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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.
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.
The Fernando Pineda Lab uses advanced computational and mathematical techniques to devise solutions to problems in modern biology and public health. We develop analysis algorithms, software tools and models that help biologists characterize biological systems. For example, we have studied the life cycle of the Plasmodium falciparum parasite, which is responsible for more than 1 million malaria deaths per year, with the goal of treating and preventing the disease. We are developing an ab initio computational strategy for finding rapidly evolving ncRNA genes in the parasite.
The GI Biomarkers Laboratory studies gastrointestinal cancer and pre-cancer biogenesis and biomarkers. The lab is led by Dr. Stephen Meltzer, who is known for his research in the molecular pathobiology of gastrointestinal malignancy and premalignancy. Research in the lab has led to several groundbreaking genomic, epigenomic and bioinformatic studies of esophageal and colonic neoplasms, shifting the gastrointestinal research paradaigm toward genome-wide approaches.
The Institute for Computational Medicine's mission is to develop quantitative approaches for understanding the mechanisms, diagnosis and treatment of human disease through biological systems modeling, computational anatomy, and bioinformatics. Our disease focus areas include breast cancer, brain disease and heart disease.
The institute builds on groundbreaking research at both the Johns Hopkins University Whiting School of Engineering and the School of Medicine.
The In-vivo Cellular and Molecular Imaging Center conducts multidisciplinary research on cellular and molecular imaging related to cancer. We provide resources, such as consultation on biostatistics and bioinformatics and optical imaging and probe development, to understand and effectively treat cancer. Our molecular oncology experts consult on preclinical studies, use of human tissues, interpretation of data and molecular characterization of cells and tumor tissue.
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.
Researchers in the Nicholas Zachos Lab work to understand variations in protein trafficking that occur during pathophysiological conditions that cause ion and water transport that result in diarrhea. We recently identified a clathrin-independent endocytic pathway responsible for elevated intracellular calcium-mediated inhibition of NHE3 activity in intestinal epithelial cells. We use advanced imaging techniques, including confocal and multi-photon microscopy, to characterize protein trafficking of intestinal transporters. We also perform functional assays using fluorescent probes (ratiometric and non-ratiometric) to measure ion transport in cell culture models, intact intestinal tissues and human small intestinal enteroids.
The Systems Biology Lab applies methods of multiscale modeling to problems of cancer and cardiovascular disease, and examines the systems biology of angiogenesis, breast cancer and peripheral artery disease (PAD).
Using coordinated computational and experimental approaches, the lab studies the mechanisms of breast cancer tumor growth and metastasis to find ways to inhibit those processes.
We use bioinformatics to discover novel agents that affect angiogenesis and perform in vitro and in vivo experiments to test these predictions. In addition we study protein networks that determine processes of angiogenesis, arteriogenesis and inflammation in PAD. The lab also investigates drug repurposing for potential applications as stimulators of therapeutic angiogenesis, examines signal transduction pathways and builds 3D models of angiogenesis.
The lab has discovered over a hundred novel anti-angiogenic peptides, and has undertaken in vitro and in vivo studies testing their activity unde...r different conditions. We have investigated structure-activity relationship (SAR) doing point mutations and amino acid substitutions and constructed biomimetic peptides derived from their endogenous progenitors. They have demonstrated the efficacy of selected peptides in mouse models of breast, lung and brain cancers, and in age-related macular degeneration.
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Combining microbiology and bioinformatics, the Cohen Lab conducts translational research on mycobacteria. By application of advanced genomic techniques to the problems of tuberculosis and nontuberculous mycobacteria, the Cohen Lab aims to develop improved tools for the diagnosis and management of mycobacterial disease.
The Tom Woolf Lab studies the quarter of the genome devoted to membrane proteins. This rapidly growing branch of bioinformatics, which includes computational biophysics, represents the main research direction of our group. We aim to provide insight into critical issues for membrane systems. In pursuit of these goals, we use extensive computer calculations to build an understanding of the relations between microscopic motions and the world of experimental measurements. Our calculations use our own Beowulf computer cluster as well as national supercomputer centers. An especially strong focus has been on the computed motions of proteins and all-atom models of the lipid bilayers that mediate their influence. To compute these motions, we use the molecular dynamics program CHARMM. We hope to use our understanding of the molecular motions for the prediction of membrane protein structures using new computational methods.
Wilmer Bioinformatics has been mainly focused on ocular informatics. Specifically, the group develops and applies bioinformatics approaches to study gene regulation and signaling networks, with particular but not exclusive attention to the mammalian retina. Understanding the molecular basis of tissue specific gene regulation and signaling will contribute to better prevention, diagnosis and treatment of retinal disease.
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