The overall goal of the Auditory Brainstem Library is to understand how abnormal auditory input from the ear affects the brainstem, and how the brain in turn affects activity in the ear through efferent feedback loops. Our emphasis is on understanding the effects of different forms of acquired hearing loss (genetic, conductive, noise-induced, age-related, traumatic brain injury-related) and environmental noise. We are particularly interested in plastic changes in the brain that compensate for some aspects of altered auditory input, and how those changes relate to central auditory processing deficits, tinnitus, and hyperacusis. Understanding these changes will help refine therapeutic strategies and identify new targets for treatment. We collaborate with other labs in the Depts. of Otolaryngology, Neuroscience, Neuropathology, the Wilmer Eye Institute, and the Applied Physics Laboratory at Johns Hopkins, in addition to labs outside the university to increase the impact and clinical relevance of our research.

Work in the Ayse Gurses Lab examines several topics related to human factors, including methods for improving patient safety in the cardiac operating room, care coordination, transitions of care and compliance of providers with evidence-based guidelines. Our team also has an interest in research that explores the working conditions of nurses. We collaborate on studies related to the development of geriatrics health service delivery at all levels of the health system.

Research in the Bakker Memory Laboratory is focused on understanding the mechanisms and brain networks underlying human cognition with a specific focus on the mechanisms underlying learning and memory and the changes in memory that occur with aging and disease. We use a variety of techniques including neuropsychological assessments, experimental behavioral assessments and particularly advanced neuroimaging methods to study these questions in young and older adults and patients with mild cognitive impairment, Alzheimer’s disease, Parkinson’s disease and epilepsy. Through our collaborations with investigators in both basic science and clinical departments, including the departments of Psychiatry and Behavioral Sciences, Psychological and Brain Sciences, Neurology and Public Health, our research also focuses on brain systems involved in spatial navigation and decision-making as well as cognitive impairment in neuropsychiatric conditions such as schizophrenia, eating disorders, obsessive-compulsive disorders, depression and anxiety.

The Balagopal Lab has adapted high-resolution tools to study viruses in situ. Specifically, we were the first to quantify hepatitis C virus (HCV) infection in single hepatocytes by developing single-cell laser capture microdissection (scLCM) and integrating this tool with highly sensitive quantitative real-time PCR. We reported that HCV infects a minority of hepatocytes that are found in geospatial clusters. More recently, we (PIs Balagopal and Thio) integrated scLCM with droplet digital PCR (ddPCR) to reveal the first observations of hepatitis B virus (HBV) infection at single cell resolution in the liver. We found that HBV infects nearly all hepatocytes prior to antiviral therapy. However, during antiviral therapy, HBV infection is diminished while viral transcription is markedly attenuated. Our lab has also focused on HIV-1 infection and immune activation for over a decade. Most recently, we have studied type 1 interferon responses to HIV-1 using RNA sequencing (RNAseq). Using this technology, we identified novel interferon-stimulated genes (ISGs) that are associated with HIV-1 restriction in vivo.

The goal of research in the Beer Lab is to understand how gene regulatory information is encoded in genomic DNA sequence. Our work uses functional genomics DNase-seq, ChIP-seq, RNA-seq, and chromatin state data to computationally identify combinations of transcription factor binding sites that operate to define the activity of cell-type specific enhancers. We are currently focused on improving SVM methodology by including more general sequence features and constraints predicting the impact of SNPs on enhancer activity (delta-SVM) and GWAS association for specific diseases, experimentally assessing the predicted impact of regulatory element mutation in mammalian cells, systematically determining regulatory element logic from ENCODE human and mouse data, and using this sequence based regulatory code to assess common modes of regulatory element evolution and variation.

Research in the Benjamin Bodnar Lab focuses on global health, particularly the application of quality-improvement techniques in resource-limited and developing health care environments. Lab work utilizes insights gained through Dr. Bodnar's past work with projects including Partners in Health, The Millennium Villages Project and the Mulago University-Yale University Collaboration in Uganda.

The Berger Lab's research is focused on understanding how multi-subunit assemblies use ATP for overcoming topological challenges within the chromosome and controlling the flow of genetic information. A long-term goal is to develop mechanistic models that explain in atomic level detail how macromolecular machines transduce chemical energy into force and motion, and to determine how cells exploit and control these complexes and their activities for initiating DNA replication, shaping chromosome superstructure and executing myriad other essential nucleic-acid transactions. Our principal approaches include a blend of structural (X-ray crystallography, single-particle EM, SAXS) and solution biochemical methods to define the architecture, function, evolution and regulation of biological complexes. We also have extensive interests in mechanistic enzymology and the study of small-molecule inhibitors of therapeutic potential, the development of chemical approaches to trapping weak protein/protein and protein/nucleic acid interactions, and in using microfluidics and single-molecule approaches for biochemical investigations of protein dynamics.

The Bert Vogelstein Laboratory seeks to develop new approaches to the prevention or treatment of cancers through a better understanding of the genes and pathways underlying their pathogenesis. Our major focus is on cancers of the colon and rectum. We have shown that each colon neoplasm arises from a clonal expansion of one transformed cell. This expansion gives rise to a small benign colon tumor (called a polyp or adenoma). This clonal expansion and subsequent growth of the tumors appears to be caused by mutations in oncogenes and tumor suppressor genes, and the whole process is accelerated by defects in genes required for maintaining genetic instability. Mutations in four or five such genes are required for a malignant tumor to form, while fewer mutations suffice for benign tumorigenesis. As the mutations accumulate, the tumors become progressively more dangerous. Current studies are aimed at the further characterization of the mechanisms through which these genes act, the identification of other genes that play a role in this tumor type, and the application of this knowledge to patient management.

The Best Laboratory focus on therapeutic vaccine development for HPV-related diseases by developing a murine model of papilloma analogous to Recurrent Respiratory Papillomatosis (RRP) for testing of DNA vaccine technology. We also work to understand the immunosuppressive tumor microenvironment that facilitates RRP development, and translate this work into novel therapies and clinical practice.

Research in the Hansoti Lab centers on the intersection of public health interventions for vulnerable populations and emergency department care. The lab employs implementation science methodologies, with a particular emphasis on mixed-methods research to design, develop, and evaluate innovative, evidence-based strategies that support socially vulnerable patients.

In South Africa, the team is pioneering strategies to enhance HIV prevention and intervention delivery within emergency departments, focusing on improving HIV service delivery for patients missed within the health system and delivering preventative care strategies to patients at high risk of HIV acquisition. These efforts are concentrated at Tygerberg Hospital and Gugulethu Clinic, in partnership with the Desmond Tutu HIV Foundation.

Domestically, the lab conducts research on opioid use disorder (OUD), specifically addressing post-discharge health system challenges related to linkage to care and retention for patients prescribed medications for opioid use disorder (MOUD). This includes addressing social determinants of health to strengthen HIV services for patients who present to the ED.

Additionally, Dr. Hansoti has a dedicated focus on surveillance strategies for high-consequence pathogens in emergency departments. She serves as the Principal Investigator for the Clinical Characterization Protocol for Severe Emerging Infections (CCPSEI) and manages cohorts for both COVID-19 and mpox, in collaboration with experts in public health, epidemiology, and infectious diseases from the Johns Hopkins School of Public Health.