Ongoing Projects

Enhancing Outbreak Analytics and Forecasting with Electronic Health Records

Sponsor/Partner:   CDC/Kaiser

Project Description/Goals: A collaboration between research scientists at Kaiser Permanente Southern California (KPSC) and academic modeling team based in University of California, Berkeley and University of California, San Francisco as part of the Outbreak Analytics and Disease Modeling (OADM) Network to improve existing pathogen surveillance toolkit (i.e., computational intractability of existing high-dimensional models and the need for enhanced nowcasting) and methodological innovations will be conducted in parallel with assessment of STLT public health department needs.  

 CTML Faculty Involved: Alan Hubbard Ph.D., Alejandro Schuler Ph.D

Evaluating Unassessed Chemicals Using Precision Prevention Methodologies

Sponsor/Partner:   State of California, OEHHA

Project Description/Goals: To develop and implement rapid computational and molecular toxicology approaches for identifying toxic chemicals and safer alternatives.

CTML Faculty Involved: Alan Hubbard Ph.D.

Toxic Substances in the Environment

Sponsor/Partner:  NIEHS

Project Description/Goals:   Identify problems associated with hazardous waste sites that have proven intractable to current methods, applying a new approach called ‘exposomics’ to address these problems and employ novel cutting-edge scientific methods and direct engagement with key stakeholders and communities in a concerted effort to make a public health impact.

 CTML Faculty Involved: Alan Hubbard Ph.D.

Targeted Learning using Adaptive Designs for HIV Epidemic Control in East Africa

Sponsor/Partner: NIH/NIAID

Project Description/Goals: This project leverages the rich data increasingly generated in the course of the HIV epidemic response, and applies targeted machine learning to advance adaptive design and analytic approaches.

 CTML Faculty Involved: Maya Petersen M.D. Ph.D. and Mark van der Laan Ph.D.

Causal and consequences of child growth failure

Sponsor/Partner: Bill and Melinda Gates Foundation

Project Description/Goals: Scalable online super-learner for targeted learning estimation of risk factor associations with child growth faltering and an online scalable super learner of an optimal individualized treatment rule for improving these health outcomes.

CTML Faculty Involved: Alan Hubbard Ph.D., Mark van der Laan Ph.D.

Joint Initiative for Causal Inference

Sponsor/Partner: Novo Nordisk

Project Description/Goals: To create an international powerhouse for statistical methods within casual inference to be used on RCT and observational data with a hub at Copenhagen University as well as at University of California, Berkeley by developing, implementing and disseminating methods for exploiting vast, new health datasets using state-of-the art advances in machine learning, causal inference, and statistical theory, and to build industry-wide consensus around best practices for answering pressing health questions in the modern methodological and data ecosystem.

CTML Faculty Involved: Maya Petersen M.D. Ph.D. and Mark van der Laan Ph.D.


Sponsor/Partner: University of Manitoba (Prime: Bill & Melinda Gates Foundation)

Project Description/Goals: The International Milk Composition Consortium's (iMic) study goal is to disentangle the complex relationship of breastmilk composition and other relevant factors on childhood development, including factors that increase the risk of stunting and wasting.

CTML Faculty Involved: Alan Hubbard Ph.D.

Socio-spatial Networks and TB Infection in Youth in Rural Uganda

Sponsor/Partner: NIH National Institute of Allergy & Infectious Diseases

Project Description/Goals: To characterize, on a population-level, where and from which social network youth acquire TB infections and to assess variations throughout stages in the early life-course (early childhood: 1-5 years; school-age: 6-11 years; adolescence: 12-18 years).

CTML Faculty Involved: Maya Petersen M.D. Ph.D. and Laura Balzer Ph.D

Harnessing Data Science to Promote Equity in Injury and Surgery for Africa

Sponsor/Partner:  NIH National Institutes of Health - Miscellaneous

Project Description/Goals: The project consists of four major projects: researching a cluster-based algorithm to estimate socioeconomic status for health equity surveillance in sub-Saharan Africa, using data-adaptive methods to optimize follow up of injured patients in Cameroon, developing the Data Management and Analysis Core, and creating a Capacity Building Core.

CTML Faculty Involved: Alan Hubbard Ph.D.

Enteric Pathogen Force of Infection among Children using Serology

Sponsor/Partner: NIH National Institute of Allergy & Infectious Diseases

Project Description/Goals: High resolution measurements of pathogen infection in stool were paired with antibody response to i) verify that seroincidence estimated from IgG response qualitatively reflects incidence based on infection in stool; ii) develop new methods to estimate force of infection for enteric pathogens in low-resource settings that combine information from PCR testing in stool and antibody response in blood (IgG); and, iii) develop methods to estimate enteric pathogen force of infection from cross sectional surveys.

CTML Faculty Involved: Alan Hubbard Ph.D.

SEARCH Community Precision Health Study

Sponsor/Partner: NIH National Institute of Health  (Subaward through UCSF)

Project Description/Goals: The Sustainable East Africa Research in Community Health (SEARCH) consortium designs and tests evidence based treatment and prevention interventions that will guide a global effort to end AIDS using a multi-disease, multi-sector approach.  

CTML Faculty Involved: Maya Petersen M.D. Ph.D. and Laura Balzer Ph.D.

Local Epidemic Modeling for the San Francisco and California Departments of Public Health

Sponsor/Partner: SFDPH; CDPH

Project Description/Goals: Mathematical modeling support for public health decision-making in the COVID-19 response. 

CTML Faculty Involved: Maya Petersen M.D. Ph.D. 

Strategic antiretroviral therapy and HIV testing for youth in rural Africa (SEARCH Youth)

Sponsor/Partner: NIH National Institute of Allergy & Infectious Diseases (Subaward through UCSF)

Project Description/Goals:  Improve the health and well-being of adolescents and young adults (10-24 years) with HIV in rural Uganda and Kenya. Results from the project's first phase are available in Mwangwa, et al.

CTML Faculty Involved: Laura Balzer Ph.D.

Simplified Isoniazid Preventive Therapy Strategy to Reduce TB Burden (SPIRIT) SEARCH-IPT

Sponsor/Partner: NIH National Institute of Allergy & Infectious Diseases (Subaward through UCSF)

Project Description/Goals: Design and evaluate a network-based intervention to increase TB prevention among persons with HIV and improve overall community health in 82 districts in Uganda. Results from the project's first phase are available in Kakande et al., with corresponding statistical analysis plan

CTML Faculty Involved: Laura Balzer Ph.D.

Enhancing Causal Inference in the Sentinel system: An Evaluation of Targeted Learning and Propensity Scores for Confounding Control in Drug Safety

Sponsor/Partner: Harvard Pilgrim Health Care

Project Description/Goals: The project involves selecting safety analysis type data sets; using outcome blind parts of the data to specify 1) a statistical model; 2) causal estimand, and 3) set up a superlearner and TMLE-based statistical analysis plan (SAP). Subsequently, the project involves carrying out the SAP and interpreting the results

CTML Faculty Involved: Mark van der Laan Ph.D.

ICLIC-MS for Enhancing Outcomes Research and Clinical Care in Multiple Sclerosis

Sponsor/Partner: NIH (PI Barcellos) 

Project Description/Goals: Our team has developed and validated an assisted web-based interface for longitudinal clinical data collection of cognitive function measures, physical disability and depression measures that are not reliably captured in the electronic health record (EHR) of multiple sclerosis (MS) patients. We will integrate several sources ofpatient data including genomic, clinical and EHR for 3,000 individuals to facilitate research and improve clinical care.

CTML Faculty Involved: Mark van der Laan Ph.D.

Community Violence and Disparities in Maternal and Infant Health: Effects and Mechanisms

Sponsor/Partner: NIH (PI Ahern)

Project Description/Goals: To inform population health and clinical care approaches to address maternal and infant health disparities by race/ethnicity and foreign-born status, and motivate violence prevention programs that both reduce immediate injuries and deaths, and ultimately improve maternal and infant health and reduce health disparities in the US.

CTML Faculty Involved: Mark van der Laan Ph.D.

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