Research in the Salzberg Lab focuses on the development of new computational methods for analysis of DNA from the latest sequencing technologies. Over the years, we have developed and applied software to many problems in gene finding, genome assembly, comparative genomics, evolutionary genomics and sequencing technology itself. Our current work emphasizes analysis of DNA and RNA sequenced with next-generation technology.

The Seth Blackshaw Lab uses functional genomics and proteomics to rapidly identify the molecular mechanisms that regulate cell specification and survival in both the retina and hypothalamus. We have profiled gene expression in both these tissues, from the start to the end of neurogenesis, characterizing the cellular expression patterns of more than 1,800 differentially expressed transcripts in both tissues. Working together with the lab of Heng Zhu in the Department of Pharmacology, we have also generated a protein microarray comprised of nearly 20,000 unique full-length human proteins, which we use to identify biochemical targets of developmentally important genes of interest.

The Gail Geller Lab primarily conducts empirical quantitative and qualitative research on the ethical and social implications of genetic testing in the adult, pediatric and family contexts. We have focused on clinical-patient communication under conditions of uncertainty; professionalism and humanism in medical education; cross-cultural variation in concepts of health and disease; and clinician suffering and moral distress. We explore these topics in a range of health care contexts, including genomics, complementary and alternative medicine (CAM) and palliative care. Our researchers have a longstanding interest in medical socialization, provider-patient communication under conditions of uncertainty and cultural differences in attitudes toward health and disease. We also explore the intersection of CAM and bioethics, as well as the role of palliative care in chronic diseases, such as muscular dystrophy and sickle cell disease.

Work in the Christopher Chute Lab involves the management of clinical data to enable effective evidence-based clinical practice and translational research. Recently, we developed an EHR-based genetic testing knowledge base to be integrated into the genetic testing ontology (GTO) and identified potential barriers to pharmacogenomics clinical decision support (CDS) implementation.

Research in the Casey Overby Lab focuses on the intersection of public health genomics and biomedical informatics. We’re currently developing applications to support the translation of genomic research to clinical and population-based health care settings. We’re also working to develop knowledge-based ways to use big data — including electronic health records — to improve population health.

The Phenotyping Core promotes functional genomics and other preclinical translational science at Johns Hopkins. We assist and collaborate in the characterization and use of genetically and phenotypically relevant animal models of disease and gene function.

The Feinberg Laboratory studies the epigenetic basis of normal development and disease, including cancer, aging and neuropsychiatric illness. Early work from our group involved the discovery of altered DNA methylation in cancer as well as common epigenetic (methylation and imprinting) variants in the population that may be responsible for a significant population-attributable risk of cancer. Over the last few years, we have pioneered the field of epigenomics (i.e., epigenetics at a genome-scale level), founding the first NIH-supported NIH epigenome center in the country and developing many novel tools for molecular and statistical analysis. Current research examines the mechanisms of epigenetic modification, the epigenetic basis of cancer, the invention of new molecular, statistical, and epidemiological tools for genome-scale epigenetics and the epigenetic basis of neuropsychiatric disease, including schizophrenia and autism.

Human induced pluripotent stem cells (hiPSCs) provide unprecedented opportunities for cell replacement approaches, disease modeling and drug discovery in a patient-specific manner. The Gabsang Lee Lab focuses on the neural crest lineage and skeletal muscle tissue, in terms of their fate-determination processes as well as relevant genetic disorders. Previously, we studied a human genetic disorder (familial dysautonomia, or FD) with hiPSCs and found that FD-specific neural crest cells have low levels of genes needed to make autonomous neurons--the ones needed for the ""fight-or-flight"" response. In an effort to discover novel drugs, we performed high-throughput screening with a compound library using FD patient-derived neural crest cells. We recently established a direct conversion methodology, turning patient fibroblasts into ""induced neural crest (iNC)"" that also exhibit disease-related phenotypes, just as the FD-hiPSC-derived neural crest. We're extending our research to the neural crest's neighboring cells, somite. Using multiple genetic reporter systems, we identified sufficient cues for directing hiPSCs into somite stage, followed by skeletal muscle lineages. This novel approach can straightforwardly apply to muscular dystrophies, resulting in expandable myoblasts in a patient-specific manner.

Dr. Colantuoni and his colleagues explore human brain development and molecular mechanisms that give rise to risk for complex brain disease. His team uses genomic technologies to examine human brain tissue as well as stem models and vast public data resources.

The Bigos Lab focuses on a Precision Medicine approach to the treatment of psychiatric illness. In addition, this lab employs functional neuroimaging and genetics as biomarkers in neuropsychiatric drug development. A recent study used functional MRI to test the neural effects of a drug with the potential to treat cognitive dysfunction in schizophrenia. Other studies aim to identify patient-specific variables including sex, race, and genetics that impact drug clearance and clinical response to better select and dose antipsychotics and antidepressants.