Author Archives: Emma Butturini

Fall Course Offering, Info 550: Data Science Toolkit

Category : Student Opportunities

Instructor 

Dr. David Benkeser 

Course Description

This course is an elective for Masters and PhD students interested in learning some fundamental tools used in modern data science. Together, the tools covered in the course will provide the ability to develop fully reproducible pipelines for data analysis, from data processing and cleaning to analysis to result tables and summaries. By the end of the course students will have learned the tools necessary to: develop reproducible workflows collaboratively (using version control based on Git/GitHub), execute these workflows on a local computer (using command line operations, RMarkdown, and GNU Makefiles), execute the workflows in a containerized environment allowing end-to-end reproducibility (using Docker), and execute the workflow in a cloud environment (using Amazon Web Services EC2 and S3 services). Along the way, we will cover a few other tools for data science including best coding practices, basic python, software unit testing, and continuous integration services.

Pre-Requisites 

Many topics covered will involve the R programming language and so familiarity with R is needed (e.g., BIOS 544/545 or similar level of competency). Necessary skills include: reading data into R, basic data cleaning in R (e.g., subsetting data, finding missing values, merging data), operating on data.frames (e.g., changing column names, row names, summarizing rows/columns of data using simple statistics), basic graphics (e.g., plot or ggplot2).

Given the similarities between python and R, students with a background in python programming should also be equipped to succeed in the class, but will possibly require more effort to get up to speed with R.

Course Learning Objectives 

  • -Understand why automation is a key element of reproducible data science.
  • Develop reproducible workflows for data cleaning, analysis and report generation using the suite of tools learned in the class.
  • Understand the importance of version control and best practices for collaborative coding projects.
  • Use Docker to develop containerized workflows.
  • Set up and work in Jupyter notebooks.
  • Utilize cloud computing services for computation and storage.

Click here to view a PDF of the course syllabus! 

COVID-19 & the Cruise Ship Task Force, PHI/CDC Global Health Podcast

Category : News/Events

About the Podcast

The PHI/CDC Global Health Podcast features stories from the PHI/CDC Global Health Fellowship Program, a U.S. Centers for Disease Control and Prevention-funded program, implemented by the Public Health Institute, where Fellows are guided by leading global health experts from the CDC. Fellows work on the front lines of global health, developing the technical and professional skills needed to make meaningful contributions to today’s global health challenges.

Episode 1 Description

This episode features Riley Wagner, MPH, who is a Global Program Management Fellow for CDC’s Center for Global Health Headquarters in Atlanta, Georgia. Riley was the first of currently 24 Fellows to be assigned to CDC’s Emergency Operations Center in response to the COVID-19 Pandemic. Riley discusses her experience on the EOC and elaborates on her work with the Cruise Ship Task Force.

Click here to listen to the first episode in this exciting, new podcast! 

Epidemiologist II, Public Health Institute

Category : Alumni

Program Summary

PHI and OPHI are organizing teams of community contact tracing staff across Washington County, Oregon as a key strategy for preventing further spread of COVID-19.

The Epidemiologist conducts investigations used in the prevention and control of communicable or chronic diseases, injuries, and other health conditions and in the planning of health programs. This is a single classification and not part of a series. The Epidemiologist is an advanced- level professional classification. Positions in this class perform duties of considerable complexity, with the exercise of professional judgment regularly applied to complex and sensitive public health issues. The Epidemiologist works under the direction of a Research and Evaluation Supervisor. The incumbent in this classification will exercise coordination, leadership, and will supervise the Data Analysts.

Minimum Qualifications

  • Master’s Degree with a focus in epidemiology and at least two (2) years of work experience in epidemiology with a public health agency; OR A doctoral-level degree in epidemiology; OR Other non-epidemiology graduate degree or certification (e.g., RN, MD/DO, DDS/DMD, DVM, PhD, RS) with specific epidemiology training (e.g., MPH degree, CDC Epidemic Intelligence Service or CSTE Applied Epidemiology Fellowship).
  • Perform statistical analysis in Stata
  • Perform epidemiologic assessment and analysis:
  • Identify public health problems pertinent to the population;
  • Conduct surveillance activities;
  • Investigate acute and chronic conditions or other adverse outcomes in the population;
  • Apply principles of efficacious ethical/legal practice as they relate to study design and data collection, dissemination, and use;
  • Manage data from surveillance, investigations, or other sources;
  • Analyze data from an epidemiologic investigation or study

Important Information

  • This is a full-time (40 hours per week) position.
  • This is a time-limited position that is funded through December 30, 2020 with the possibility of being extended.
  • This is a remote position based in Washington County, Oregon.
  • As part of the application process, you must submit contact information for at least one managerial reference.
  • The offer of a position is conditional upon an applicant’s successful completion of a background check.

Apply 

  • Click here to read the full position description and apply online! 

 

Research Computing Specialist, University of Chicago

Category : Alumni

Center Overview 

The Chicago Center for HIV Elimination (CCHE), is situated within the Biological Sciences Division at the University of Chicago Medicine. CCHE aims to eliminate all new HIV transmission events by 2041. The University of Chicago’s position on the South Side makes it uniquely situated to test, treat, and prevent new HIV infections in a highly affected population. The South Side communities and majority Black suburbs connected to them to the South represents the largest contiguous Black population in the United States. By using our integrated HIV transmission elimination approaches, we are beginning to make new infections in these communities less frequent.

Responsibilities

The job uses best practices and knowledge of data manipulation, statistical applications, programming, analysis and modeling in order to implement projects related to the University’s various internal data systems as well as from external sources. The job is responsible for managing operational protocols.

  1. Has a deep understanding of methods to analyze complex data sets for the purpose of extracting and purposefully using applicable information. May develop and maintain infrastructure that connects data sets.
  2. Guides staff or faculty members in defining the project and applies principals of data science in manipulation, statistical applications, programming, analysis and modeling.
  3. Calibrates data between large and complex research and administrative datasets. Guides and may set the operational protocols for collecting and analyzing information from the University’s various internal data systems as well as from external sources.
  4. Designs and evaluates statistical models and reproducible data processing pipelines using expertise of best practices in machine learning and statistical inference. Provides expertise for high level or complex data-related requests and engages other IT resources as needed. Partners with other campus teams to assist faculty with data science related needs.
  5. Performs other related work as needed.

Minimum Qualifications 

  1. College or university degree in related field.
  2. Knowledge and skills developed through 5-7 years of work experience in a related job discipline.

Preferred Qualifications 

  • Master’s or higher in Computer Science
  • Working in a research environment, especially academic
  • Use of Python-based packages and platforms for analytic computing such as NumPy, Pandas and Dask
  • Working with medical record data and/or health research data including clinical trials and population-based studies of health; working with PHI
  • Use of REDCap for data capture; developing against its API
  • Using Continuous Integration/Continuous Delivery (CI/CD) in GitLab or GitHub
  • Use of PostgreSQL database
  • Open-source development

Apply

Click here to view the full position description and to apply online! 

Racial Disparities in COVID-19 Webinar, 5/27

Category : News/Events

Overview 

COVID-19 has highlighted the critical role that public health plays in the US and it also has demonstrated that this virus does not affect everyone equally. While it has affected the lives of all Americans, some racial and ethnic groups have been more likely to contract and die from COVID-19 than others. In this webinar, we will discuss some of the biological, behavioral and contextual factors that affect COVID-19 transmission and severity, and what public health professionals can and have been doing to reduce the impact of this virus on individuals and communities.

Register 

  • This is a live webinar on May 27, 2020 from 11:30am to 1pm ET.
  • Click here to register! 

 

#InsideAPE – Summer Spotlights

Category : #WeAreEmoryEPI

Now that the semester has officially ended and students look excitedly toward applying the skills and knowledge they have honed over their first year of epidemiology training, the Confounder Team is excited to reintroduce a familiar #IamEmoryEPI segment: #InsideAPE. We will be profiling students on a biweekly basis throughout the summer to share the important work they are doing, as well as their creativity and resiliency in adapting their APE project plans during the current pandemic.

While we look forward to reading about all of the exciting, new projects our students will be working on in the coming months, let’s look back at some of the great projects our Class of 2020 students worked on last summer: 

 

Christina Chandra (GLEPI ’20) & TREAT Asia/amfAR

“My project is called “Assessing Barriers and Facilitators to Integrating Mental Health Services and Related Guidelines into HIV Clinical Care among HIV Providers in Bangkok, Thailand” and… As the principal investigator, I am responsible for everything from study design, IRB compliance, data collection, and data analysis.”

 

Christopher Elmlinger (GLEPI ’20) & Tennessee Department of Health 

“My role has primarily been researching and updating the state’s 12 Vital Signs and the associated intervention strategies and policy recommendations that local health councils can pursue. Tennessee’s Vital Signs are a set of 12 metrics selected to measure the pulse of health in Tennessee (examples include preventable hospitalizations, infant mortality, youth obesity, and access to parks and greenways). “

 

Cassie Kersten (GLEPI ’20) & CDC Division of Global Migration and Quarantine 

“For my project, I am collaborating with the Division of Adolescent and School Health to examine the presence of policies and procedures in public school districts that would facilitate the implementation of non-pharmaceutical interventions (NPIs) in the case of a pandemic. By examining these factors in relation with geographic region, urbanicity, district enrollment size, and socioeconomic status indicators, we hope to identify opportunities for improving pandemic preparedness and response plans in school districts.” 

 

Madison Hayes (GLEPI ’20) & World Bank Group & CSIS 

“This summer, I am splitting time between two organizations, CSIS and the World Bank Group, where I research topics related to global health security. I contribute to the writing of new publications and multimedia through drafting and editing of products including topical analysis, reports, discussion papers, commentaries, and website content.”

 

Alejandra Alvarez (EPI ’20) & World Water Relief

“The main goal of my APE is to implement a WASH themed summer camp for the youth in San Rafael. I am in charge of making lesson plans which include the activities and discussion questions that will engage the youth in WASH topics that directly affect them. … My other responsibility for the summer is to look through the logs and see how WASH behaviors and attitudes, such as how often school children wash their hands and whether or not a school bathroom has soap, changes throughout the school year.” 

 

Be sure to tune in every other week for stories about how our students are addressing pressing public health challenges through their APEs!

 

Featured image from: https://webstockreview.net/explore/office-clipart-intern/

Contact Tracers, Georgia DPH

Category : Student Opportunities

Program Mission: 

To protect State of Georgia employees by preventing disease, injury and disability through the promotion of health and wellbeing.

Description:

The Georgia Department of Public Health is seeking Contact Tracers to support the Department of Public Health and Local Boards of Health to perform COVID-19 contact tracing.

The Department of Public Health (DPH) will hire, train and supervise a team of community contact tracing staff across Georgia. The aim of this will be to call every person diagnosed with COVID-19, gather their contacts, and proceed to call every contact in Georgia. This will fortify efforts to control the pandemic in Georgia.

 

Job Responsibilities:

The Contact Tracer will call all every case and either call or virtually monitor every contact of anyone diagnosed with COVID-19 to document a symptom check, refer them for testing according to established protocols, and provide them with instructions for quarantine. Contact Tracers are required to follow all scripts, policies and procedures provided by DPH, and comply with DPH training regarding confidential information related to personal information.

  • Understand Contact Interviewing and Contact Tracing in the context of a pandemic
  • Basic introduction into the standardized processes of Contact Interviewing and Contact Tracing
  • Conducting Interviews
  • Documentation of Interviews in a digital system
  • Introduction to Daily Workflow
  • Response to Common Requests and Referral for Testing

All applicants will need computer access and wifi access.

May work various hours and weekends.

Minimum Qualifications:

  • High School Diploma
  • Ability to exhibit a professional, positive attitude and work ethic
  • Excellent interpersonal skills required and ability to interact professionally with culturally diverse individuals during a time of crisis and distress
  • Ability to show empathy to distressed individuals
  • Excellent organizational and communication skills
  • Ability to speak, read, and write English
  • Second or multiple languages a plus
  • Critical thinking and sound judgment required
  • Ability to handle confidential information with discretion and professionalism
  • Proficiency with computers

Preferred Qualifications:

  • Bilingual
  • Bachelor’s degree
  • Current College Student (Undergraduate or Graduate) majoring in Public Health or a closely related field or Recent Graduate. 
  • Completion of coursework in Epidemiology
 

Additional Information:

This is temporary or hourly paid work performing professional health care services. Positions in this job are established for less than 9 months or scheduled for less than 30 hours per week and are not eligible for benefits if the position status is temporary (i.e., SCOA 513). Positions in this job are established for greater than 9 months and scheduled for greater than 30 hours per week if the position status is permanent labor (i.e., SCOA 512). Normally permanent labor positions are eligible for Health Insurance benefits.

Apply: 

  • Click here to learn more about the position and apply on Handshake! 

Lessons Learned and Opportunities Ahead for Academic Public Health During the COVID-19 Pandemic (Recording)

Category : News/Events

Click here to watch the closing panel for the ASPPH’s virtual annual meeting where Dean  Curran joined other deans of public health to discuss the unique challenges posed by COVID-19 and the lessons learned so far, particularly how the pandemic has impacted academic public health. 

Birth Defects Surveillance and Research Fellowship, CDC

Category : Alumni

Description: 

Three research opportunities are currently available with the Birth Defects Monitoring and Research Branch of the National Center on Birth Defects and Developmental Disabilities (NCBDDD) at the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia.

NCBDDD’s mission is to improve the health of children and adults by preventing birth defects and developmental disabilities, and complications of heredity blood disorders; promoting optimal child development, and the health and wellness among children and adults living with disabilities. The Birth Defects Monitoring and Research Branch conducts birth defects surveillance and research into the possible causes and long term outcomes of birth defects. The purpose of this fellowship program is to provide an educational experience to individuals interested in the field of public health and reproductive and birth defects epidemiology. Opportunities are aimed at furthering the health science, epidemiological and analytical knowledge of participants. Under the direction of senior scientists, participants will train within the Birth Defects Monitoring and Research Branch in the analysis of public health data, and learn about how surveillance and research can impact public health policy. Participants are assigned to train on various projects and can expect to gain valuable learning experiences in surveillance and research study management, database cleaning, data analyses, and interpretation of the results, writing manuscripts and giving oral presentations. They will get an overview of the practice and application of public health policy used to support public health programs. Participant training involves:

  • literature searches
  • review of databases
  • use of statistical software
  • analyses of data and summarization of findings
  • participation in surveillance and research projects
  • preparation of scientific manuscripts, posters, presentations, and fact sheets, and other information
  • utilization of MarketScan or other claims or health record data
  • determining the effects of medications during pregnancy
  • assessing risk factors for birth defects
  • assessing the long term morbidity and mortality of infants born with birth defects or neonatal abstinence syndrome
  • verbal and written presentations of epidemiologic studies or surveillance activities at scientific conferences
  • development of manuscripts for disseminating the results in peer-reviewed publications

Qualifications

The qualified candidate should have received a master’s degree in one of the relevant fields, or be currently pursuing the degree and will reach completion by the start date of the appointment. Degree must have been received within five years of the appointment start date.

Preferred Skills:

  • Experience in qualitative and quantitative research using SAS, SPSS, R or other statistical software
  • Experience with reference management software
  • Experience with claims data (Marketscan, HCUP, Medicaid Max)

Apply: 

  • Click here to learn more about the position and apply online! 
  • Application Deadline: June 1st, 2020 3PM EST

Graduate Research Assistant, RSPH

Category : Student Opportunities

Position Description

Dr. Cam Escoffery seeks to hire a Graduate Research Assistant for federally funded cancer related projects. Primary responsibilities may include:

  • Data collection and quality control of surveys of parents, young adolescents, adolescents about SurvivorLink and cancer care and clinics about program delivery
  • Assist with mixed methods data collection and analyses
  • Data cleaning
  • Conducting descriptive data analyses and presenting data in tables
  • Report writing
  • Assist with administrative research tasks (i.e., research-related mailings)
  • Other tasks may include: attend research meetings and assist in manuscript writing

Background

Many evidence-based interventions (EBIs) exist. However, their adoption and implementation in clinical and community setting is not optimal. Capacity building and active dissemination are required to enhance their update.. The main project will package, evaluate and disseminate an educational and electronic personal health record for pediatric cancer survivors (SurvivorLink) among pediatric cancer centers.  GRAs will assist in program training, data collection  and data analyses.

Minimum Qualifications

Highly motivated, efficient, organized, detail-oriented and interested in or experience working on research projects.

Preferred Qualifications

Prior work experience and research preferred. Excellent written and verbal communication skills. Experience with Microsoft Office products and databases, especially Excel, and online data collection. Experience with SAS and REDCap preferred.

Additional Information 

  • Hours per week: 10-12 hours/week
  • Position Type: Part Time
  • Organization: Rollins School of Public Health
  • Operating Unit: Rollins School of Public Health
  • Department: Behavioral Sciences and Health Education
  • Compensation:  $12/hour.
  • Start Date: as early as May 17, 2020

Apply 

  • Application Deadline: May 24, 2020 (Applications will be screened as they arrive; positions may be filled prior to this deadline.)         
  • Please send resume and cover letter by email to: Cam Escoffery, PhD, MPH, CHES, (cescoff [at] emory [dot] edu) and Hallie Udelson, MPH, CHES, (hudelso [at] emory [dot] edu)

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  • GCDTR Seminar Series Presents: "Utilizing Genomics to Study the Role of Ancestry in Racial Disparities" May 6, 2024 at 12:00 am – 1:00 am Guest Lecture Event Type: Guest LectureSeries: HybridSpeaker: Melissa B. Davis, PhDContact Name: Wendy GillContact Email: wggill@emory.eduRoom Location: RRR_R809Link: https://tinyurl.com/Melissa-Davis"Utilizing Genomics to Study the Role of Ancestry in Racial Disparities"
  • 2024 Charles C. Shepard Award Symposium May 8, 2024 at 12:00 pm – 1:15 pm zoom.us… Online Location: https://zoom.us/j/96537866614The Charles C. Shepard Award is given to thegraduating masters student who is deemed bythe faculty to have prepared the most scholarlyresearch paper. Please join us to recognize andcelebrate this year’s finalists who will present aposter of their work.
  • RSPH Staff Council Presents: Cheers and Beers - Schoolhouse Edition May 16, 2024 at 5:00 pm – 8:00 pm Networking and Special Event Event Type: Networking,Special EventContact Name: Staff CouncilContact Email: rsphstaffcouncil@emory.eduRSPH staff and post-docs are invited to an evening of camaraderie and delicious bites, presented by the RSPH Staff Council. Space is limited. Watch your email for a link to RSVP.

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  • GCDTR Seminar Series Presents: "Utilizing Genomics to Study the Role of Ancestry in Racial Disparities" May 6, 2024 at 12:00 am – 1:00 am Guest Lecture Event Type: Guest LectureSeries: HybridSpeaker: Melissa B. Davis, PhDContact Name: Wendy GillContact Email: wggill@emory.eduRoom Location: RRR_R809Link: https://tinyurl.com/Melissa-Davis"Utilizing Genomics to Study the Role of Ancestry in Racial Disparities"
  • 2024 Charles C. Shepard Award Symposium May 8, 2024 at 12:00 pm – 1:15 pm zoom.us… Online Location: https://zoom.us/j/96537866614The Charles C. Shepard Award is given to thegraduating masters student who is deemed bythe faculty to have prepared the most scholarlyresearch paper. Please join us to recognize andcelebrate this year’s finalists who will present aposter of their work.
  • RSPH Staff Council Presents: Cheers and Beers - Schoolhouse Edition May 16, 2024 at 5:00 pm – 8:00 pm Networking and Special Event Event Type: Networking,Special EventContact Name: Staff CouncilContact Email: rsphstaffcouncil@emory.eduRSPH staff and post-docs are invited to an evening of camaraderie and delicious bites, presented by the RSPH Staff Council. Space is limited. Watch your email for a link to RSVP.
  • The Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID) July 15, 2024 – July 31, 2024 Conference / Symposium Event Type: Conference / SymposiumSeries: The Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID)Speaker: Leaders in the FieldContact Name: Pia ValerianoContact Email: pvaleri@emory.eduLink: https://sph.emory.edu/SISMID/index.htmlThe Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID) is designed to introduce infectious disease researchers to modern methods of statistical analysis and mathematical modeling.
  • The Second Annual RSPH Staff and Post-Doctoral Ice Cream Social August 14, 2024 at 1:00 pm – 2:00 pm Networking and Special Event Event Type: Networking,Special EventContact Name: Staff CouncilContact Email: rsphstaffcouncil@emory.eduRoom Location: RRR_Terrace 2nd FloorRSPH staff and post-docs are invited to join us for ice cream and delightful conversation. This event is hosted by the RSPH Staff Council.
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