Kyle Allison

Kyle Allison

Kyle Allison

Assistant Professor, Department of Medicine/Infectious Disease, Emory University

kyle.allison@bme.gatech.edu

404-727-6974

Office Location:
Emory HSRB E146

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    Research Focus Areas:
    • Systems Biology
    Additional Research:
    Our lab studies the response of bacteria to antibiotics in order to develop new methods for eradicating persistent bacteria. Bacterial persistence is a form antibiotic resistance in which a transient fraction of bacterial cells tolerates severe antibiotic treatment while the majority of the population is eliminated. These 'persisters' can contribute to chronic infections and are a major medical problem. Despite their medical and scientific importance, presistence is not fully understood. A crucial challenge in studying bacterial persistence results from a lack of methods to isolate persisters from the heterogeneous populations in which they occur. As a result, systems-level analysis of persisters is beyond current techniques, and fundamental questions regarding their physiological diversity remain unanswered. Our lab seeks to develop methods to isolate persisters and study them with systems-wide, molecular techniques. The resulting findings will be used to engineer improved antibiotic therapies. Dr. Allison's previous research included development of a novel method to eradicate pathogenic bacteria, includingEscherichia coliandStaphylococcus aureus,by metabolic stimulation and the finding that bacteria communicate with each other to alter their tolerance to antibiotics.

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    Ahmet Coskun

    Ahmet Coskun

    Ahmet Coskun

    Assistant Professor of Biomedical Engineering

    Ahmet Coskun is a systems biotechnologist and bioengineer, working at the nexus of multiplex imaging and quantitative cell biology.

    Single Cell Biotechnology Lab is strategically positioned for imaging one cell at a time for spatial context. We are multi-disciplinary researchers interested in photons, ions, and electrons and their interactions with cells and tissues.  Using large-scale experiments and computational analysis, we address fundamental challenges in cancers, immunology, and pediatric diseases. Variability of single cell profiles can be used to understand differences in therapeutic response, as well as satisfy our curiosity on understanding how cells are spatially organized in nature.

    Our lab aims to deliver biotechnologies for spatial multi-omics profiling vision at the single cell level.

    1) Spatial genomics: Our lab was part of an early efforts to demonstrate spatially resolved RNA profiling in single cells using a sequential FISH method. We will continue leveraging seqFISH and correlation FISH (another computational RNA imaging method) for exploring spatial dynamics of cellular societies.

    2) Spatial proteomics: Our lab develops expertise on antibody-oligonucleotide based barcoding for multiplex protein imaging using CODEX technology. We combine CODEX with super-resolution and 3D imaging to visualize and quantify subcellular epigenetic states of immune and cancer cells.

    3) Spatial metabolomics: Our lab works on computational and isotope barcoding approaches for small molecule profiling using MIBI (Multiplexed ion beam imaging). 3D and subcellular metabolic state of individual cells are used to model functional modes of cellular decision making in health and disease.

    We also develop machine learning and deep learning algorithms to make sense of imaging based single cell big data.

    In a nutshell, we create image-based ‘omic technologies to reveal spatial nature of biological systems. We benefit from enabler tools:  Super-resolution bioimaging, barcoded biochemical reagents, advanced algorithms and automated microfludics. Topical interests include Spatial Biology, Liquid Biopsy, and Global Oncology.

    Ahmet Coskun trained at Stanford (Postdoc/Instructor with Garry Nolan), Caltech (Postdoc with Long Cai) and UCLA (PhD with Aydogan Ozcan). His lab is currently funded by NIH K25, BWF CASI, Georgia Tech & Emory.

    acoskun7@gatech.edu

    404-894-3866

    Office Location:
    Petit Biotechnology Building, Office 1311

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    University, College, and School/Department
    Research Focus Areas:
    • Bioinformatics
    • Cancer Biology
    • Cell Manufacturing
    • Chemical Biology
    • Computational Genomics
    • Public Health
    • Regenerative Medicine
    • Systems Biology
    Additional Research:
    The Single Cell Biotechnology Lab aims to study spatial biology in health and disease. Our research lies at the nexus of multiplex bioimaging, microfluidic biodynamics, and big data biocomputation. Using high-dimensional nanoscale imaging datasets, we address fundamental challenges in immuno-engineering, cancers, and pediatric diseases. Our lab pursues a transformative multi-omics technology to integrate spatially resolved epigenetics and spatial genomics, proteomics, and metabolomics, all in the same platform. We uniquely benefit from super-resolution microscopy, imaging mass spectrometry, combinatorial molecular barcoding, and machine learning to enhance the information capacity of our cellular data. Variability of single cell images can be used to understand differences in therapeutic responses, as well as satisfy our curiosity on understanding how cells are spatially organized in nature.

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    Todd Streelman

    Todd Streelman

    Todd Streelman

    Professor and Chair

    Streelman grew up in Chestertown Md, where he developed a keen interest in the outdoors. He graduated with a BS in Biology from Bucknell University. While there, he attended a semester (plus one cold winter-mester) at the Marine Biological Laboratory in Woods Hole Massachusetts — where a chance encounter with Les Kaufman, Karel Liem, a few jars of pickled fish and a dental X-ray technician led to his lifelong love of cichlids. Streelman won the Pangburn Scholar-Athlete award (lacrosse) at BU. As a PhD student with Stephen Karl, Streelman developed approaches to identify, clone and sequence multiple, independent single-copy nuclear loci to reconstruct accurate phylogenies for cichlid fishes and their relatives. These phylogenies changed perspective about how these species groups evolved, and allowed new and improved inference about the evolutionary history of key ecological traits. Multi-locus phylogenies are now the standard in the field. 

    As a postdoc in Tom Kocher’s lab and then a young investigator at Georgia Tech, Streelman worked on the first unbiased quantitative genetic (QTL) studies in Malawi cichlids, some of the first such studies in evolutionary systems. In particular, work showed that adaptive features of the cichlid jaw and the striking orange-blotch color polymorphism had a simple genetic basis.  

    Streelman was an Alfred P. Sloan Foundation Postdoctoral Fellow, an Alfred P. Sloan Foundation Faculty Research Fellow and a NSF CAREER Awardee.  

    Over the past two decades as an independent investigator, with support from the NSF, NIH and the Human Frontier Science Program, Streelman’s group has pioneered genomic and molecular biology approaches in the Malawi cichlid system to solve problems difficult to address in traditional model organisms. Major projects include (i) tooth and taste bud patterning and regeneration; (ii) the underpinnings of complex behavior; and (iii) developmental diversification of the face and brain.  

    Generally, we are captivated by context-dependent traits like development and behavior because they must be executed in space and time with exquisite control. We analyze and manipulate genomes and development in multiple species of Malawi cichlids, spanning divergence in embryonic/adult traits and behavior – and collaborate with folks studying these same traits in zebrafish, mouse and human. In 2014, Streelman helped to coordinate a large effort to sequence the genomes of five East African cichlids, including one from Lake Malawi. This was a landmark for our research community and has recast attention to genome-wide approaches. We are motivated by the prospect to dissect evolutionary change with genetic and cellular precision.  

    In his free time, Streelman likes mountaineering, skipping rocks and pickling.

    todd.streelman@biology.gatech.edu

    404-894-3700

    Office Location:
    EBB 3007

    Website

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    Research Focus Areas:
    • Molecular Evolution
    • Neuroscience
    Additional Research:
    Researchers in the Streelman lab use the cichlid fish model to address fundamental questions in ecology and evolution. We are fascinated by context-dependent processes like embryonic development, the regeneration of organs and complex behavior. Context-dependency is interesting because it reveals new rules of biological systems that are not necessarily operational during homeostasis. For instance, recent results suggest that stem-like cells in the brain may tune the evolution of male social behavior. We raise cichlids from Lake Malawi in custom fish facilities at Georgia Tech. We invent automated assays to quantify behavior, we sequence genomes and the transcriptomes of cells, and we collaborate with computational scientists, engineers and colleagues working in zebrafish, mouse and human. Members of the lab are keen to learn new things by working together, compelled by mechanism and comparative approaches.

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    Shuichi Takayama

    Shuichi Takayama

    Shuichi Takayama

    Professor, Wallace H. Coulter Department of Biomedical Engineering
    GRA Eminent Scholar, Wallace H. Coulter Department of Biomedical Engineering
    Price Gilbert, Jr. Chair in Regenerative Engineering andMedicine

    Shu Takayama earned his BS and MS in Agricultural Chemistry at the University of Tokyo. He earned a Ph.D. in Chemistry at The Scripps Research Institute in La Jolla, California studying bio-organic synthesis with Dr. Chi‐Huey Wong. He then worked as a postdoc with Dr. George Whitesides at Harvard University where he focused on applying microfluidics to studying cell and molecular biology.

    Takayama began his career at the University of Michigan, where led his lab in the Department of Biomedical Engineering and Macromolecular Science & Engineering for over 17 years. In 2017, the lab moved to Georgia Tech where Shu became the Georgia Research Alliance Price Gilbert Chair Professor of Biomedical Engineering in the Wallace H. Coulter Department of Biomedical Engineering.

    Takayama’s research interests are diverse and motivated by clinical and biotechnology needs. He is always interested in hearing from stakeholders in these areas who are seeking engineering collaboration.

    takayama@gatech.edu

    404.385.5722

    Office Location:
    EBB 4018

    Takayama lab

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    Research Focus Areas:
    • Bioengineering
    • Biomaterials
    • Cancer Biology
    • Cell Manufacturing
    • Medical Device Design, Development and Delivery
    • Micro and Nano Device Engineering
    • Miniaturization & Integration
    • Molecular, Cellular and Tissue Biomechanics
    • Nanomaterials
    • Systems Biology
    Additional Research:
    Use of micro/nanofluidics for cell analysis; diagnostics; and chromatin analysis; High throughput 3D cell cultures; Organs-on-a-chip construction and design; Role of rhythm in cell signaling; Self-switching fluidic circuits; Fracture fabrication

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    Young-Hui Chang

    Young-Hui Chang

    Young-Hui Chang

    Professor

    Dr. Chang is the director of the Comparative Neuromechanics Laboratory. His research program focuses on trying to understand how animals move through and interact with their environment.

    yh.chang@ap.gatech.edu

    404-894-9993

    Office Location:
    1309 B

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    Research Focus Areas:
    • Molecular, Cellular and Tissue Biomechanics
    • Neuroscience
    Additional Research:
    Current projects involve studying how gait compensations are made both from biomechanical and motor control perspectives. To this end, we study the control of human and non-human vertebrate legs within the conceptual framework of the Uncontrolled Manifold hypothesis. This idea suggests neuromechanical redundancy is not only helpful, but is exploited by the nervous system to simplify control of and completion of specific behavioral tasks, such as those involved in limb function during locomotion. We integrate concepts and tools from comparative biomechanics, neurophysiology and computational neuroscience.

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    Greg Gibson

    Greg Gibson

    Greg Gibson

    Professor
    Director, Center for Integrative Genomics
    Adjunct Professor, School of Medicine, Emory University

    Greg Gibson is Professor of Biology and Director of the Center for Integrative Genomics at Georgia Tech. He received his BSc majoring in Genetics from the University of Sydney (Australia) and PhD in Developmental Genetics from the University of Basel. After transitioning to quantitative genetic research as a Helen Hay Whitney post-doctoral fellow at Stanford University, he initiated a program of genomic research as a David and Lucille Packard Foundation Fellow at the University of Michigan. He joined the faculty at Georgia Tech in Fall of 2009, after ten years at North Carolina State University where he developed tools for quantitative gene expression profiling and genetic dissection of development in the fruitfly Drosophila. He is now collaborating with the Center for Health Discovery and Well Being on integrative genomic analyses of the cohort. Dr Gibson is an elected Fellow of the American Association for the Advancement of Science, and serves as Section Editor for Natural Variation for PLoS Genetics. He has authored a prominent text-book, a "Primer of Genome Science" as well as a popular book about genetics and human health, "It Takes a Genome".

    greg.gibson@biology.gatech.edu

    404-385-2343

    Office Location:
    EBB 2115A

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    Research Focus Areas:
    • Cancer Biology
    • Molecular Evolution
    • Systems Biology
    Additional Research:
    Quantitative Evolutionary Genetics. After 15 years working on genomic approaches to complex traits in Drosophila, my group has spent much of the past 10 years focusing on human quantitative genetics. We start with the conviction that genotype-by-environment and genotype-by-genotype interactions are important influences at the individual level (even though they are almost impossible to detect at the population level). We use a combination of simulation studies and integrative genomics approaches to study phenomena such as cryptic genetic variation (context-dependent genetic effects) and canalization (evolved robustness) with the main focus currently on disease susceptibility.​ Immuno-Transcriptomics.As one of the early developers of statistical approaches to analysis of gene expression data, we have a long-term interest in applications of transcriptomics in ecology, evolution, and lately disease progression. Since blood is the mostaccessible human tissue, we've examined how variation is distributed within and among populations, across inflammatory and auto-immune states, and asked how it relates to variation in immune cell types. Our axes-of-variation framework provides a new way of monitoring lymphocyte, neutrophil, monocyte and reticulocyte profiles from whole peripheral blood. Most recently we have also been collaborating on numerous studies of specific tissues or purified cell types in relation to such diseases as malaria, inflammatory bowel disease, juvenile arthritis, lupus, and coronary artery disease. Predictive Health Genomics. Personalized genomic medicine can be divided into two domains: precision medicine and predictive health. We have been particularly interested in the latter, asking how environmental exposures and gene expression, metabolomic and microbial metagenomics profiles can be integrated with genomesequencing or genotyping to generate health risk assessments. A future direction is incorporation of electronic health records into genomic analyses of predictive health. Right now it is easier to predict the weather ten years in advance than loss of well-being, but we presume that preventative medicine is a big part of the future of healthcare.​

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    Yuhong Fan

    Yuhong Fan

    Yuhong Fan

    Associate Professor
    Georgia Research Alliance Distinguished Scholar

    yuhong.fan@biology.gatech.edu

    404-385-1312

    Office Location:
    Petit Biotechnology Building, Office 2313

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    Research Focus Areas:
    • Cancer Biology
    • Regenerative Medicine
    • Systems Biology
    Additional Research:
    Epigenetics, Epigenomics, Chromatin, Gene Expression, Stem Cell Biology, Epidrugs, Mouse Genetics, Cancer, Function of Linker Histones in Mammalian Development, and Stem Cell Differentiation

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    Andrés J. García

    Andrés J. García

    Andrés García

    Executive Director, Parker H. Petit Institute for Bioengineering and Bioscience
    The Petit Director’s Chair in Bioengineering and Bioscience
    Regents’ Professor, George Woodruff School of Mechanical Engineering

    Andrés Garcia's research centers on cellular and tissue engineering, areas which integrate engineering and biological principles to control cell function in order to restore and/or enhance function in injured or diseased organs. Specifically, his research focuses on fundamental structure-function relationships governing cell-biomaterials interactions for bone and muscle applications. Current projects involve the analysis and manipulation of cell adhesion receptors and their extracellular matrix ligands. For example, a mechanochemical system has been developed to analyze the contributions of receptor binding, clustering, and interactions with other cellular structural proteins to cell adhesion strength. In another research thrust, bio-inspired surfaces, including micropatterned substrates, are engineered to control cell adhesion in order to direct signaling and cell function. For instance, biomolecular surfaces have been engineered to target specific adhesion receptors to modulate cell signaling and differentiation. These biomolecular strategies are applicable to the development of 3D hybrid scaffolds for enhanced tissue reconstruction,"smart" biomaterials, and cell growth supports. Finally, genetic engineering approaches have been applied to engineer cells that form bone tissue for use in the development of mineralized templates for enhanced bone repair.

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    andres.garcia@me.gatech.edu

    404-894-9384

    Office Location:
    Petit Biotechnology Building, Office 2310

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    Research Focus Areas:
    • Biomaterials
    • Cell Manufacturing
    • Chemical Biology
    • Drug Design, Development and Delivery
    • Molecular, Cellular and Tissue Biomechanics
    • Regenerative Medicine

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