The Computational Health Informatics Program (CHIP) at Boston Children’s Hospital hosts a training program for postdoctoral fellows to be trained in Informatics, Genomics, Machine Learning, Artificial Intelligence, and Biomedical Data Science. The program is funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) at the National Institutes of Health (T32HD040128) and is open to US citizens and permanent residents.
Founded in 1994, CHIP is a multidisciplinary applied research and education program. Biomedical informatics has become a major theme and methodology for biomedical science, health care delivery, and population health, involving high-dimensional modeling and understanding of patients from the molecular to the population levels. We design information infrastructure for medical decision making, diagnosis, care redesign, public health management, and re-imagined clinical trials. The field is inherently interdisciplinary, drawing on traditional biomedical disciplines, the science and technology of computing, data science, biostatistics, epidemiology, decision theory, omics, implementation science, and health care policy and management. Our faculty are trained in medicine, data science, computer science, mathematics and epidemiology. Our faculty have been featured in The New York Times, Wall Street Journal, ABC News, CNBC, Bloomberg, CNN, Forbes, Financial Times, NBC News, GQ Magazine, U.S. News & World Report, Politico, and BBC News for their expertise on COVID-19.
We seek outstanding candidates passionate about advancing the ability to acquire and then reason over an entire spectrum of data types ranging from molecular and genomic all the way to clinical, epidemiological, environmental and social. Focus areas may include, but are not limited to research applications of machine learning/AI including COVID-19, medical applications of machine learning/AI including clinical decision support and predictive medicine, genomic and precision medicine, population health, health IT architectures and standards (e.g. SMART on FHIR apps and infrastructure), re-imagined clinical trials, real-world evidence, data visualization, and integrative omics. Candidates should have strong quantitative backgrounds.
Over the past two decades, the program has trained a mix of MDs and PhDs. More than 90 percent have gone on to receive independent funding in faculty positions in academic medicine.
The training grant favors applicants who have a strong focus on pediatric acute care, and pediatric emergency physicians are especially encouraged to apply.
Faculty
Core Faculty - Informatics Track
Michael Agus, MD is HMS Professor of Pediatrics, BCH Division Chief, Division of Medical Critical Care; Endowed Chair in Critical Care; Medical Director, Medical Intensive Care Unit and Intermediate Care Program; and Co-Medical Director, Biocontainment Unit. His work on his third NIH-funded grant supporting investigations of endocrinopathies in critical illness is examining stress hydrocortisone in pediatric septic shock, including aspects of precision medicine wherein specific panels of biomarkers are being evaluated as predictors of clinical response. His research program provides access to trial design, grant writing, colleagues and patients, forming a sound basis for new studies by an affiliated trainee.
Paul Avillach, MD is HMS Assistant Professor of Pediatrics and Biomedical Informatics, and Faculty in CHIP at BCH. He focuses on translational bioinformatics, developing novel methods for integrating multiple heterogeneous clinic cohorts, EHR data, and multiple types of genomics data to encompass biological observations. Avillach has extensive federal funding, and has led informatics cores on projects of major national significance, including the Global Rare Diseases Registry project. He also directs the NIH AIM-AHEAD Research Fellowship program, engaging early-career researchers from under-represented populations to participate in biomedical research using AI/ML methodologies on EHR data. Trainees under his mentorship can develop projects using multiscale, multi-omics databases developed from our BCH populations, including patients with rare and common diseases seen in the ED.
William Bosl, PhD is HMS Visiting Associate Professor and Faculty in CHIP at BCH. He has two PhDs, in Physics and Neurocognition. His primary research focus is in applying informatics to biomarker discovery for neurological and neurodevelopmental disorders in pediatric populations, such as ED patients with seizures.
Florence Bourgeois, MD, MPH is HMS Associate Professor of Pediatrics and Assistant Professor of Emergency Medicine, and Faculty in CHIP at BCH. She Co-directs the Harvard-MIT Center for Regulatory Science, and is Scientific Director of the BCH PrecisionLink Biobank. She has held multiple R grants. Trainees can participate in her many projects applying big data analytics to evaluate regulation and use of medications in children.
John S. Brownstein, PhD is HMS Professor of Pediatrics and Biomedical Informatics. He directs the Computational Epidemiology Group of CHIP, and the Innovation and Digital Health Accelerator at BCH, and is the BCH Chief Innovation Officer. He has had a rich tapestry of funding from the NIH, industry, and major. He was awarded the Presidential Early Career Award for Scientists and Engineers and the Lagrange Prize for international achievements in complexity sciences, and leads major international efforts in informatics and real-time public health surveillance.
Tim Miller, PhD, is HMS Assistant Professor of Pediatrics and Faculty in CHIP at BCH. He is a leader in the subfield of clinical NLP of medical text. He adapts NLP to new domains and holds R01 funding. Trainees in his program work on computational phenotyping, temporal information extraction, or text summarization.
Chirag Patel, PhD is HMS Associate Professor of Biomedical Informatics. He is developing bioinformatics approaches extracting knowledge from large-scale environmental exposure and genomic data spanning from molecules to populations. He has R01, and RF1 funding. Trainees under Dr. Patel can work on environmental influences and genetic interactions leading to acute illnesses.
Ben Reis, PhD is HMS Associate Professor of Pediatrics and leads the Predictive Medicine Group of CHIP at BCH. He focuses on using novel computational approaches for predicting disease. He has conducted large-scale population studies of COVID-19 vaccine effectiveness and safety, and developed novel methods for tracking and understanding pandemics through digital information sources. He holds multiple R01s and has been recognized for his work with an award from the White House.
Guergana Savova, PhD is HMS Patricia F. Brennan Professor of Pediatrics, and Senior Faculty in CHIP at BCH. She is an international leader in the field of NLP, and developed the leading medically-related pipeline for NLP, cTakes, now a top-level open source Apache Software Foundation project. She holds multiple R01 and U awards. She has an extensive history of mentorship, particularly to women in medical research.
Griffin Weber, MD, PhD is HMS Associate Professor of Biomedical Informatics and Associate Professor of Medicine at Beth Israel Deaconess Medical Center (BIDMC). He also directs the Biomedical Research Informatics Core at BIDMC, and is an investigator on Informatics for Integrating Biology and the Bedside (i2b2). He created the original software for the Shared Health Research Information Network (SHRINE), a federated query tool that connects i2b2 databases across multiple institutions.
Core Faculty - Genomics Track
Robert Green, MD, MPH, is HMS Professor of Medicine (Genetics), and the Director of the G2P (Genomes to People) Research Program at Brigham and Women’s Hospital, Broad Institute and Ariadne Labs. Internationally recognized for research and policy efforts accelerating the implementation of genomic/precision medicine, Dr. Green co-leads the first NIH funded randomized trial of sequencing in newborns (BabySeq Project), Dr. Green is a Fellow of the American Neuropsychiatric Association. He has had continuous NIH funding for 26 years and has considerable experience mentoring fellows in patient-oriented research.
Bruce Horwitz, MD, PhD, a PEM physician, is HMS Associate Professor of Pediatrics. His lab is working to understand the regulating of inflammatory responses at mucosal surfaces including the respiratory tract. They have developed experimental and computational pipelines to analyze mucosal immune cells. His lab provides outstanding opportunities for fellows to investigate the role of inflammation regulation in respiratory conditions with which children frequently present to the ED, such as SARS-CoV-2 and respiratory syncytial virus.
Benjamin Raby, MD, MPH, is HMS Leila and Irving Perlmutter Professor of Pediatrics, Director of the Pulmonary Genetics Center at Brigham and Women’s Hospital, and Pulmonary Medicine Division Chief at BCH. A pulmonologist and genetic epidemiologist, he is PI of three NHLBI-sponsored grants focused on genomic approaches in asthma and childhood interstitial lung disease. Fellows in his laboratory will have access to highly characterized asthma cohorts for genomic study.
Core Faculty—Trans-Disciplinary Group
Donald Goldmann, MD, is HMS Professor of Pediatrics, and Chief Scientific Officer, Emeritus, of the Institute for Healthcare Improvement, founded by Don Berwick (past director of CMS). He was long-time Director of the Harvard-wide Child Health Services Research Training Program, and mentored scores of fellows and faculty, including K and R awardees. As a trans-disciplinary scientist, he participates on mentorship teams for projects with a health services component in care delivery, quality improvement, or evaluation.
Richard Malley, MD, trained as a pediatric emergency physician. He is HMS Professor of Pediatrics and the Kenneth McIntosh Chair, Pediatric Infectious Diseases at BCH. His laboratory is focused on pneumococcal pathogenesis and novel vaccine strategies for Streptococcus pneumoniae and other pathogens, including, recently, SARS-CoV-2. He has had extensive federal and foundation funding. His trainees will study vaccine development for diseases commonly seen in the pediatric ED.
Rebekah Mannix, MD, MPH, is HMS Associate Professor of Pediatrics and EM, and Senior Associate, Division of PEM, BCH. She Co-directs the BCH Brain Injury Center. Her translational lab studies traumatic brain injury and repetitive head trauma, and her work has been funded by the NIH, DOD, and the NFL Charitable Foundation.
Lise Nigrovic, MD, MPH, a PEM physician, is HMS Associate Professor in Pediatrics and Emergency Medicine. Her research focus is the appropriate diagnostic evaluation and treatment of children with infectious emergencies. As founding chair, she has established the first pediatric Lyme disease biobank, housed at BCH, and she is a nationally-recognized leader in evaluation of diagnostic tests for Lyme disease. She has federal (NIH R01, DOD) and foundation funding.
Kathleen Walsh, MD, MSc is Director of the Harvard-wide Pediatric Health Services Research Fellowship (PEMRTP PI Mandl is a founding faculty member). As a trans-disciplinary faculty, she ensures synergy between the Harvard-wide fellowship and PEMRTP. Dr. Walsh also directs the BCH Patient Safety Research Center, and has AHRQ R18 funding focused on patient safety.
Supporting Faculty - (PEMRTP Graduates)
Chris Cassa, PhD, is Assistant Professor of Medicine, HMS. His laboratory conducts research on clinical risk assessment and predictions of functional impact for genetic variants. One of the greatest challenges in the translation of clinical genetics is the analysis of germline sequence variants in genes with established disease associations. Healthy individuals often carry genetic variants in genes that have been previously associated with disease, and there is a pressing need to distinguish between causal variants that increase disease risk and those that are either incompletely penetrant or false positives.
Andrew Fine, MD, MPH, has focused his intellectual and innovative efforts on delivering clinical epidemiology, big data and digital medicine to the bedside in real time, with a focus on three major areas: clinical prediction models, clinical pathways, and clinical tools to improve efficiencies in care. His group has developed and validated models to improve the diagnosis and management of communicable diseases such as group A streptococcal pharyngitis and Lyme disease, as well as to improve clinical operations by the early prediction of the need for hospital admission among patients in the ED.
Lois Lee, MD, MPH is a clinical researcher whose primary areas of research focus are injury prevention, trauma care, health policy and health disparities. She has published seminal research examining changes in pediatric injuries after state and federal level policy changes. In addition, her work includes examining policy changes at the institutional and state level which could potentially address health disparities in the US.
Shannon Manzi, PharmD, is HMS Assistant Professor of Pediatrics, Director of Safety & Quality, Department of Pharmacy at BCH, and Faculty in CHIP at BCH. Her research areas include the application of clinical pharmacogenomics and medication safety related outcomes. The medication use process in the Emergency Medicine and Disaster Medicine settings are of particular interest, given their fast-paced, sometimes austere, environments and lack of patient history.
William Meehan, MD, MPH, is dual trained in PEM and sports medicine. He is Director of the Micheli Center for Sports Injury Prevention and Director of Research for the Brain Injury Center at BCH, and PI of the Neurologic Function across the Lifespan: A LONGitudinal, Translational Study for Former National Football League Players (NFL-Long Study).
Marc Neuman, MD, MPH, is an outcomes researcher whose research focuses on improving the accuracy of the clinical and radiographic diagnosis of pneumonia. His work has identified patients at low risk of radiographic pneumonia, such as children with wheezing, and has identified hypoxia as the single best predictor of pneumonia in children. He is the Director of Research, Division of PEM at BCH.
Alon Geva, MD, MPH, focuses on clinical and epidemiologic research at the intersection of pediatric critical care medicine and biomedical informatics. Incorporating methods from machine learning, NLP, and AI, he harnesses the power of “big data” to bring meaningful insight to how critical care is delivered to children, with a quality improvement lens. He also collaborates with DBMI colleagues to advance methods to improve identification of high-precision cohorts for clinical research studies.
Leadership
Program Director
Dr. Mandl is the director of CHIP at Boston Children’s Hospital and is the Donald A.B. Lindberg Professor of Pediatrics and Biomedical Informatics at Harvard Medical School. He is trained as a pediatrician and pediatric emergency physician. His work at the intersection of population and individual health has greatly influenced the burgeoning field of biomedical informatics. He pioneered real-time biosurveillance using ED data, and championed patient involvement in data production and access, leading to the creation of the first personal health and participatory surveillance systems. Dr. Mandl's advancements in 'SMART' programming interfaces, in conjunction with his influence on the 21st Century Cures Act, have streamlined universal access to individual and population health data. These capabilities enhance interoperability in healthcare systems and foster substantial economies of scale. He leads the Genomic Information Commons across eight leading children’s hospitals, participating in a federated model for genomic intelligence. He directs the BCH PrecisionLink Biobank. He is an elected member of the National Academy of Medicine, American Society for Clinical Investigation, Society for Pediatric Research, American College of Medical Informatics and American Pediatric Society. He is a recipient of the Presidential Early Career Award for Scientists and Engineers, the Donald A.B. Lindberg Award for Innovation in Informatics and the Barger Award for top mentors at HMS. He was advisor to two Directors of the CDC and chaired the Board of Scientific Counselors of the NIH’s National Library of Medicine. He is co-chair of the National Academy of Medicine’s Digital Health Action Committee.
Informatics Track Director
Dr. Kohane is Chair of DBMI at HMS and is the Marion V. Nelson Professor of Biomedical Informatics. He is also Faculty in CHIP at BCH. Dr. Kohane is an internationally recognized leader in biomedical informatics, heading collaborations at HMS and its hospital affiliates in the application of genomics and computer science in medicine. He leads 3 large NIH-funded projects: the Coordinating Center for the Undiagnosed Disease Network, a Center for Excellence in Big Data to Knowledge, and a Center for Excellence in Genomic Science. Kohane is a prolific and award-winning mentor who has received the highest recognition for mentoring at HMS, the William H. Silen Lifetime Achievement in Mentoring Award. He was also the founding PI of the pre-doctoral Bioinformatics and Integrated Genomics training program.
Genomics Track Director
Dr. Hirschhorn is the Concordia Professor of Pediatrics and Professor of Genetics at HMS, Co-director of the Broad Institute’s Metabolism Program, and Division Chief of Endocrinology at BCH. He has been a leader in shaping the design of genome-wide association studies to understand the genetic basis of polygenic traits and diseases. He was awarded the American Pediatric Society’s Norman J. Siegel New Member Outstanding Science Award and the Society for Pediatrics Research E. Mead Johnson Award. His trainees can apply genetic, computational, and genomic methods to a range of endocrine disorders (including diabetic kidney disease).
Applications are open (click here), and admissions are available on a rolling basis.
