People





   

Kevin Janes

Center Director and Institute Lead
Professor
Department of Biomedical Engineering, University of Virginia

http://bme.virginia.edu/janes/

Changes in cellular behavior underlie development, disease, and tissue homeostasis. The response of cells to external factors depends upon posttranslational signals and changes in gene expression. These biomolecules are wired together in cells to form networks. Intracellular signaling and gene-expression networks are highly interconnected and time dependent, making them difficult to study and even harder to understand at the systems level. Our lab designs new experimental and computational approaches for analyzing such networks. We draw from engineering principles to inspire new techniques that can be applied to network-level questions about signal transduction and gene expression. We are particularly interested in using our methods for problems in cancer biology, where the molecular “signal processing” has gone awry and cellular responses are inappropriate.

   

Doug Lauffenburger

Deputy Director and Institute Lead
Professor and Head
Department of Biological Engineering, M.I.T.

http://web.mit.edu/dallab/index.html

Molecular cell bioengineering is the application of engineering approaches to develop quantitative understanding of cell function in terms of fundamental molecular properties, and to apply this understanding for improved design of molecular- and cell-based technologies. Our research group focuses on elucidating important aspects of receptor-mediated regulation of mammalian blood and tissue cell behavioral functions such as proliferation, adhesion, migration, differentiation, and death. A central paradigm of our work is development and testing of computational models -- based on principles from engineering analysis and synthesis -- for receptor regulation of cell function by exploiting techniques of molecular biology to alter parameters characterizing receptor or ligand properties in well-characterized cell systems. Quantitative experimental assays are used to measure cell functions, receptor/ligand interaction parameters, and signaling network dynamics. Problems are primarily motivated by health care technologies of interest to pharmaceutical and biotechnological companies, and emphasize multi-disciplinary collaborative interactions, including colleagues in both academia and industry.

   

Preethi Chandran

Institute Lead
Assistant Professor
Department of Chemical Engineering, Howard University

http://www.che.cea.howard.edu/users/pchandran

We are interested in the engineering design behind self-assembled nanoscale structures of semiflexible biopolymers (DNA, aggrecan, and collagen, etc), and in using these nanostructures as physical containers for drug delivery and tissue regeneration. We have developed an integrated approach to study these bioassemblies, from the single-molecule interactions to the group polymer dynamics to the nanomechanics of the final complex. Techniques like Atomic Force Microscopy, Dynamic Light Scattering, and Rheology allow us to interrogate the biomolecule physics at different stages of self-assembly. We are also engaged in developing a multi-scale modeling theory for semidilute biopolymers. This theory is based on our string-of-continuous-beams polymer model. The theory enables us to model coarse-grain biopolymer self-assembly at reduced cost but with high orders of polymer interaction.

   

Philip Bourne

Industrial Co-Lead
Professor and Director
Department of Biomedical Engineering
Data Science Institute, University of Virginia

https://dsi.virginia.edu/people/phil-bourne/profile

From 2014-2017, I was the Associate Director for Data Science at the National Institutes of Health. In this role I led the Big Data to Knowledge Program, coordinating access to and analyzing biomedical research from across the globe and making it available to scientists and researchers. While there, I was also responsible for governance and strategic planning activities for data and knowledge management, and established multiple trainings in data science. Prior to my time at the NIH, I spent 20 years on the faculty at the University of California-San Diego, eventually becoming Associate Vice Chancellor of Innovation and Industrial Alliances.

   

Legand Burge III

Industrial Co-Lead
Professor
Department of Computer Science, Howard University

http://www.cs.cea.howard.edu/user/14

My research interests lie in the field of distributed computing. I am interested in the application of distributed high-performance computing to solve computational science problems in Biology, Physics, and Chemistry. I am currently the director of the Distributed Systems Research Group (DSRG) and associate director of the Center for Applied High Performance Computing at Howard University. I am also interested in Computer Science Education and Diversity as a Member of the Howard West Initiative with Google, as well asTech Innovation and Entrepreneurship as Director of the HowU Innovate Foundry.

   

Jeff Saucerman

Industrial Co-Lead
Associate Professor
Department of Biomedical Engineering, University of Virginia

http://bme.virginia.edu/saucerman/

Heart function and failure are controlled by complex signaling and transcriptional networks that are just beginning to be mapped out. My laboratory combines computational modeling and live-cell microscopy to identify these molecular networks and understand how they mediate cell decisions. We are tackling a number of unexplained cellular decisions that are fundamental to the development of heart failure. For example, after myocardial infarction, what causes a given myocyte to choose enhanced contractility, growth, or death? Why do certain stresses cause myocyte lengthening, while other stresses increase myocyte thickness? Why are certain forms of heart growth reversible while others are irreversible? Answers to these basic science questions are being translated into novel strategies to re-engineer the failing heart.

   

John Gates

Engagement Director
Associate Dean for Diversity and Inclusion
Office of Diversity & Engagement

https://engineering.virginia.edu/about/diversity-and-engagement

The vision for UVA Engineering's diversity efforts, led by the Office of Diversity and Engagement, is to harness the strategic value of diversity, inclusion and engagement in UVA Engineering's educational and research programs. We are cultivating an environment in which every person is optimally valued and supported, so our students, faculty and staff can make their best contributions to society. The Office of Diversity and Engagement provides a vision of strategic diversity for the School of Engineering, supports diversity initiatives benefiting the School and University, and seeks external support for diversity research and education. The office also operates the Center for Diversity in Engineering, a student support center.

   

Roseanne Ford

Education Co-Lead
Professor
Department of Chemical Engineering, University of Virginia

http://faculty.virginia.edu/ford/

Our research focuses on the application of chemical engineering principles to problems in microbial ecology. The aim is to develop a fundamental understanding of mechanisms underlying microbial behavior which will provide insights for future technological innovation. Our focus is on fundamental studies of bacterial chemotaxis, including microbial processes such as nitrogen fixation, the development of infection, and the growth of biofilms on medical implants and marine surfaces. Applications include bioremediation of hazardous waste, specifically investigating microbial transport limitations on the overall rates of in situ biodegradation and strategies for overcoming these limitations.

   

Kimberlei Richardson

Education Co-Lead
Assistant Professor
Department of Pharmacology, Howard University

http://connect.rtrn.net/profilesweb/Richardson

I am a research mentor and lecturer for the Leadership Alliance Program and the First Year Research Experience at Howard University and I also serve as a mentor for the Louis Stokes Alliances for Minority Participation Program to promote STEM undergraduate research training for underrepresented minorities. I studied Chemistry as an undergraduate at Howard University, completed by doctoral degree in Pharmacology at Howard University College of Medicine, and conducted postdoctoral work at Johns Hopkins Medical Institutions and the Medical University of South Carolina. I am also an active member of the graduate studies committee in the Department of Pharmacology since returning to Howard as a faculty member.

   

Natalie Kuldell

Education Co-Lead
Instructor
Department of Biological Engineering, M.I.T.

http://educationgroup.mit.edu/HHMIEducationGroup/?page_id=2918

I am the Education Outreach Coordinator for MIT's Department of Biological Engineering and leader of BioBuilder, a nonprofit organization that takes cutting-edge research projects in synthetic biology and transforms them into teachable modules that students and teachers can investigate together. I studied Chemistry as an undergraduate at Cornell, completed my doctoral and post-doctoral work at Harvard Medical School, and taught at Wellesley College before joining the faculty at MIT.

   

Jason Papin

Director of Research
Professor
Department of Biomedical Engineering, University of Virginia

http://bme.virginia.edu/csbl/home.html

The completed sequences of multiple genomes have catalyzed a phase transition in bioengineering research. Systems analysis has become a requirement for making sense of high-throughput data and for characterizing properties of biological networks. In order to extend these recent developments to medical applications, there is a pressing need for reconstructing and analyzing the biochemical networks that direct cellular processes. The subsequent analysis of these networks requires high-performance computing and sophisticated mathematical techniques. Our research goals consist of the construction and analysis of large-scale biochemical networks and their application to human disease. Currently, we are working to develop methods for incorporating high-throughput data with integrated signaling, metabolic, and regulatory network reconstructions, and we are using these tools to study fundamental problems in infectious disease, cancer, and bioenergy. The development and application of computational methods to analyze large biological networks will revolutionize medical research and lead to the characterization of novel therapeutic targets that would be impossible otherwise.

   

Linda Griffith

Thrust #1 Co-Lead
Professor
Department of Biological Engineering, M.I.T.

http://lgglab.mit.edu

Our research encompasses molecular-to-systems level analysis, design and synthesis of biomaterials, scaffolds, devices and micro-organs for a range of applications in regenerative medicine, tissue engineering, and in vitro drug development. A central theme is connecting the experimental systems to systems biology measurements. Most projects are highly interdisciplinary and translational, involving basic scientists, clinicians, and engineers, often with industry partners, to solve important problems in medicine and biology.

   

Shayn Peirce-Cottler

Thrust 3 Leader
Professor
Department of Biomedical Engineering, University of Virginia

http://bme.virginia.edu/peirce/

The microvasculature, a complex network of highly specialized blood vessels, is capable of growing and altering its structure and function to regulate blood flow and accommodate the changing metabolic needs of the body's tissues. Microvascular growth and remodeling are important in pathological conditions, such as wound healing, ischemic disease (e.g. peripheral vascular disease and heart disease), and tumor growth. We study microvascular growth and remodeling using novel computational and experimental techniques, including agent-based computational models and thin tissues that enable visualization and manipulation of entire microvascular networks in vivo. We also develop therapeutic approaches to grow and regenerate injured and diseased tissues by manipulating the structure and composition of the microvasculature.

   

Bill Southerland

Thrust #2 Co-Lead
Professor and Director
Center for Computational Biology & Bioinformatics, Howard University

https://ccbb.howard.edu/content/home

The mission of the Howard University Center for Computational Biology and Bioinformatics (CCBB) is to encourage and promote the application of computational approaches to the study of biomedical and disease processes. The application of those research approaches and methods that are at the interface of the biomedical and the physical science is of particular interest.

   

Mete Civelek

Thrust #2 Co-Lead
Assistant Professor
Department of Biomedical Engineering, University of Virginia

http://civeleklab.org

The goal of our laboratory is to understand the genetic mechanisms that lead to increased susceptibility to cardiovascular and metabolic diseases. The interactions among hundreds of genes and gene networks along with environmental factors such as diet affect our health status. We use systems genetics to uncover this complexity. We employ a range of experimental and computational methods to quantitate and integrate intermediate phenotypes, such as transcript, protein or metabolite levels in human and mouse populations. We also test our predictions using standard biochemistry and molecular biology approaches in cell cultures and animal models. Our results provide insights into both the molecular underpinnings of complex traits and the understanding of common, complex diseases.

   

Forest White

Core Investigator
Professor
Department of Biological Engineering, M.I.T.

http://white-lab.mit.edu

The focus of our research is the quantitative analysis of protein phosphorylation events regulating signal transduction cascades associated with cancer and other biological processes. With its mass spectrometry-based technology, analysis of protein phosphorylation occurs on a global scale, allowing for quantitative mapping of complex signal transduction cascades in a variety of biological samples. Currently, the group is applying this technology to understand signaling processes regulating biological response to exogenous stimuli in a variety of cancer model systems. Elucidation of signal transduction cascades involved in oncogenesis, cancer progression, and metastasis will generate both novel drug targets and a host of biological markers, allowing for early diagnosis and tracking of cancer progression.

   

Matthew Lazzara

Thrust #3 Co-Lead
Associate Professor
Department of Chemical Engineering, University of Virginia

http://faculty.virginia.edu/lazzara/

Cell signaling is the biochemical process cells use to make decisions about virtually everything they do – migrate, differentiate, survive, die, and more. Signaling involves networks of intracellular proteins whose concentrations, modification states, or localization change in response to events such as receptor-ligand binding. Cells interpret these signaling network changes, using rules scientists are only beginning to decipher, to execute decision processes. While proper signaling is critical to normal development and health, aberrant signaling leads to numerous diseases, including cancer. Thus, the ability to engineer signaling processes or intervene effectively in aberrant signaling has huge medical implications. Our lab integrates experimental and computational methods to study fundamental aspects of cell signaling regulation and applied aspects of cell signaling including the efficacy of therapeutics that target particular signaling pathways in cancer.

   

Thomas Barker

Core Investigator
Professor
Department of Biomedical Engineering, University of Virginia

http://www.matrixbiology.net

My lab is primarily focused on both understanding and manipulating cell-ECM mechanotransduction pathways in homeostasis and disease. Our primary interest is in understanding how cells' changing microenvironment direct their phenotype and initiate pathological programs, primarily tissue fibrosis and scar formation. Both cells and their extracellular matrix (ECM) are exquisitely sensitive to mechanical forces and slight perturbations in the mechanical homeostasis between cells and their ECM can initiate pathological programs that lead to tissue destruction and even death. For example, pulmonary fibrosis is a fatal disease driven in large part by stiffening of lung tissue due to chronic wound repair. Once the tissue becomes stiff, normal cells are recruited into a pathological program that ultimately leads to complete destruction of the lung and death of the patient. There are no cures and very few viable medical options for treating the disease. For these reasons, understanding how the fibrotic program is both initiated and persists will lead to new breakthroughs in treating these fatal diseases.

   

Silvia Blemker

Core Investigator
Professor
Department of Biomedical Engineering, University of Virginia

http://bme.virginia.edu/muscle/

The goal of our research is to identify the principles of muscle design by characterizing the relationships between muscle structure, mechanical properties, biology, and function. We are applying these findings to understanding and improving the treatments for musculoskeletal impairments associated with movement disorders, such as cerebral palsy. We create computational models of the musculoskeletal system that describe the complex three-dimensional architecture and geometry of muscles. We also develop nonlinear constitutive relationships for muscle that represent the properties of muscle cells and extra-cellular connective tissues. We use dynamic magnetic resonance imaging techniques to study the deformation and motion of muscles during joint movement. We perform anatomical measurements and tissue testing to characterize the arrangements of proteins in muscle and to determine the material properties of muscle tissue.

   

Graham Casey

Core Investigator
Professor
Center for Public Health Genomics, University of Virginia

https://med.virginia.edu/faculty/faculty-listing/gc8r/

My research focuses on unravelling the complex genetic mechanisms underlying risk of colorectal cancer in order to enhance disease surveillance leading to improved health outcome. Our approach integrates large-scale human genetic association data with epigenetic and transcriptomic profiling, and incorporates genome editing and in vitro human 3D normal colon organoid models to better understand causal mechanisms of disease.

   

Jeff Holmes

Core Investigator
Professor
Department of Biomedical Engineering, University of Virginia

http://bme.virginia.edu/holmes/

The Cardiac Biomechanics Group focuses on the interactions between mechanics, function, and growth and remodeling in the heart. The mechanical properties of normal and diseased myocardium are important determinants of overall heart function. These mechanical properties change during growth, remodeling or disease, often in part as a response to changes in the mechanical environment. Our group studies this interplay between mechanical environment, tissue response, and heart function, not only to better understand the basis for heart disease but also to identify new opportunities to intervene.

   

Peter Kasson

Core Investigator
Associate Professor
Department of Molecular Physiology & Biophysics, University of Virginia

https://kassonlab.wordpress.com

Our research centers on the membrane biology of virus-host cell interactions, with a focus on influenza as both a common model system and an important human pathogen. We wish to address three fundamental questions in influenza infection: how does influenza recognize cell-surface glycans on the cells it infects, how do fusion proteins catalyze membrane fusion and bring about viral entry, and how does cellular lipid metabolism permit or inhibit viral replication. We use a combination of novel computational methods and targeted experiments to generate robust quantitative and mechanistic models for these processes. This will yield important insight into the biochemistry of viral infection and should also generalize well to similar problems in vesicle trafficking and cell recognition.

   

Sean Moore

Core Investigator
Associate Professor
Department of Pediatrics, University of Virginia

https://med.virginia.edu/sean-moore-lab/

We study the structure and function of the GI tract in the context of childhood nutrition, growth, immunity, and host-microbe interactions. This work is inspired locally by the children with digestive diseases we care for at the University of Virginia Children’s Hospital, and globally, by a desire to accelerate progress towards the Sustainable Development Goals for children. We use enteroids and organoids as model systems to better understand host processes and are refining mouse models of environmental enteric dysfunction as pre-clinical platforms for discovery.

   

Kristen Naegle

Core Investigator
Associate Professor
Department of Biomedical Engineering, University of Virginia

https://engineering.virginia.edu/faculty/naegle-kristen-m

Our lab seeks to understand the regulation and function of tyrosine phosphorylation in complex networks. Tyrosine phosphorylation is key to important cell signaling processes that convert extracellular cues, like growth factors and insulin, into biochemical networks that result in a change to the cell. We use both computational and molecular technologies to predict and test the role of tyrosine phosphorylation on proteins and in cellular networks. We incorporate new mathematical and computational methods as needed to tackle the fundamental problems of our research, using techniques that have a foundation in statistical robustness.

   

Gustavo Rohde

Core Investigator
Associate Professor
Department of Biomedical Engineering, University of Virginia

http://faculty.virginia.edu/rohde/

We combine techniques from applied mathematics, signal processing, image analysis, and machine learning to build end to end computation predictive models for biomedical, mobile and remote sensing applications. Transport transforms, and CellOrganizer are examples of the latest methods and technologies our laboratory has developed.

   

Aidong Zhang

Core Investigator
Professor
Department of Computer Science, University of Virginia

https://engineering.virginia.edu/faculty/aidong-zhang

My laboratory is interested in data mining/data science, machine learning, bioinformatics, and health informatics and will join the University of Virginia in January 2019. We are especially interested in tackling the “big p, small n” problem for applying machine learning in biology and medicine.

   

Michael Campbell

Core Investigator
Assistant Professor
Department of Biology, Howard University

http://www.biology.howard.edu/faculty/campbell/campbell.html

One of the major goals of my lab is to understand the genetic basis of complex diseases (for example, prostate cancer, prostate cancer and hypertension) that disproportionately affect African and African American populations using wet laboratory and computational methods. In the end, we aim to generate new information regarding the distribution and frequency of variants specific to populations of African descent, which will be informative for the development of targeted treatments based on more personalized genomic variation.

   

Yayin Fang

Core Investigator
Associate Professor and Co-Director
Center for Computational Biology & Bioinformatics, Howard University

https://ccbb.howard.edu/content/home

The mission of the Howard University Center for Computational Biology and Bioinformatics (CCBB) is to encourage and promote the application of computational approaches to the study of biomedical and disease processes. The application of those research approaches and methods that are at the interface of the biomedical and the physical science is of particular interest

   

Courtney Robinson

Core Investigator
Assistant Professor
Department of Biology, Howard University

http://www.biology.howard.edu/faculty/robinson/robinson.html

My research group studies the ecology of host-associated microbial communities. Model systems are necessary in order to learn about the complex interactions between hosts and their microbes, and between community members. Insects, like other animals, depend on their microbial communities for a number of functions related to host health. Additionally, insects often contain relatively simple microbial communities. We use a number of insect models and techniques from molecular biology to study questions related to fundamental ecological concepts such as community response to invasion and perturbation, as well as the impact of diet and host development on the microbiota, host selection of microbial communities, and the role of microbiota structure in susceptibility to disease.

   

Patrick Ymele-Leki

Core Investigator
Assistant Professor
Department of Chemical Engineering, Howard University

http://www.pylbiocheglab.com

Our research program focuses on (i) the development and implementation of high- and low- throughput screening assays for the identification of novel small molecules with antimicrobial activity, (ii) the development and characterization of physiologically and industrially relevant multispecies in vitro biofilm models for the identification of potential drug targets, and (iii) the in vivo assessment of cytotoxicity and pharmacokinetics parameters and hypothesis-driven validation of antimicrobial drug targets for site colonization related to biofilm formation. This approach combines the benefits of physiologically and industrially relevant assays with a target validation approach superior to that typically encountered for either drug discovery screening or biofilm resistance studies. Current work and collaborative research projects include (i) the investigation of the impact of biofilm structural features (i.e., porosity, diffusional distance, biomass, and biovolume) and physical fluid forces on the efficacy of known antimicrobial agents; (ii) the evaluation of potential antimicrobial challenge mechanisms as a strategy for in situ biofilm control; and (iii) the identification of novel chemical probes and microbial targets and development of novel drug delivery strategies in biofilm settings.

   

Katharina Ribbeck

Core Investigator
Assistant Professor
Department of Biological Engineering, M.I.T.

http://biogels.mit.edu

My lab focuses on basic mechanisms by which mucus barriers exclude, or allow passage of different molecules and pathogens, and the mechanisms pathogens have evolved to penetrate mucus barriers. We hope to provide the foundation for a theoretical framework that captures general principles governing selectivity in mucus, and likely other biological hydrogels such as the extracellular matrix, and bacterial biofilms. Our work may also be the basis for the reconstitution of synthetic gels that mimic the basic selective properties of biological gels.

   

Omer Yilmaz

Core Investigator
Assistant Professor
Department of Biology, M.I.T.

https://ki.mit.edu/people/faculty/yilmaz

The goal of our laboratory is to understand how adult stem cells and their microenvironment adapt to diverse diets in the context of tissue regeneration, aging, and cancer initiation. Towards this end, we are studying the effects of dietary interventions such as calorie restriction and high fat diet-induced obesity on intestinal stem cell (ISC) function in the mammalian intestine. Since ISCs, like all adult stem cells, possess the ability to self-renew and the capacity for differentiating in tissue-specific cell types, they likely play an important role in remodeling the intestine in response to diet-induced physiologies.

   

Paul Blainey

Core Investigator
Assistant Professor
Department of Biological Engineering, M.I.T.

http://web.mit.edu/Blainey-lab/

Broadly, research in my group integrates new microfluidic, optical, and molecular tools for application in biology and medicine. We emphasize quantitative single-cell and single-molecule approaches, aiming to enable multiparametric studies with the power to reveal the workings of natural and engineered biological systems across a range of scales.

   

Clary Clish

Core Investigator
Institute Scientist
Broad Institute

https://www.broadinstitute.org/bios/clary-clish

My lab works in collaboration with groups, from both within the Broad Institute and the external research community, on projects that range in scope from metabolic phenotyping of model systems to large human cohort studies. Contributions from the platform have included the discovery of plasma metabolic signatures that indicate future risk of developing diabetes in the Framingham Heart Study Offspring cohort, 4-12 years before clinical diagnosis of type 2 diabetes, as well as the discovery of early indicators of pancreatic cancer in humans years before clinical diagnosis. Prior to joining the Broad Institute, I held senior and executive management positions in the biotechnology industry from 2001-2008, including vice president of discovery at Gene Logic Inc. and director of metabolite biochemistry at Beyond Genomics Inc.

   

Daniel Gioeli

Affiliated Faculty
Associate Professor
Department of Microbiology, Immunology & Cancer Biology, UVA

https://mic.med.virginia.edu/gioeli/

My primary research interest has focused on understanding the mechanistic underpinnings of the cell signaling networks that contribute to cancer progression and resistance to therapy. My laboratory is currently focused on two research areas: 1) We are testing the hypothesis that progression of prostate cancer to castration-resistance is frequently driven by changes in CHK2 signaling that regulate androgen receptor (AR) activity, facilitate cell proliferation, and minimize hormone dependence. 2) We are developing an in vitro tumor microenvironment system for solid tumors that utilizes multiple cell types and recapitulates tumor capillary hemodynamics and biological transport. The applicability of this system is multifaceted and includes facilitating drug discovery and development, mechanistic analysis of drug responses, and development of biomarkers of response. In addition to the two above focus areas, my collaborative interactions are focused on the molecular mechanisms of combinations of targeted molecular agents in order to overcome inherent and acquired resistance associated with traditional therapeutic approaches.

   

Eli Zunder

Affiliated Faculty
Assistant Professor
Department of Biomedical Engineering, University of Virginia

http://bme.virginia.edu/people/zunder.html

Research in our laboratory is focused on discovering the mechanisms that control stem cell fate. We study in vitro differentiation to gain insight into stem cell behavior during normal development and disease, and we study in vivo development to gain insight into the derivation of clinically relevant cell types for regenerative therapy. In order to study the complex mixtures of rapidly changing cell types that exist in these in vitro and in vivo systems, we are building experimental and computational tools that track cell populations as they change over time with molecular characterization at the single-cell level. Using these tools, our goal is to define the fundamental principles of cellular pluripotency and differentiation.