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Research Lab Results for functional genomics

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  • Beer Lab

    Lab Website

    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 Areas: computational biology, biomedical engineering, DNA, genomics, RNA
  • Li Gao Lab

    Principal Investigator:
    Li Gao, M.D., Ph.D.
    Medicine

    The Li Gao Lab researches functional genomics, molecular genetics and epigenetics of complex cardiopulmonary and allergic diseases, with a focus on translational research applying fundamental genetic insight into the clinical setting. Current research includes implementation of high-throughput technologies in the fields of genome-wide association studies (GWAS), massively parallel sequencing, gene expression analysis, epigenetic mapping and integrative genomics in ongoing research of complex lung diseases and allergic diseases including asthma, atopic dermatitis (AD), pulmonary arterial hypertension, COPD, sepsis and acute lung injury/ARDS; and epigenetic contributions to pulmonary arterial hypertension associated with systemic sclerosis.

    Research Areas: pulmonary arterial hypertension, molecular genetics, cardiopulmonary diseases, asthma, epigenetics, complex lung disease, allergies, genomics, COPD, atopic dermatitis
  • Phenotyping and Pathology Core

    Lab Website
    Principal Investigator:
    Cory Brayton, D.V.M.
    Molecular and Comparative Pathobiology

    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.

    Research Areas: pathobiology, phenotyping, translational research, genomics
  • Seth Blackshaw Lab

    Lab Website
    Principal Investigator:
    Seth Blackshaw, Ph.D.
    Neuroscience

    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.

    Research Areas: retina, central nervous system, biochemistry, hypothalamus, proteomics, genomics
  • Tamara O'Connor Lab

    The O'Connor Lab studies the molecular basis of infectious disease using Legionella pneumophila pathogenesis as a model system.

    We are looking at the network of molecular interactions acting at the host-pathogen interface. Specifically, we use L. pneumophila pathogenesis to examine the numerous mechanisms by which an intracellular bacterial pathogen can establish infection, how it exploits host cell machinery to accomplish this, and how individual proteins and their component pathways coordinately contribute to disease.

    We are also studying the role of environmental hosts in the evolution of human pathogens. Using genetics and functional genomics, we compare and contrast the repertoires of virulence proteins required for growth in a broad assortment of hosts, how the network of molecular interactions differs between hosts, and the mechanisms by which L. pneumophila copes with this variation.

    Research Areas: infectious disease, Legionella pneumophila, genomics, pathogenesis, molecular biology
  • Zhaozhu Qiu Laboratory

    Lab Website
    Principal Investigator:
    Zhaozhu Qiu, Ph.D.
    Neuroscience
    Physiology

    Ion channels are pore-forming membrane proteins gating the flow of ions across the cell membrane. Among their many functions, ion channels regulate cell volume, control epithelial fluid secretion, and generate the electrical impulses in our brain. The Qiu Lab employs a multi-disciplinary approach including high-throughput functional genomics, electrophysiology, biochemistry, and mouse genetics to discover novel ion channels and to elucidate their role in health and disease.

    Research Areas: ion channel, neurological disease, electrophysiology, functional genomics, sensory neuroscience
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