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Christopher Walsh

M.D., Ph.D.

Chief, Division of Genetics and Genomics, Boston Children’s Hospital

Bullard Professor of Pediatrics and Neurology at Harvard Medical School

Investigator, Howard Hughes Medical Institute

Director and co-PI, Allen Discovery Center for Human Brain Evolution

Associate Member, Broad Institute of MIT and Harvard

Dr. Walsh completed his MD and PhD degrees at The University of Chicago, neurology residency and chief residency at Massachusetts General Hospital, and postdoctoral training in Genetics with Professor Connie Cepko at Harvard Medical School. In 1993 he became Assistant Professor of Neurology at Harvard and Beth Israel-Deaconess Medical Center and was promoted to Bullard Professor of Neurology in 1999. In 2002 he was appointed an Investigator of the Howard Hughes Medical Institute. From 2003-2007 he served as Director of the Harvard-MIT Combined MD-PhD training program. He moved to Boston Children’s Hospital in 2006, becoming Chief of Genetics, which in 2014 merged with the Program in Genomics to become the Division of Genetics and Genomics.  The Division contains more than thirty full-time faculty members, roughly evenly divided between clinicians treating children with rare genetic disease, and researchers studying the genetic causes of human illness.

Dr. Walsh’s research has focused on the development and function of the human cerebral cortex, pioneering the analysis of genetic diseases that affect the developing brain, resulting in epilepsy, intellectual disability, autism spectrum disorders, and other conditions. His lab has identified more than three dozen neurological disease genes by establishing world-wide collaborations and pioneering the analysis of recessive brain disorders in countries where marriage between distant relatives is common. He has described how a few disease genes essential for constructing the brain were also important targets of the evolutionary processes that shaped the human brain, resulting in the founding of the Allen Discovery Center for Human Brain Evolution in 2017. Recent work has pioneered the understanding of clonal somatic mutations as important causes of human focal epilepsy and autism, and the remarkable genomic diversity of single neurons in human brain.

Dr. Walsh’s research has been recognized by a Javits Award from the NINDS, the Dreifuss-Penry Epilepsy Award from the American Academy of Neurology, the Derek Denny-Brown and Jacoby Awards from the American Neurological Association, the Clinical Research Award from the American Epilepsy Society, the Pruzhansky Award from the American College of Medical Genetics, the Cajal Club Discoverer Award, the Perl-Neuroscience Award from the University of North Carolina, the Distinguished Alumni Award from the University of Chicago, and the Gruber Neuroscience Prize in 2021. Dr. Walsh is an elected fellow of the American Association for the Advancement of Sciences, and an elected member of the American Association of Physicians, the National Academy of Medicine, the American Academy of Arts and Sciences, and the National Academy of Sciences.

Christopher Walsh

M.D., Ph.D.

Chief, Division of Genetics and Genomics, Boston Children’s Hospital

Bullard Professor of Pediatrics and Neurology at Harvard Medical School

Investigator, Howard Hughes Medical Institute

Director and co-PI, Allen Discovery Center for Human Brain Evolution

Associate Member, Broad Institute of MIT and Harvard

Dr. Walsh completed his MD and PhD degrees at The University of Chicago, neurology residency and chief residency at Massachusetts General Hospital, and postdoctoral training in Genetics with Professor Connie Cepko at Harvard Medical School. In 1993 he became Assistant Professor of Neurology at Harvard and Beth Israel-Deaconess Medical Center and was promoted to Bullard Professor of Neurology in 1999. In 2002 he was appointed an Investigator of the Howard Hughes Medical Institute. From 2003-2007 he served as Director of the Harvard-MIT Combined MD-PhD training program. He moved to Boston Children’s Hospital in 2006, becoming Chief of Genetics, which in 2014 merged with the Program in Genomics to become the Division of Genetics and Genomics.  The Division contains more than thirty full-time faculty members, roughly evenly divided between clinicians treating children with rare genetic disease, and researchers studying the genetic causes of human illness.

Dr. Walsh’s research has focused on the development and function of the human cerebral cortex, pioneering the analysis of genetic diseases that affect the developing brain, resulting in epilepsy, intellectual disability, autism spectrum disorders, and other conditions. His lab has identified more than three dozen neurological disease genes by establishing world-wide collaborations and pioneering the analysis of recessive brain disorders in countries where marriage between distant relatives is common. He has described how a few disease genes essential for constructing the brain were also important targets of the evolutionary processes that shaped the human brain, resulting in the founding of the Allen Discovery Center for Human Brain Evolution in 2017. Recent work has pioneered the understanding of clonal somatic mutations as important causes of human focal epilepsy and autism, and the remarkable genomic diversity of single neurons in human brain.

Dr. Walsh’s research has been recognized by a Javits Award from the NINDS, the Dreifuss-Penry Epilepsy Award from the American Academy of Neurology, the Derek Denny-Brown and Jacoby Awards from the American Neurological Association, the Clinical Research Award from the American Epilepsy Society, the Pruzhansky Award from the American College of Medical Genetics, the Cajal Club Discoverer Award, the Perl-Neuroscience Award from the University of North Carolina, the Distinguished Alumni Award from the University of Chicago, and the Gruber Neuroscience Prize in 2021. Dr. Walsh is an elected fellow of the American Association for the Advancement of Sciences, and an elected member of the American Association of Physicians, the National Academy of Medicine, the American Academy of Arts and Sciences, and the National Academy of Sciences.

Recent Publications

The Somatic Mosaicism across Human Tissues Network

Published On 2025 Jul 03

Journal article

From fertilization onwards, the cells of the human body acquire variations in their DNA sequence, known as somatic mutations. These postzygotic mutations arise from intrinsic errors in DNA replication and repair, as well as from exposure to mutagens. Somatic mutations have been implicated in some diseases, but a fundamental understanding of the frequency, type and patterns of mutations across healthy human tissues has been limited. This is primarily due to the small proportion of cells...


High-resolution detection of copy number alterations in single cells with HiScanner

Published On 2025 Jul 02

Journal article

Improvements in single-cell whole-genome sequencing (scWGS) assays have enabled detailed characterization of somatic copy number alterations (CNAs) at the single-cell level. Yet, current computational methods are mostly designed for detecting chromosome-scale changes in cancer samples with low sequencing coverage. Here, we introduce HiScanner (High-resolution Single-Cell Allelic copy Number callER), which combines read depth, B-allele frequency, and haplotype phasing to identify CNAs with high...