NIH Funded Postdoc Training in Informatics, Genomics, Machine Learning, Artificial Intelligence, and Biomedical Data Science

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, 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 (T32HD040128-16) and is open to US citizens and permanent residents.

Over the past two decades, the program has trained a mix of 19 fellows with MDs and PhDs. More than 90% have gone on to receive independent funding in faculty positions in academic medicine.

The unparalleled learning environment at Boston Children’s Hospital, a teaching hospital of Harvard Medical School, enables access to world-class mentors. Fellows are able to leverage research networks and multi-site collaborations with storied institutions such as Harvard Medical School, Massachusetts Institute of Technology, the Broad Institute, and Dana Farber Cancer Institute.

Program Structure

Fellows in the training program work toward independence in two interrelated phases: 

(1) Mentored research project

Fellows will be mentored by a faculty member of choice and will select a research topic. 

(2) Formal course work

Trainees may have the option of formal coursework. The Program Director and faculty mentor work with the fellow to tailor the curriculum based on the skills required for the fellow’s research project and long-term objectives. Often, this can lead to coursework at the Harvard Department of Biomedical Informatics or the Harvard School of Public Health. Many projects have an emphasis on pediatric emergency and acute care.

Faculty

Informatics and Genomics
Michael Agus MDMichael Agus, MD, is HMS Associate Professor of Pediatrics and BCH Division Chief, Division of Medicine Critical Care; Endowed Chair in Critical Care; Medical Director, Medicine Intensive Care Unit and Intermediate Care Program; and Co-Medical Director, Biocontainment Unit. His research utilizes data from continuous glucose monitoring paired with advanced computer algorithm-based modeling techniques to generate therapy recommendations for tight glycemic control. He is PI for NIH-funded R01 grants, including national multi-center trials. 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, PhDPaul Avillach, MD, is HMS Assistant Professor of Biomedical Informatics and Faculty in CHIP at BCH. He focuses on the development of novel methods for integrating of multiple heterogeneous clinic cohorts, EHRs, and multiple types of genomics data to encompass biological observations. Avillach has extensive federal funding, leading informatics cores on projects of major national significance, including the BD2K PIC-SURE Center of Excellence and the Global Rare Diseases Registry project. 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.
Alan Beggs, PhD, is the Sir Edwin and Lady Manton Professor of Pediatrics at HMS, and the Director of the Manton Center for Orphan Disease Research at BCH. His research focuses on the molecular genetics of inherited diseases, particularly muscular dystrophies, many of which present in the ED with acute complications. He is one of the foremost investigators in the area of mutations that cause congenital myopathies and a former Investigator of the Howard Hughes Medical Institute. He has mentored numerous post-doctoral trainees, include multiple previous K-awardees. 
William (Bill) Bosl, PhD 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 clinical neurophysiology and neuro-diagnostics, using EEG signal processing. Fellows working with Dr. Bosl can investigate digital biomarker-based assessments of patients in the ED with seizures.
Florence Bourgeois, MD, MPH Florence Bourgeois, MD, MPH, is HMS Associate Professor of Pediatrics (Pending) and Assistant Professor of Emergency Medicine and Faculty in CHIP at BCH. She has expertise and a strong publication track record using multiple national databases pertinent to emergency care, including The National Hospital Ambulatory Medical Care Survey (NHAMCS) and Clinical Trials.gov. She has held multiple R grants. Her trainees can participate in her many projects on the regulatory science of pediatric pharmaceuticals or PEM-related epidemiological research. She was trained in this program. 
John Brownstein, PhDJohn S. Brownstein, PhD, is HMS Professor of Pediatrics and Biomedical Informatics. He directs the Computational Epidemiology Group of CHIP at BCH, and is the BCH Chief Innovation Officer. He has had a rich tapestry of funding from the NIH, industry, and major foundations such as The Bill and Melinda Gates Foundation. He was awarded the Presidential Early Career Award for Scientists and Engineers and leads major international efforts in informatics and social-media-based infectious disease surveillance. He did his postdoctoral fellowship at CHIP.
 Jonathan Finkelstein, MD, MPH Jonathan Finkelstein, MD, MPH, is HMS Professor of Pediatrics and Population Medicine and Co-Director of the Harvard Pediatric Health Services Research Fellowship Program. He is a winner of the HMS Clifford A. Barger Award for Excellence in Mentoring. He is also Vice President of Quality for BCH. He has particular methodological expertise in study designs and analytic approaches needed to translate evidence to the clinical care setting. He is PI on two NIH T32 grants and an AHRQ K12. Dr. Finkelstein will provide strong synergy between the health services research program and the PEMRTP program.
Donald A. Goldmann, MD Donald Goldmann, MD, is Clinical Professor of Pediatrics at BCH. He is a senior leader of the Institute for Health Care Improvement, founded by Don Berwick, past director of the Centers for Medicaid and Medicare Services (CMS). Dr. Goldman has been Director of the Harvard-wide Child Health Services Research Training Program since 1995. As a trans-disciplinary mentor, Dr. Goldmann will participate on mentorship teams where informatics and genomics projects have a health services component in care delivery, quality improvement, or evaluation, and provide synergy through shared didactics. Importantly, the Health Services Research program is located on the same floor as the laboratory of the PI, Dr. Mandl, providing a solid geographic basis for collaboration.
Robert GreenRobert Green, MD, MPH, is Associate Professor of Medicine at Brigham and Women’s Hospital and HMS, and the Associate Director of the Partners Center for Personalized Genetic Medicine. His work explores emerging themes in translational genomics such as the impact of genetic and genomic information on the lives of people who receive this information, and on the practice of medicine. Dr. Green is a Fellow of the American Neuropsychiatric Association. He has a K24 mentoring award and considerable experience mentoring Fellows and junior faculty in patient-oriented research. He holds multiple R and U grants and provides an outstanding opportunity for PEMRTP fellows to study the role of whole exome sequencing in the evaluation of conditions presenting to EDs. 
Bruce HorwitzBruce Horwitz, MD, PhD, a PEM physician, is an Associate Professor of Pediatrics at BCH and HMS. His lab is internationally recognized for work in NF kappaB signaling, a central modulator of innate immune responses. A key focus is on innate immunity to bacteria, a central problem in PEM in diseases induced by acute inflammatory response (e.g., pneumonia, cellulitis, and abscesses). His laboratory provides outstanding opportunities for fellows to investigate the role of innate immunity in conditions frequently presenting to the ED, such as appendicitis, diverticulitis, and inflammatory bowel disease.
Louis Kunkel, PhDLouis Kunkel, PhD, is HMS Professor of Pediatrics and Genetics and a former Investigator of the Howard Hughes Medical Institute. Dr. Kunkel’s research focuses on the molecular biology of genetic muscular dystrophies and autism spectrum disorders. He is internationally known for identifying the Duchenne-Becker muscular dystrophy gene dystrophin.Kunkel is a member of the National Academy of Sciences. Dr. Kunkel has trained approximately 50 Fellows over the past 30 years, including the current President of Tufts University. Most have of his former fellows now have academic positions, and the majority of those who were clinical now have physician-scientist roles. Fellows in his laboratory will study genetic contributions to diseases presenting to the ED. 
Richard Malley, MDRichard Malley, MD, trained as a pediatric emergency physician. He is HMS Professor of Pediatrics and the Kenneth McIntosh Chair, Pediatric Infectious Diseasesat BCH. His laboratory is focused on pneumococcal pathogenesis and novel vaccine strategies for Streptococcus pneumoniae and other pathogens. 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, MPHRebecca Mannix, MD, MPH, is HMS Assistant Professor of Pediatrics and Emergency Medicine, and Faculty in the Division of Emergency Medicine at BCH. Her laboratory studies both animal models of closed head injury and the epidemiology and clinical management of concussion. She is PI of a U01. Fellows under her mentorship will study closed head injury. She herself completed a PEMRTP postdoctoral fellowship.
Timothy Miller, PhDTim Miller, PhD, is HMS Assistant Professor of Pediatrics (Pending) and Faculty in CHIP at BCH. He is a leader in the basic science of natural language processing (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. Dr. Miller completed his postdoctoral training at CHIP.
Chirag PatelChirag Patel, PhD, is HMS Assistant Professor of Biomedical Informatics and a new DBMI faculty member for this cycle. He is developing bioinformatics approaches extracting knowledge from large-scale environmental exposure and genomic data spanning from molecules to populations. He is one of multiple PIs of an NIDDK training program and has R01, R00, and R21 funding. Trainees under Dr. Patel can work on environmental influences and genetic interactions leading to acute illnesses. 

Benjamin Raby, MD, MPHBenjamin Raby, MD, MPH, is HMS Associate Professor of Medicine, and recently appointed Pulmonary Medicine Division Chief at BCH. He is an investigator at the Channing Laboratory studying the genomics of asthma. He developed gene expression signatures for asthma-associated traits and methods to facilitate quantitative trait locus (QTL) mapping. These efforts resulted in the identification of regulatory variants that influence the expression of 1,585 genes, including novel asthma susceptibility variants, and the development of a pipeline to functionally characterize the identified asthma genes. Fellows in his laboratory will have access to highly characterized asthma cohorts for genomic study.

Ben Reis, PhDBen Reis, PhD, is HMS Assistant Professor of Pediatrics and leads the Predictive Medicine Group of CHIP at BCH. He uses advanced computational techniques to analyze large health care databases with the goal of predicting clinical and public health risks. He holds multiple R01s and has been recognized for his work with an award from the White House. Fellows working with Dr. Reis can develop a wide range of predictive modeling projects focused on topics such as clinical risk, drug safety, or public health outbreaks. Or they can develop novel methods for using social networks to identify or monitor public health trends. Reis is a successful mentor and was himself a postdoctoral fellow at CHIP.
Mauricio Santillana, PhD Mauricio Santillana, PhD, is an Assistant Professor at HMS, a faculty member at CHIP at BCH, and an associate at the Harvard Institute for Applied and Computational Sciences. In recent years, his main focus has been to develop mathematical models to improve healthcare. Specifically, he has leveraged information from big data sets from Internet-based services (such as Google, Twitter, Flu Near You, Weather) and electronic health records to predict disease incidence in multiple locations worldwide and to predict outcomes in hospitalized patients. Dr. Santillana has advised the CDC and the White House on the development of population-wide disease forecasting tools.
Guergana Savova, PhD Guergana Savova, PhD, is HMS Associate Professor of Pediatrics, and Senior Faculty in CHIP at BCH. She is an international leader in the field of natural language processing, and developed the leading medically-related pipeline for NLP, cTakes, which is the only top level open source project in the Apache Foundation. She holds multiple R01s. Trainees in her program work on computational phenotyping, temporal information extraction, or medical text summarization. 
Sebastian Schneeweiss, M.D., Sc.D.Sebastian Schneeweiss, MD, ScD, is Professor of Medicine and Epidemiology at Harvard Medical School and Chief of the Division of Pharmacoepidemiology and Pharmacoeconomics in the Department of Medicine, Brigham and Women’s Hospital. His research focuses on the comparative effectiveness and safety of biopharmaceuticals and developing methods to reach causal conclusions from analyzing complex healthcare databases (NASEM video). He focuses on newly marketed medications and how real-world evidence can be generated expeditiously at highest quality without compromising the accuracy of findings. He teaches courses in principled database analytics in pharmacoepidemiology at Harvard and in Europe. 

Griffin WeberGriffin Weber, MD, PhD, is HMS Associate Professor of Biomedical Informatics and Associate Professor of Medicine at Beth Israel Deaconess Medical Center. He developed a novel approach to studying health systems across multiple scales, called health system dynamics, which involves reasoning over multiple scales of biomedical informatics data, including EHR and claims data. He completed his postdoctoral training at HMS DBMI.

Michael WhalenMichael Whalen, MD, is Associate Professor of Pediatric Critical Care Medicine at the Massachusetts General Hospital. His laboratory studies the molecular basis for traumatic brain injury, including concussion, and participates in the Pediatric Emergency Care Applied Research Network. He has held multiple investigator awards from the NIH and a Department of Defense award. He has successfully mentored two of our trainees, one during his fellowship and the other as she transitions to independence. He continues to provide a laboratory for the study of concussion and closed head injury.
Leadership
Advisory Committee

Admissions

Applications are open, and admissions are available on a rolling basis.

Eligibility

Citizens or permanent residents of the United States enrolled in a research doctoral, research postdoctoral, clinical doctoral, or clinical postdoctoral are eligible to apply. Preference will be given to candidates, who have, or are seeking, board certification in pediatric emergency medicine, or who have research interests that are aligned with CHIP’s core research areas.

The program has been committed to recruiting and retaining postdoctoral trainees who are URiM. We have maintained our commitment to diversity through prioritizing applications from diverse and disadvantaged backgrounds. Women and underrepresented minority groups are strongly encouraged to apply.

How to Apply

Click here to ask questions.

To apply, send a CV and a personal statement to megan.rollins@childrens.harvard.edu and have three letters of reference sent to her as well.

Admissions Statistics

91% of past graduates are employed in academic medicine

93% of past graduates are actively engaged in biomedical research

A large fraction of the fellows have achieved independent funding