred.
Ability to work under pressure and in teams.
Ability and willingness to travel internationally, approximately 15%.
US Citizenship or US Permanent Residency.
Ability to obtain and maintain a Secret security clearance or at minimum a FAC.

To apply, click HERE.

Mathematical modeling of host-parasite dynamics, PhD positions

Category : Alumni

The Hall Lab ( is seeking to recruit Ph.D. students who are passionate about mathematical modeling of host-parasite dynamics for admission in fall 2020. Successful applicants will join multi-disciplinary teams working on exciting projects funded through the National Science Foundation’s Dynamics of Integrated Socio-Environmental Systems, Ecology and Evolution of Infectious Diseases, and Population and Community Ecology programs. Positions are available for the following three projects:

• Modeling habitat and coinfection as drivers of heterogeneity in infection processes, applied to transmission of Puumala hantavirus in voles in Finland. For project details, click HERE.

• Modeling the socio-ecological dynamics of land use change and infectious diseases, with application to transmission of Chagas disease and leishmaniasis in Panama. For project details, click HERE

• Modeling interactions between resident and migratory populations and the consequences for parasite infection, with application to North American monarch butterflies and their protozoan parasites. This position will be co-mentored by Dr Sonia Altizer ( HERE for project details.

Students will join the world-class Ecology graduate program at the Odum School of Ecology (, and may also be eligible for admittance to the NSF-funded Graduate Research Training program in Interdisciplinary Disease Ecology Across Scales ( or the Integrative Conservation Program ( at UGA. We seek motivated graduate students with strong interests in applying mathematical models to ecological and epidemiological problems. Prior experience of working with mathematical models is highly desirable. Interested applicants should send a cover letter indicating their research and training interests, and a copy of their CV, to rjhall [at] uga [dot] edu. Applications from students from diverse and underrepresented backgrounds are especially welcome.

For more information, click HERE.

Recruiting 26 PhD students, in the Netherlands

We are now recruiting 26 PhD students for our NWA project – Preparing for vector-borne virus outbreaks in a changing world – a One Health approach.

Preparing for vector-borne virus outbreaks in a changing world: an One Health Approach

The Netherlands, with its dense population of humans and livestock, international transport and travel hubs, and water-dominated landscape is particularly vulnerable to infectious disease outbreaks. The One Health Consortium aims to understand if and how changes in climate, farming, water management and travel lead to mosquito-borne disease outbreaks, to be better prepared.

Interacting changes
Infectious disease outbreaks are increasingly common due to multiple, interacting global changes and developments in the human, animal or environment domains.

These changes can trigger processes that disturb the fragile balance in the complex human-animal-environment ecosystem, up to the point where the conditions are created for (new) infectious disease outbreaks, in animals and/or humans. In these situations, the state of the system has reached a pathogen-specific vulnerability threshold ( ‘tipping point’), making the system receptive to outbreaks of that pathogen if it is introduced. The Netherlands, with its dense population of humans and food animals, international transport and travel hubs (Schiphol, Rotterdam), and unique water-dominated landscape is particularly vulnerable to the occurrence of such tipping points and hence, outbreaks of (newly emerging) infectious diseases. In this project we will consider four change scenarios that could lead to the occurrence of such tipping points and disease emergence:

changes in the climate,
changes in water management,
changes in farming methods and
changes concerning international travel and import risks.
Despite this expected vulnerability, emerging disease outbreaks in the Netherlands are still relatively rare. We currently study these outbreaks – when they occur – reactively, individually and within relatively isolated silos (e.g., human vs animal vs ecological health, academic research vs public health research, public vs private sector). This ad-hoc, reactive and fragmented approach is ineffective and inefficient. Instead, the partners collaborating in this project will adopt a pro-active, integrated, multisectoral, One Health approach in studying emerging infectious disease outbreaks.

We will develop and implement a forward-looking integrated research agenda, measuring and modelling how projected demographic, climatological, ecological, and planological changes will impact the risk of emergence of infectious diseases in the Netherlands, and translate this understanding into effective, integrated outbreak preparedness and response actions.

Focus on vector-borne diseases (VBD)
To prevent spreading our efforts and resources too thinly, we will focus our research agenda on a specific category of infectious diseases, namely vector-borne diseases (VBD), which are particularly relevant to the Netherlands, due to its water-dominated ecosystems and abundant wildlife as potential amplifying hosts. VBD are infectious diseases that are transmitted through arthropods (e.g. mosquitoes). They have been expanding massively in (sub)tropical regions of the world through trade and habitat changes.

Scientific and societal breakthroughs we aim to achieve
Our ambition is to prepare for VBD outbreaks in a rapidly changing environment. The One Health Consortium will do this by

providing pathogen specific and generic early warning indicators that measure whether our human-livestock-wildlife ecosystem is (becoming) vulnerable for VBD outbreaks,
developing novel catch all tools for outbreak detection and risk assessment,
translating the knowledge into interventions based on in depth knowledge of the entire ecosystem and interactions in which such outbreaks may occur.
Our approach consists of four complementary, interacting pillars. The One Health Consortium will gain a deep understanding of suitability of ecosystems in the Netherlands for VBD introduction, circulation, and expansion, and – conversely – the actionable factors that determine ecosystem resilience.

Pillar A: Ecosystem mapping

PhDs will be involved in studies aimed at mapping at high-resolution the complex interplay between factors that drive arbovirus introduction, circulation and expansion in the Netherlands. They will be involved in a series of uniquely interconnected research studies addressing reservoir hosts, disease hosts, viruses, vectors, and their interactions, and through their work provide critical baseline data for the PhDs in pillar B, responsible for model development.

Wild-animals are important as reservoir for arboviruses, both by introducing viruses through migration, and by serving as amplifiers of locally present viruses, if conditions are favourable. In addition, specific vectors are needed for arbovirus establishment. The group of PhDs involved in this work will jointly design smart surveillance strategies, involving well-trained citizen scientists coordinated by Vogeltrekstation, as well as studies in dead birds and other wild-life reported to the Dutch Wildlife Health Centre. Where needed, this will be complemented with targeted sampling of rodents, bats, and wild herbivores to provide information regarding circulation of (emerging) arboviruses. Dried blood spot samples, throat- and cloacal swabs will be tested for antibodies and/or target viruses, using protein microarrays and multiplex PCRs, developed as part of this project (Pillar D).

Analytical methods will be harmonized across species, including humans. Spatial and temporal avian host dynamics will be studied through citizen-science projects combined with detailed longitudinal studies in selected host species and in relation to virus exposure. We will gather data on density and movements of competent avian hosts for (invasive) mosquito vectors for animal and human AVD by combining and modifying existing citizen science projects (Sovon, Vogeltrekstation, Eurobirdportal, Trektellen) to monitor avian host occurrence in time and space. For rodents, bats and mammals, data will be gathered through “” and the Network Ecological Monitoring of CBS and through direct consultation of landowners that use large grazers as management tool.

If an actual VBD outbreak occurs in the Netherlands during the project period, the efforts and associated resources will be realigned to target the specific disease, if agreed with the funder and in collaboration with co-financing partners with a mandate for outbreak response. Sanquin and the blood bank of Curacao will prepare a rapid response protocol for population exposure testing during a health threat, and will provide access for establishing baselines for systems serology studies. To do this, joint preparedness protocols will be developed under coordination of PhD project 21.

PhD projects 1 through 5 are tightly linked and will collaborate closely to optimise sampling of various taxa and to allow for cross-taxa analyses and integration of data from virus phylogeny and pathogenicity to vector and host population dynamics and, ultimately, risk mapping and early warning.

PhD vacancies
PhD position 1: Citizen science for mosquito surveillance

PhD position 2: Wildlife surveillance

PhD position 3: Impact of emerging arboviruses on wild bird populations

PhD position 4: Tracking of movement, density and mortality of susceptible amplifying hosts (birds, rodents, bats, mammals)

PhD position 5: Dynamic risk based early warning risk maps

PhD position 6: Travelers as sentinel and source of arboviruses

PhD position 7: Citizens and surveillance with focus on high schools

PhD position 8: Arbovirus impact in livestock

Pillar B: Forecasting and early detection

PhDs will be involved in studies aimed at mapping the complex interplay between factors at high-resolution that drive arbovirus introduction, circulation and expansion in the Netherlands. They will be involved in a series of uniquely interconnected research studies addressing reservoir hosts, disease hosts, viruses, vectors, and their interactions, building from field and experimental data (collected in Pillars A and D), supplemented with data relevant to model VBD life-cycles collected from public sources (e.g., KNMI, CBS, literature, data from the EDEN/EDENext EU-funded projects). We will develop a method and practical tools for early warning to quantify and predict when the critical emergence threshold will be reached for VBD. The model-based approach will be used to analyse scenarios that could lead to disease emergence: 1) changes in climate, 2) changes in water management, 3) changes in farming practices, and 4) changes in importation risk. Critical knowledge gaps for the change scenario’s will be addressed through targeted experimental studies that generate essential data for the scenario modelling.

PhD vacancies
PhD position 9: Tracing and retracing mosquito-borne disease emergence

PhD position 10: Tools to explore risk of emergence of vector-borne diseases in ecosystems

PhD position 11: Generic early warning indicators for vector-borne infections

PhD position 12: Predictors of tipping points of mosquito populations in a changing world

PhD position 13: Vector competence studies in change scenario’s

PhD position 14: Vector immunity in change scenario’s

PhD position 15: Experimental work on effects of global change scenarios on vector population parameters

Pillar C: Impact and severity assessment

In Pillar C we address key knowledge gaps that are crucial to model the potential impact of an outbreak through a suite of in vitro and in vivoexperiments in mosquitoes and (reservoir and disease) hosts, respectively. The work in pillar c will address a select group of critical parameters to answer key questions for risk assessment: 1) what vector and vertebrate species can be infected, 2) can the virus efficiently spread between vectors, animals and humans, and 3) can the virus cause (severe) disease in animals or humans?

PhD vacancies
PhD position 16: Prediction of host range and reservoir potential

PhD position 17: Understanding the role of vector, host and virus variations in transmission and disease

PhD position 18: Models to study and prioritize neuropathogenic arboviruses

PhD position 19: Role of host innate immune responses and arbovirus innate immune evasion in transmissibility, host range and disease outcome

PhD position 20: Arbovirus systems serology: antibody profiling for exposure and impact assessment

Pillar D: Interventions

The findings from the studies in pillars a, b, and c will be used to guide development of targeted early warning systems and tools for rapid assessment of risk of emerging VBD to humans and animals, to be transferred to institutes with primary responsibility for early warning.

A cross-cutting toolkit of advanced assays will be developed, including targeted and metagenomic NGS, protein microarrays, eDNA metabarcoding, targeted to field studies and for rapid outbreak response. To allow deployment for use in regions with limited research infrastructure, such as the Dutch Caribbean, fieldable versions of the key assays will be developed. A suite of bio-informatic tools, coupled with a data sharing and analysis platform will be developed for the entire project in collaboration with the European data infrastructure EBI/ELIXIR and the COMPARE project.

PhD vacancies
PhD position 21: From theory to practice: what to do, when and where?

PhD position 22: Serological tools for surveillance across species

PhD position 23: Pathogen detection, metagenomics and genomic epidemiology for early warning surveillance

PhD position 24: Modulating mosquito immunity

PhD position 25: Arbovirus pathogenesis and development of innovative vaccine candidates

PhD position 26: Universal vaccines

Partners in this project: Erasmus Medical Center, Utrecht University, Wageningen University Research, Leiden University Medical Center, Radboud University Medical Center, NIOO, Avans Hogescholen, Leiden University, Utrecht University Medical Center, Deltares, RIVM, KNMI, Red Cross Blood bank foundation, Sanquin, Techncasium, NVWA, CEAB-CSIC (Spain), SOVON

For more information, click HERE.