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Displaying 1 to 20 of 74 results for genomics

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  • Alan Scott Lab

    Research in the Alan Scott Lab involves several important areas of genomics. Our team collaborates on a study to investigate the exon and genome sequence variants that determine phenotype, with a specific focus on the genetic bases of cleft lip and palate. We are also involved in assessing and improving genomic technologies to provide next-generation sequencing and analysis of sequence data to the clinical environment. In addition, we have a longstanding interest in the problem of gene annotation and the evolutionary genomics of vertebrates, especially endangered species.

    Research Areas: evolutionary genomics, sequence analysis, genomics, genome annotation, genomic technologies, cleft lip and palate

    Principal Investigator

    Alan Scott, Ph.D.

    Department

    Medicine

  • Alison Moliterno Lab

    The Alison Moliterno Lab studies the molecular pathogenesis of myeloproliferative disorders (MPDs), including polycythemia vera, essential thrombocytosis and idiopathic myelofibrosis. Our research is focused on the genetic and epigenetic lesions associated with MPDs, with the goal of improving diagnosis and treatment for these disorders.

    Research Areas: blood disorders, idiopathic myelofibrosis, essential thrombocytosis, epigenetics, genomics, polycythemia vera, myeloproliferative disorders

    Principal Investigator

    Alison Moliterno, M.D.

    Department

    Medicine

  • Andrew Feinberg Laboratory

    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.

    Research Areas: autism, cancer, epigenetics, schizophrenia, human development, aging, DNA, genomics, neuropsychiatric disease

    Lab Website

    Principal Investigator

    Andrew Feinberg, M.D., M.P.H.

    Department

    Medicine

  • Andrew McCallion Laboratory

    The McCallion Laboratory studies the roles played by cis-regulatory elements (REs) in controlling the timing, location and levels of gene activation (transcription). Their immediate goal is to identify transcription factor binding sites (TFBS) combinations that can predict REs with cell-specific biological control--a first step in developing true regulatory lexicons.

    As a functional genetic laboratory, we develop and implement assays to rapidly determine the biological relevance of sequence elements within the human genome and the pathological relevance of variation therein. In recent years, we have developed a highly efficient reporter transgene system in zebrafish that can accurately evaluate the regulatory control of mammalian sequences, enabling characterization of reporter expression during development at a fraction of the cost of similar analyses in mice. We employ a range of strategies in model systems (zebrafish and mice), as well as analyses in the human population, to illu...minate the genetic basis of disease processes. Our long-term objective is to use these approaches in contributing to improved diagnostic, prognostic and therapeutic strategies in patient care. view more

    Research Areas: cell biology, genomics, gene regulation, nervous system

    Principal Investigator

    Andrew McCallion, Ph.D.

    Department

    Molecular and Comparative Pathobiology

  • Beer Lab

    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

  • Berger Lab

    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/p...rotein and protein/nucleic acid interactions, and in using microfluidics and single-molecule approaches for biochemical investigations of protein dynamics. view more

    Research Areas: biochemistry, proteomics, ATP, DNA, genomics

  • Bert Vogelstein Laboratory

    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 ident...ification of other genes that play a role in this tumor type, and the application of this knowledge to patient management. view more

    Research Areas: rectal cancer, colon cancer, genomics, pathogenesis

    Lab Website

    Principal Investigator

    Bert Vogelstein, M.D.

    Department

    Oncology

  • Brady Maher Laboratory

    The Brady Maher Laboratory is interested in understanding the cellular and circuit pathophysiology that underlies neurodevelopmental and psychiatric disorders. Our lab focuses on trying to understand the function of genes that are associated with neurodevelopment problems by manipulating their expression level in utero during the peak of cortical development. We then use a variety of approaches and technologies to identify resulting phenotypes and molecular mechanisms including cell and molecular biology, optogenetics, imaging and electrophysiology.

    Current projects in the lab are focused on understanding the function of transcription factor 4 (TCF4), a clinically pleiotropic gene. Genome-wide association studies have identified genetic variants of TCF4 that are associated with schizophrenia, while autosomal dominant mutations in TCF4 result in Pitt Hopkins syndrome. Using our model system, we have identified several interesting electrophysiological and cell biological phenotypes as...sociated with altering the expression of TCF4 in utero. We hypothesize that these phenotypes represent cellular pathophysiology related to these disorders and by understanding the molecular mechanisms responsible for these phenotypes we expect to identify therapeutic targets for drug development.
    view more

    Research Areas: cell biology, neurodevelopment, imaging, schizophrenia, psychiatric disorders, Pitt Hopkins syndrome, elecrophysiology, genomics, drugs, optogenetics, molecular biology, phenotypes

  • Carlo Colantuoni Laboratory

    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.

    Research Areas: stem cells, brain tissue, brain development, genomics

    Principal Investigator

    Carlo Colantuoni, Ph.D.

    Department

    Neurology
    Neuroscience

  • Casey Overby Lab

    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.

    Research Areas: public health, genomics, electronic health records, bioinformatics

    Principal Investigator

    Casey Taylor, Ph.D.

    Department

    Medicine

  • Chloe Thio Lab

    Research in the Chloe Thio lab focuses on several areas. First, HBV virology and immunology in HBV monoinfected and HIV-HBV co-infected individuals that will ultimately help develop a cure for HBV. Second, HCV infection in men who have sex with men. Third, non-alcoholic fatty liver disease with a focus on HIV-infected individuals. Fourth, host genetic determinants of spontaneous HBV recovery and HCV clearance.

    Research Areas: HIV-HBV co-infection, hepatitis B, genomics, hepatitis C, fatty liver

    Principal Investigator

    Chloe Thio, M.D.

    Department

    Medicine

  • Christopher Chute Lab

    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 Areas: pharmacogenomics, genomics, electronic health records, bioinformatics, evidence-based medicine, phenotypes

  • Daniel Weinberger Laboratory

    The Daniel Weinberger Laboratory focuses on the neurobiological mechanisms of genetic risk for developmental brain disorders. We study the genetic regulation of the transcriptome in normal human brain across the human life span and in brains from patients with various psychiatric disorders. We also study the impact of genetic variation on aspects of human brain development and function linked with risk for schizophrenia and related psychiatric disorders. Our lab uses unique molecular and clinical datasets and biological materials from a large sample of families with affected and unaffected offspring and normal volunteers. These datasets include DNA, lymphoblast and fibroblast cell lines, and extensive quantitative phenotypes related to genetic risk for schizophrenia, including detailed cognitive assessments and various neuroimaging assays. In other research, we are working on a human brain transcriptome project that is RNA sequencing over 1,000 human brain samples in various regi...ons and based also on sorting of specific celliular phentypes. We are exploring the molecular processing of the gene and its implications for cognition and aspects of human temperament. view more

    Research Areas: neurobiology, brain, transcriptome, schizophrenia, psychiatric disorders, genomics, developmental disorders, RNA

  • Daria Gaykalova Lab

    The Daria Gakalova Lab defines the functional role of epigenetics in transcriptional regulation of head and neck squamous cell carcinoma (HNSCC) progression. To evaluate the whole-genome distribution of various histone marks, her team is using chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-Seq) for primary tissues, a method recently developed by her lab. The research group of Daria Gaykalova was the first to demonstrate the cancer-specific distribution of H3K4me3 and H3K27ac marks and their role in cancer-related gene expression in HNSCC. The research showed that an aberrant chromatin alteration is a central event in carcinogenesis and that the therapeutic control of chromatin structure can prevent the primary of secondary cancerization. Further preliminary data suggest that the differential enrichment of these disease-specific histone marks and DNA methylation correlate with alternative splicing events (ASE) formation. For this project, Dr. Gaykalova... and her team employed a novel bioinformatical tool for the detection of cancer-specific ASEs. Through thorough functional validation of the individual ASEs, the lab demonstrated that each of them has a unique mechanism of malignant transformation of the cells. Due to high disease specificity, ASEs represent the perfect biomarkers of the neoantigens and have direct application to clinical practice. view more

    Research Areas: Head and neck squamous cell carcinoma, Human papillomavirus, Alternative splicing, epigenetics, Chromatin structure, Cancer genomics, head and neck cancer

  • David Moller Lab

    Research in the David Moller Lab focuses on sarcoidosis, a potentially fatal inflammatory disease characterized by tiny clumps of inflammatory cells that scar the lungs, lymph nodes, skin and other major organs. We’re currently involved in a clinical trial related to genomic research in sarcoidosis and a clinical trial related to genomic research in Alpha-1 antitrypsin deficiency. Previously, we led a project that identified a potential protein trigger responsible for sarcoidosis.

    Research Areas: Alpha-1 antitrypsin deficiency, sarcoidosis, genomics

    Principal Investigator

    David Moller, M.D.

    Department

    Medicine

  • Devreotes Laboratory

    The Devreotes Laboratory is engaged in genetic analysis of chemotaxis in eukaryotic cells. Our long-term goal is a complete description of the network controlling chemotactic behavior. We are analyzing combinations of deficiencies to understand interactions among network components and carrying out additional genetic screens to identify new pathways involved in chemotaxis. A comprehensive understanding of this fascinating process should lead to control of pathological conditions such as inflammation and cancer metastasis.

    Research Areas: biochemistry, cell biology, chemotaxis, cancer, genomics, inflammation

    Lab Website

    Principal Investigator

    Peter Devreotes, Ph.D.

    Department

    Cell Biology

  • Dhananjay Vaidya Lab

    Research conducted in the Dhananjay Vaidya Lab focuses on the prevention of heart disease, with special emphasis on cardiometabolic risk factors, genetics in high-risk families, cardiovascular epidemiology, statistics and vascular biology. We also provide consultation on study design as well as plan and oversee data analyses for projects supported by the Center for Child and Community Health Research.

    Research Areas: heart disease, epidemiology, data analysis, cardiometabolic risk factors, statistics, study design, cardiovascular, genomics, vascular biology

    Principal Investigator

    Jay Vaidya, M.B.B.S., M.P.H., Ph.D.

    Department

    Medicine

  • Erika Matunis Laboratory

    The Erika Matunis Laboratory studies the stem cells that sustain spermatogenesis in the fruit fly Drosophila melanogaster to understand how signals from neighboring cells control stem cell renewal or differentiation. In the fruit fly testes, germ line stem cells attach to a cluster of non-dividing somatic cells called the hub. When a germ line stem cell divides, its daughter is pushed away from the hub and differentiates into a gonialblast. The germ line stem cells receive a signal from the hub that allows it to remain a stem cell, while the daughter displaced away from the hub loses the signal and differentiates. We have found key regulatory signals involved in this process. We use genetic and genomic approaches to identify more genes that define the germ line stem cells' fate. We are also investigating how spermatogonia reverse differentiation to become germ line stem cells again.

    Research Areas: stem cells, spermatogenesis, genomics, molecular biology

    Lab Website

    Principal Investigator

    Erika Matunis, Ph.D.

    Department

    Cell Biology

  • Erwin Lab

    Schizophrenia, autism and other neurological disorders are caused by a complex interaction between inherited genetic risk and environmental experiences. The overarching goal of the group are to reveal molecular mechanisms of gene by environment interactions related to altered neural development and liability for brain disorders. Our research uses a hybrid of human stem cell models, post-mortem tissue and computational approaches to interrogate the contribution of epigenetic regulation and somatic mosaicism to brain diseases. Our previous work has demonstrated that the human brain exhibits extensive genetic variability between neurons within the same brain, termed "somatic mosaicism" due to mobile DNA elements which mediate large somatic DNA copy number variants. We study environment-responsive mechanisms and consequences for somatic mosaicism and are discovering the landscape of somatic mosaicism in the brain. We also study the epigenetic regulation of cell specification and activity-d...ependent states within the human dorsal lateral prefrontal cortex and striatum. view more

    Research Areas: autism, Cellular and Molecular Neuroscience, stem cells, Developmental Neuroscience, Neurobiology of Disease, Induced Pluripotent Stem Cell Models, Organoids, schizophrenia, genomics, Dystonia, Epigenomics

    Lab Website

    Principal Investigator

    Jennifer Erwin, Ph.D.

    Department

    Neurology

  • Francis Giardiello Lab

    Research in the Francis Giardiello Lab focuses on the study of cancer and cancer chemoprevention in the gastrointestinal tract. This has included the investigation of the genetic basis of familial colorectal cancer and the use of genetic testing in the hereditary forms of colorectal cancer. We have a continuing interest in the study of the genotypic-phenotypic correlations in polyposis syndromes, which include familial adenomatous polyposis, juvenile polyposis and Peutz-Jeghers syndrome.

    Research Areas: gastrointestinal system, colorectal cancer, cancer, genomics, polyposis syndromes

    Principal Investigator

    Francis Giardiello, M.D.

    Department

    Medicine

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