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Displaying 1 to 7 of 7 results for computational biology

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  • Albert Lau Lab

    The Lau Lab uses a combination of computational and experimental approaches to study the atomic and molecular details governing the function of protein complexes involved in intercellular communication. We study ionotropic glutamate receptors (iGluRs), which are ligand-gated ion channels that mediate the majority of excitatory synaptic transmission in the central nervous system. iGluRs are important in synaptic plasticity, which underlies learning and memory. Receptor dysfunction has been implicated in a number of neurological disorders.

    Research Areas: central nervous system, synaptic plasticity, computational biology, intracellular communication, ionotropic glutamate receptors, neurological disorders

  • 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

  • David Shortle Lab

    The principal research interest of the Shortle Lab is protein folding--how amino acid sequence information encodes three-dimensional structure. We are taking a combined experimental and computational approach to this longstanding puzzle of fundamental biochemistry. In addition, the laboratory is working to predict protein structure from sequence in ways that make the underlying physical chemistry transparent and the relative contributions of different interactions quantifiable.

    Research Areas: biochemistry, computational biology, protein folding, protein structure

  • Mihaela Pertea Lab

    The Mihaela Pertea Lab develops computational tools for RNA sequence analysis, gene finding, splice-site prediction and sequence-motif finding. Previous research projects led to the development of open-source software systems related to finding genes.

    Research Areas: computational biology, DNA, genomics, RNA

    Lab Website

    Principal Investigator

    Mihaela Pertea, M.S., M.S.E., Ph.D.

    Department

    Medicine

  • Salzberg Lab

    Research in the Salzberg Lab focuses on the development of new computational methods for analysis of DNA from the latest sequencing technologies. Over the years, we have developed and applied software to many problems in gene finding, genome assembly, comparative genomics, evolutionary genomics and sequencing technology itself. Our current work emphasizes analysis of DNA and RNA sequenced with next-generation technology.

    Research Areas: computational biology, DNA, genomics, sequencing technology, biostatistics, RNA

  • Systems Biology Laboratory

    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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    Research Areas: peripheral artery disease, breast cancer, systems biology, computational biology, cancer, cardiovascular, age-related macular degeneration, bioinformatics, angiogenesis, microcirculation

    Principal Investigator

    Aleksander Popel, Ph.D.

    Department

    Biomedical Engineering

  • Wheelan Lab

    The Wheelan Lab focuses on DNA sequence analysis. Her team creates new techniques to mathematically analyze and biologically interpret high-throughput sequencing data and other high-dimensional biological datasets. The team examines spatial relationships across genomes and uses transposons to query genomic sequence/structure relationships.

    Research Areas: computational biology, DNA, genomics, sequencing

    Principal Investigator

    Sarah Wheelan, M.D., Ph.D.

    Department

    Oncology

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