Alisa Stephens-Shields, PhD

Director, Biostatistics and Data Science Core

Mary Putt, PhD, ScD

Co-Director, Biostatistics and Data Science Core

Yun Li, PhD

Core Investigator

Ted Barrell, BA

CRCU Data Manager

Chris Helker, MSPH

Database Design & Management

The Biostatistics and Data Science (BDS) Core provides CFAR investigators with statistical collaboration  and consultation for proposal development, pilot studies, and data management and informatics expertise for research planning.

The Core Director is Dr. Alisa Stephens-Shields, Associate Professor of Biostatistics at the University of Pennsylvania. Mr. Chris Helker, Director of Clinical Data Management at Penn’s Clinical Research Computing Unit (CRCU), is the Core representative for data management needs.

Dr. Alisa Stephens-Shields, and supporting data analyst Ms. Antoneta Karaj, provide collaboration and consultation on study design and data analysis issues requested via the Core. Dr. Stephens-Shields has substantial experience and expertise in designing, conducting and analyzing data from clinical trials, including cluster-randomized trials, as well as laboratory studies and observational studies. The Core’s ongoing statistical research program includes the development and application of novel causal inference approaches to enhance the design and analysis of randomized trialsaddresses the analysis of data that include error-prone or misclassified covariates, such as exposures and outcomes derived from the EHR, and/or outcomes in HIV-related epidemiological and clinical investigations.

Every attempt will be made to link investigators with statistical collaborators who have particular expertise in the methods relevant to the types of data to be generated in their study; other faculty and research staff may become involved in CFAR projects to provide specialized expertise when needed.

Available Services

  • Statistical Expertise
  • Help Desk
  • Database Design and Management Expertise
  • Using the Clinical Core Database and Specimen Repository
  • Biostatistics Training

Statistical Expertise

The Biostatistics and Data Science Core offers advice to CFAR Investigators on study design and data analysis issues. It also provides statistical collaborations for research funding applications, and analytical help for small studies without formal funding for statistical collaboration. Areas of application include:

  • laboratory and animal studies
  • clinical studies relating to prognostic characteristics and disease course
  • clinical trials of therapeutic and preventive regimens
  • analysis of EHR data

To request consultation regarding statistical issues, please contact Dr. Alisa Stephens-Shields at

Help Desk

The Biostatistics and Data Science Core enthusiastically supports trainees at various levels in navigating statistical design and analysis challenges in proposed and ongoing research. Core personnel advise on methodology and provide example analysis code to graduate students and postdoctoral fellows for a wide range of study designs.  Recent requests have included tutorials on principal components analysis for the analysis of immunoassay data, zero-inflated Poisson models for the analysis of rates in animal studies, and multivariate time-to-event analysis in animal studies.

Interested trainees may submit a request for statistical support toHelp Desk. Individuals receiving funding through the HIV Pathogenesis, Vaccination and Cure training grant are especially encouraged.

Database Design and Management Expertise

Informatics expertise is provided by staff of the Clinical Research Computing Unit (CRCU) and covers all aspects of data management, including:

  • Proposal development and submission coordination
  • Database design, construction and management
  • Development of data collection instruments/case report forms
  • Data quality assurance/control
  • Data mining and integration (CFAR database and Penn Data Store)

To request any of these services, contact Chris Helker at

Clinical Core Database and Specimen Repository

The Penn CFAR Biostatistics and Data Science Core maintains and facilitates access to a clinical care database for use in studying the epidemiology of HIV/AIDS, for evaluating feasibility of intervention studies, and for facilitating conduct of such studies. The Clinical Core Database and Specimen Repository can be used to identify potential subjects for study or can be used as a basis for independent clinical investigation.

Data and samples available to investigators include:

  • Demographics
  • Biological Specimens
  • Medical History
  • Previous Antiviral Treatments
  • Present Antiviral Treatments
  • Sexual History
  • Adherence Questions
  • Alcohol and Drug Use
  • Hepatitis Treatment
  • Metabolics
  • CES-D (Center for Epidemiologic Studies-Depression)
  • Clinical Laboratory Measures

To query the database please complete the Penn CFAR Clinical Core Requests Form. A member of Penn’s Clinical Research and Computing Unit will respond.

To identify the data that are available, you may download the Case Report Form (CRF) that patients are given at intake and the Follow-up CRF that is done at subsequent visits.

Consultations, queries of the Databases, and access to specimens from the Specimen Repository are provided to CFAR investigators and their collaborators by request.

For more information, to request consultation, or to request training on accessing the database, please contact Ted Barrell, CRCU Data Manager, at  Phone: 215-573-5486

Biostatistics Training

Core G biostatisticians are available to make introductory presentations on biostatistical concepts and methods that are appropriate for faculty and fellows working in other Core areas. These presentations are routinely made to Virology faculty and fellows in spring semesters and can be presented to other groups as well. Click here for a PDF of a prior training seminar.