Justin T. Baker, MD, PhD

Justin T. Baker, MD, PhD

McLean Hospital Title
Harvard Medical School Title
  • Associate Professor of Psychiatry


Justin T. Baker, MD, PhD, is the scientific director of the McLean Institute for Technology in Psychiatry (ITP) and director of the Laboratory for Functional Neuroimaging and Bioinformatics at McLean Hospital. He is also an associate professor of psychiatry at Harvard Medical School.

Dr. Baker’s research uses both large-scale studies and deep, multilevel phenotyping approaches to understand the nature and underlying biology of mental illnesses. He is a clinical psychiatrist with expertise in schizophrenia and bipolar spectrum disorders and other disorders of emerging adulthood. In 2016, Dr. Baker co-founded the ITP, a first-of-its-kind research and development center to foster tool development and novel applications of consumer technology in psychiatric research and care delivery.

Research Focus:

Dr. Baker’s Laboratory for Functional Neuroimaging and Bioinformatics conducts research to understand the nature and underlying biology of mental illnesses, particularly lifelong conditions such as schizophrenia and bipolar disorder. The goal of this work is to develop more effective strategies to both monitor the course of illness and intervene in creative ways to improve the lives of individuals struggling with these conditions.

A central focus of the Baker lab is to understand how the architecture of the human brain changes as a function of psychiatric illness. Historically, most research on the biological origins of psychiatric illness has focused on individual diagnostic categories studied in isolation. Mounting evidence indicates that nominally distinct psychiatric diagnoses are not separated by clear neurobiological boundaries. The lab uses multiple behavioral, neuroimaging, and computational approaches to experimentally disentangle how changes in human brain network function and organization ultimately give rise to changes in behavior.

One set of studies captures a narrow slice in time from many individuals to better understand how differences in the brain relate to differences in behavioral expression between individuals, such as at the level of disorder labels (i.e., “diagnoses”) or more continuous patterns of symptom expression at a single point in time. One recent study derived functional connectomic signatures in over 1,000 individuals, including patients presenting with different types and severities of impairment, and found features of both shared and specific connectomic functioning. These data have important implications for the establishment of functional connectomic fingerprints of severe mental disease that may lead toward biologically based understanding across a wide range of clinical presentations.

And yet, no two brains are identical. Moreover, individual brains change over time in ways that may be clinically significant and biologically important. A second set of studies uses “deep phenotyping” or “N-of-1” approaches to explore how changes within an individual’s brain over time reflect changes in their symptom experiences, how they perceive the world, and how they express behavior. The essence of this work is to combine multiple measurement modalities—such as audiovisual recordings, electronic health record data, activity from personal tracking devices and smartphones, as well conventional measures including subjective reports from patients and clinicians—to capture the rich interplay between clinical and behavioral responses over time at the individual level, and thereby deepen our understanding of the relationships between subjective and objective measures of psychiatric illness. This push toward understanding the brain and behavior at the individual level is critical for clinical translation as well as addressing a number of open questions about how transient brain states may influence behavior.

The lab’s current deep phenotyping projects use single-case experimental designs in individuals with severe conditions including bipolar disorder, schizophrenia, borderline personality disorder, and obsessive compulsive disorder. By applying computational approaches, such as latent construct modeling, machine learning, and dynamical systems analysis, the data collected from each study—and each individual—can reveal key relationships to advance human neuroscience and develop novel, personalized therapeutics.

In addition to basic and translational neuroscience and behavioral studies, the Baker lab conducts both clinical research and quality improvement studies to engage clinicians and other care providers to integrate tools developed in the lab into clinical practice. Past projects have included trials of smartphone apps for case management and peer support in early and chronic psychosis, respectively, as well as during the immediate period following acute hospitalization to reduce readmission rates. Current projects seek to incorporate continuous wearable actigraphy into clinical workflows for sleep and movement monitoring in several of McLean’s inpatient and residential services, and automated interview analytics into workflows for clinical assessment, using computer vision, acoustic analysis, and natural language processing.

As co-founder and scientific director of the McLean Institute for Technology in Psychiatry, Dr. Baker oversees the development of computational phenotyping approaches to be applied in both cutting-edge research and technology-enabled care. In addition to pushing the envelope of what can be achieved with current technologies to improve access to high-quality mental health care, the ITP also scrutinizes consumer technology’s potential downsides, such as overuse patterns conferring risk for psychiatric illnesses and social dysfunction. Dr. Baker currently serves as the principal or co-investigator on multiple federal and philanthropic grants to develop methods for intensive, longitudinal assessment in complex psychiatric conditions, as well as advancing study of the social, legal, and ethical implications of these novel approaches.

Dr. Baker also helped launch and currently serves as a senior faculty advisor for the MGH-McLean Adult Psychiatry Residency Training Program’s Physician Scientist Training Program in Psychiatry. This NIH R25-funded research education program fosters research and training for psychiatrists committed to pursuing a research career and addressing the critical shortage of physician-scientists in psychiatry. Over the past decade, he has mentored dozens of trainees at every level of training (from high school to clinical fellowships) and remains actively engaged in teaching and navigating careers in the clinical neurosciences.

  • Crystal Blankenbaker, Clinical Research Assistant
  • Katie Fairbank-Haynes, MA, Clinical Research Assistant
  • Einat Liebenthal, DSc, Associate Director
  • Robert Patterson, MD, Research Volunteer
  • Habib Rahimi-Eichi, PhD, Research Associate
Selected Publications:

Baker JT, Germine LT, Ressler KJ, Rauch SL, Carlezon WA Jr. Digital devices and continuous telemetry: opportunities for aligning psychiatry and neuroscience. Neuropsychopharmacology 2018;43(13):2499-2503.

Baker JT, Dillon DG, Patrick LM, Roffman JL, Brady RO Jr, Pizzagalli DA, Öngür D, Holmes AJ. Functional connectomics of affective and psychotic pathology. Proceedings of the National Academy of Sciences USA. 2019.

Mueller NE, Panch T, Macias C, Cohen BM, Öngür D, Baker JT (2018). Using smartphone apps to promote psychiatric rehabilitation in a peer-led community support program: pilot study. JMIR Mental Health 2019;5(3).

PubMed search for Dr. Baker

Education & Training

  • 1997 ScB, Brown University
  • 2007 MD, PhD, Washington University in St. Louis
  • 2007-2008 Medicine Internship, Newton-Wellesley Hospital
  • 2007-2011 Residency in Psychiatry, Massachusetts General Hospital/McLean Hospital
Board Certifications:
  • 2008 Medical License, Board of Registration in Medicine, Commonwealth of Massachusetts
  • 2011 Psychiatry, American Board of Psychiatry and Neurology


Phone: 617.855.3913
Office Address: Belmont campus - McLean Imaging Center, Room 189