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  • Alan Baer Lab

    Principal Investigator:
    Alan Baer, M.D.
    Medicine

    Research in the Alan Baer Lab focuses on Sjogren's syndrome. Previously, we conducted the Sjogr...en's International Registry (SICCA), enrolling 300 patients and creating a valuable source of clinical data and biospecimens for research we're conducting with colleagues at Johns Hopkins and the University of California-San Francisco. Currently, we're conducting a longitudinal observational study of patients with Sjogren's syndrome. We're also collaborating with Dr. Ben Larman in the Department of Pathology, using phage immuno-precipation sequencing to work on a characterization of the complete autoantibody repertoire in Sjogren's syndrome patients. view more

    Research Areas: autoantibodies, Sjogren's syndrome, autoimmune rheumatic diseases, observational data
  • Alan Scott Lab

    Principal Investigator:
    Alan Scott, Ph.D.
    Medicine

    Research in the Alan Scott Lab involves several important areas of genomics. Our team collabora...tes 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. view more

    Research Areas: evolutionary genomics, sequence analysis, genomics, genome annotation, genomic technologies, cleft lip and palate
  • Balagopal Lab - Viral Hepatitis and Translational Virology

    Principal Investigator:
    Ashwin Balagopal, M.D.
    Medicine

    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.
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    Research Areas: HIV-1, hepatitis B, hepatitis C
  • Early Detection of Pancreatic Cancer Laboratory

    Lab Website
    Principal Investigator:
    Michael Goggins, M.B.B.Ch., M.D.
    Medicine

    The goal of the lab's research is to identify molecular abnormalities that can improve the outc...ome of patients with pancreatic cancer and those at risk of developing this disease. Much of our work is focused on translational research evaluating markers and marker technologies that can help screen patients with an increased risk of developing pancreatic cancer.

    Thus, marker efforts have been focused mostly on identifying markers of advanced precancerous neoplasia (PanINs and IPMNs) that could improve our ability to effectively screen patients at risk of developing pancreatic cancer. We lead or participate in a number of clinical research protocols involved in the screening and early detection of pancreatic neoplasia including the CAPS clinical trials. We maintain a large repository of specimens from cases and controls with and without pancreatic disease and use this repository to investigate candidate markers of pancreatic cancer for their utility to predict pancreatic cancer risk.

    In addition, we have been working to identify familial pancreatic cancer susceptibility genes and identified BRCA2 as a pancreatic cancer susceptibility gene in 1996. We participate in the PACGENE consortium and the familial pancreatic cancer sequencing initiative. My lab also investigates pancreatic cancer genetics, epigenetics, molecular pathology, tumor stromal interactions and functional analysis of candidate genes and miRNAs. Dr. Goggins is the principal investigator of a phase I/II clinical trial evaluating the Parp inhibitor, olaparib along with irinotecan and cisplatin for patients with pancreatic cancer.
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    Research Areas: pancreatic cancer
  • 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 ca...rdiopulmonary 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. view more

    Research Areas: pulmonary arterial hypertension, molecular genetics, cardiopulmonary diseases, asthma, epigenetics, complex lung disease, allergies, genomics, COPD, atopic dermatitis
  • Liliana Florea Lab

    Principal Investigator:
    Liliana Florea, Ph.D., M.Sc.
    Medicine

    Research in the Liliana Florea Lab applies computational techniques toward modeling and problem... solving in biology and genetic medicine. We work to develop computational methods for analyzing large-scale sequencing data to help characterize molecular mechanisms of diseases. The specific application areas of our research include genome analysis and comparison, cDNA-to-genome alignment, gene and alternative splicing annotation, RNA editing, microbial comparative genomics, miRNA genomics and computational vaccine design. Our most recent studies seek to achieve accurate and efficient RNA-seq correction and explore the role of HCV viral miRNA in hepatocellular carcinoma. view more

    Research Areas: evolutionary genomics, vaccines, carcinoma, cancer, genomics, bioinformatics, RNA, comparative genomics
  • Loyal Goff Laboratory

    Lab Website
    Principal Investigator:
    Loyal Goff, Ph.D.
    Neuroscience

    The Loyal Goff Laboratory seeks to answer a fundamental biological question: How is the genome... properly interpreted to coordinate the diversity of cell types observed during neuronal development? We are focused on the acquisition of specific cellular identities in neuronal development and identifying the molecular determinants responsible for proper brain development. Using novel experimental approaches for the enrichment and purification of specific neuronal cell types and recent technological advances in single-cell RNA sequencing, we can discover and explore the cellular factors that contribute to neuronal cell fate decisions during mammalian brain development. view more

    Research Areas: brain, neuronal development, genomics, RNA
  • Rasika Mathias Lab

    Principal Investigator:
    Rasika Mathias, Sc.D.
    Medicine

    Research in the Rasika Mathias Lab focuses on the genetics of asthma in people of African ances...try. Our work led to the first genomewide association study of its kind in 2009. Currently, we are analyzing the whole-genome sequence of more than 1,000 people of African ancestry from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA). CAAPA’s goal is to use whole-genome sequencing to expand our understanding of how genetic variants affect asthma risk in populations of African ancestry and to provide a public catalog of genetic variation for the scientific community. We’re also involved in the study of coronary artery disease though the GeneSTAR Program, which aims to identify mechanisms of atherogenic vascular diseases and attendant comorbidities. view more

    Research Areas: heart disease, African Americans, asthma, genomics, health disparities
  • Ryuya Fukunaga Lab

    The Fukunaga Lab uses multidisciplinary approaches to understand the cell biology, biogenesis a...nd function of small silencing RNAs from the atomic to the organismal level.

    The lab studies how small silencing RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs), are produced and how they function. Mutations in the small RNA genes or in the genes involved in the RNA pathways cause many diseases, including cancers. We use a combination of biochemistry, biophysics, fly genetics, cell culture, X-ray crystallography and next-generation sequencing to answer fundamental biological questions and also potentially lead to therapeutic applications to human diseases.
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    Research Areas: biophysics, biochemistry, cell biology, cell culture, genomics, RNA
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