Postdoctoral Training in Informatics, Genomics, Machine Learning, Artificial Intelligence, 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, 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 (T32HD040128-16) and is open to US citizens and permanent residents.

CHIP, an affiliate of Harvard Medical School and a collaborating program of the Harvard Medical School Department of Biomedical Informatics, is recruiting postdoctoral fellows. 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 and Genomics

Michael 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 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.

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 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 ClinicalTrials.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 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.

Tianxi Cai, ScD is a John Rock Professor of Population and Translational Data Sciences at the Harvard T.H. Chan School of Public Health. Dr. Cai’s current research interests are mainly in the area of biomarker evaluation; model selection and validation; prediction methods; personalized medicine in disease diagnosis, prognosis and treatment; statistical inference with high dimensional data; and survival analysis.

Felix Dietlein, PhD is is a faculty member of CHIP and Harvard Medical School. He is also an Associate Member at the Broad Institute of MIT and Harvard and an Investigator at the Dana-Farber Cancer Institute. He holds an MD and PhDs in mathematics and molecular medicine. He completed his postdoctoral training at Dana-Farber. His mission is to advance precision medicine by identifying molecular vulnerabilities in tumor genomes, translating them into targeted therapies, and improving diagnostics in the clinical setting. His multidisciplinary training in medicine, biology, and mathematics allows him to approach complex problems from diverse perspectives. He is dedicated to training the next generation of interdisciplinary scientists by providing mentorship to researchers at various stages in their careers and integrating them into an inclusive and collaborative laboratory environment.

Nils Gehlenbord, PhD received his PhD from the University of Cambridge and was a predoctoral fellow at the European Bioinformatics Institute (EMBL-EBI). The goal of Gehlenborg’s research is to improve human health by developing computational techniques and interfaces that enable scientists and clinicians to efficiently interact with biomedical data. Tight integration of algorithmic approaches from biomedical informatics with advanced data visualization techniques is central to his efforts, as is close collaboration with clinicians and experimentalists. Currently, Gehlenborg is researching and developing novel tools to visualize heterogeneous data from large-scale cancer genomics studies such as The Cancer Genome Atlas, integrating visual and computational approaches to support sense-making in biology, and using software to support reproducible collaborative research in epigenomics and genomics.

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 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 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.

William (Bill) La Cava, PhD is a faculty member in CHIP at Boston Children’s Hospital and Harvard Medical School and directs the Cava Laboratory. He received his PhD from UMass Amherst with a focus on interpretable modeling of dynamical systems. Prior to joining CHIP, he was a post-doctoral fellow and research associate in the Institute for Biomedical Informatics at the University of Pennsylvania.

Maimuna (Maia) Majumder, PhD is an Assistant Professor in CHIP at Harvard Medical School and Boston Children’s Hospital. Her research applies artificial intelligence and machine learning methods to public health problems, with a focus on infectious disease surveillance using search query, mobile phone, and news+social media data. Since January 2020, Maia and her team have been actively responding to the ongoing COVID-19 pandemic.

Richard 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, 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.

Arjun (Rai) Manrai, PhD is an Assistant Professor at Harvard Medical School and Faculty in CHIP at Boston Children’s. Dr. Manrai has a PhD in Bioinformatics and Integrative Genomics from the Harvard-MIT Division of Health Sciences and Technology. His primary research focus is in cardiovascular medicine, genomics, machine learning, meta-science, and statistical methods.

Tim 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.

Lise Nigrovic, MD, MPH is HMS Associate Professor in Pediatrics and Emergency Medicine and a Senior Associate Physician in Medicine in the Division of Emergency Medicine at Boston Children's. Her research focus is the approach to diagnosis and management of children with infectious emergencies. She is the founding chair of the eight-center pediatric Lyme disease clinical research network, Pedi Lyme Net, with an associated pediatric biorepository funded by the Global Lyme Alliance, Department of Defense and NIAID. Dr. Nigrovic was recently awarded an over-the-cap R01 to support a twenty-center study to compare the effectiveness of oral doxycycline vs. IV ceftriaxone for the treatment of Lyme meningitis.  Previously she served for 15 years on the steering committee of Pediatric Emergency Medicine Applied Research Network (PECARN) and chair of the Pediatric Emergency Medicine Clinical Research Collaborative (PEM CRC) of the American Academy of Pediatrics.

Chirag 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, 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, 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.

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, 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. 

Collin Stultz, MD, PhD, is a professor in MIT’s Department of Electrical Engineering and Computer Science and co-Lead of the Harvard-MIT Division of Health Sciences and Technology, Institute of Medical Engineering and Sciences, and Research Laboratory of Electronics. He is also a cardiologist at the Massachusetts General Hospital. His Computational Cardiovascular Research Group is focused on developing and applying machine learning models that identify patients at high risk of adverse clinical events, and that identify optimal treatment strategies for high risk patients. His group combines computational modeling and machine learning to accomplish these tasks.

Kathleen Walsh, MD, MSc is Director of the Harvard-wide Pediatric Health Services Research Fellowship. Her research focuses on patient safety, particularly the safe care of children with chronic conditions in the outpatient and home setting. She has experience in the study medication errors and adverse drug events among children in the hospital, emergency department, clinic, and home. She has developed and evaluated health information technology interventions to support medication use. She visited the homes of children with sickle cell disease, cancer, and epilepsy in single site and multisite studies to understand barriers and facilitators of safe home medication use. In collaboration with parents of children with chronic conditions, she led the development, implementation, and testing of information technology interventions to improve home medication use. 

Griffin 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.

Supporting Faculty - (PEMRTP Graduates) 

Chris Cassa, PhD, 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.

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.

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. She is the one supporting faculty member who is not a graduate of PEMRTP. However, she has advised numerous PEMRTP and T15 informatics fellows on their research. 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. A PEMRTP graduate, he pioneered a new clinical subspecialty focus, the outpatient care of children after concussive injuries, and created the Concussion Clinic at BCH during his fellowship. Straight out of fellowship, he became Co-PI of a $100M grant to study sports concussion. 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.

Timothy J. Savage, MD, MPH, focuses on pediatric pharmacoepidemiology with an emphasis on real-world evidence (RWE) studies of antibiotics in children, using insurance claims data as a RWE source and conducting stratified analyses by the time before pediatric labeling and after pediatric approval.

Leadership

Program Director

Kenneth D. Mandl, MD, MPH 

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 exerts a sustained influence on the developing field of biomedical informatics. He was a real time biosurveillance  pioneer. Having long advocated for patient participation in producing and accessing data, Mandl was a designer of the first personal health and participatory surveillance systems. Cognizant of electronic health record system limitations, Mandl was a developer of SMART on FHIR (substitutable apps running universally on health IT) for innovators to reach large markets and patients and doctors to access an “app store for health.” Through his influence on the 21st Century Cures Act, federal regulations require support for SMART interfaces, ensuring standardized access to individual and population data at system scale, “without special effort.” He leads the federated Genomic Information Commons across nine top children’s hospitals and directs the Boston Children’s Hospital PrecisionLink Biobank for Health Discovery. Dr. Mandl has been elected to 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 he Presidential Early Career Award for Scientists and Engineers, the Donald A.B. Lindberg Award for Innovation in Informatics and the Clifford A. Barger Award for top mentors at Harvard Medical School. His trainees lead informatics in academia and in the world’s largest technology companies. He was advisor to two Directors of the CDC and chaired the Board of Scientific Counselors of the NIH’s National Library of Medicine. Dr. Mandl teaches and mentors extensively at the postgraduate level and leads this NIH-funded training program in biomedical informatics and genomics.

Informatics Track Director

Isaac Kohane, MD, PhD

Dr. Kohane directs the HMS Department of Biomedical Informatics 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 up collaborations at HMS and its hospital affiliates in the application of genomics and computer science in medicine. He leads the Coordinating Center for the NIH Undiagnosed Disease Network, 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

Joel Hirschhorn, MD, PhD

Dr. Hirschhorn is the Concordia Professor of Pediatrics and Professor of Genetics at HMS, a Senior Associate Member of the Broad Institute, 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, including asthma. 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 acute care populations.