Systems Biology Administration

Division Leader, Systems Biology

John Tyson

John Tyson, Division Leader

University Distinguished Professor, Biological Sciences

Email: tyson@vt.edu

Phone (Lab 1): (540) 231-5958 

Phone (Lab 2): (540) 231-5508

Welcome to the Division of Systems Biology and to the new
bachelor's degree program in Systems Biology!

Living systems—be they single cells, multicellular plants or animals, communities of interdependent organisms, or human societies—are complex networks of interacting agents whose synergistic relationships determine the behavior, development and evolution of the systems. In all cases, the behavior of the system transcends the properties of its parts and is rarely understandable by intuitive reasoning alone. Systems biologists approach the intellectual and practical challenges presented by living systems by a combination of theoretical, mathematical, computational and experimental tools to describe, simulate and understand these networks of interacting agents that underlie the basic biology of living things.  

The Division of Systems Biology at Virginia Tech offers a B.S. degree program that trains undergraduate students in the ideas, methodologies and tools of modern systems biology, including a rigorous research experience and professional development. The degree will prepare VT students for exciting careers in cutting-edge biotechnology and biomedical industries or for advanced training in the most competitive graduate programs in systems biology. 

Faculty in the Division of Systems Biology at Virginia Tech are involved in a wide range of biological problems:

  • Molecular dynamics
  • High-throughput studies of genes, proteins and metabolites
  • Network topology
  • Network dynamics and cell physiology
  • Synthetic biology
  • Metabolic control
  • Protein signaling networks
  • Cancer etiology, diagnosis and treatment
  • Immune system modeling
  • Drug development accelerated by modeling
  • Microbiome dynamics
  • Infectious disease modeling
  • Simulation of large-scale human social interactions

Have questions? Our advisors, Nora Dragovic and Cara Craze, are happy to answer any questions you might have! 


Cara Craze

Cara Craze

Academic Advisor,

Academy of Integrated Science

Email: cara1@vt.edu

Phone: 540-231-8132



Nora Sullivan

Nora Dragovic

Program Manager & Advisor,

Academy of Integrated Science

Email: nora84@vt.edu

Phone: 540-231-8131


Core and Affiliated Faculty

Dr. Abbas' research focus is on infectious disease system dynamics and public health systems research. While he has primarily focused on the epidemiological and economic scales of infectious disease dynamics, he is interested in multi-scale infectious disease dynamics of public health significance that connect with the immunological and evolutionary scales. 

Contact: 

Phone: (540) 231-1865

Email: kaja.abbas@vt.edu    

Dr. Josep Bassaganya-Riera is the Director of the Nutritional Immunology and Molecular Medicine Laboratory at the Biocomplexity Institute of Virginia Tech. He has held many research grants from various sources including the National Institutes of Health, the United States Department of Agriculture, and industrial corporations. He is the Principal Investigator and Director for the Modeling Immunity to Enteric Pathogens (MIEP) project, a $10.6 million Center that investigates the immunoregulatory mechanisms underlying infections with gut pathogens by applying mathematical systems to mucosal immunology. Dr. Bassaganya-Riera has published over 100 scientific papers, 9 patents and manages a research portfolio of $15M.

 

Dr. Baumann's interests in system biology revolve around using mathematical modeling of biological systems as a way to integrate knowledge, gain enhanced understanding, and make useful predictions. His current interest is to model the effect of anti-estrogen therapy in breast cancer cells and create optimized therapeutic protocols that enhance cancer cell death while delaying the onset of resistance and limiting side effects. More generally, Dr. Baumann is interested in deterministic and stochastic modeling of biological systems, from ecological models to pharmacological models, to cell signaling networks.

Contact: 

Phone: (540) 231-4446

Email: baumann@vt.edu
    

Dr. Bevan's research involves the application of computational molecular modeling to relate the structure and dynamics of molecular systems to function. Systems currently under investigation include the amyloid β-peptide that is associated with Alzheimer's disease and peroxisome proliferator-activated receptor that is associated with inflammation, diabetes, and obesity. We also are initiating projects involving G-protein coupled receptors (GPCRs), and irisin, a recently discovered protein with hormone-like properties. Finally, he and his research associates are using computational methods to design enzymes, with their strategy being to alter the substrate specificity of existing enzymes. 

Contact: 

Phone: (540) 231-5040

Email: drbevan@vt.edu
  

Research Groups: 

The Bevan Lab

Dr. Cao's research interests are in computational science and engineering. He has worked in the field of numerical solution of differential-algebraic equations (DAEs), sensitivity analysisfor DAEs and ordinary differential equations (ODEs), error estimation and control for linear systems and ODEs, and stochastic simulation for biochemical systems. He has made significant contribution in the stochastic algorithms related to multi-scale problems. The implicit tau-leapingmethod and the slow-scale SSA method proposed by him and his collaborators have become a hot topic in this area.

Contact: 

Phone: (540) 231-1417

Email: ycao@cs.vt.edu
    

Dr. Childs' research interests involve developing and analyzing mathematical models of biological systems as well as building innovative quantitative methods informed by experimental results. The biological focus of her work is the development of host immune responses to infectious disease and the resulting feedback on pathogen dynamics and transmission at the population level. She studies this from two perspectives: the acquisition of immunity to antigenically complex and varying pathogens and pathogen evolution as a response to adaptive immune control.

Contact: 

Phone: (540) 231-8265

Email: lchilds@vt.edu

Research Groups: 

Dr. Childs' Homepage

Professor, Biological Sciences

Dr. Chen's research focuses on mathematical modeling of biological systems. She is particularly interested in studying the coupling between biological signaling and spatiotemporal regulation/mechanical interactions. 

Biological systems self-assemble into highly heterogeneous and dynamic structures. Spatiotemporal regulation and mechanical interactions constitute critical aspects in biological signaling mechanisms, but in most cases their specific functional roles remain poorly understood. Modern experimental tools allow high resolution live-cell imaging and dynamic force measurement for these biological processes. Mathematical modeling fills the gaps in these data with physically viable assumptions, which optimizes the information obtained from the data and contributes to deeper understanding of the functional roles of spatiotemporal regulation and mechanical interactions. Previously, Dr. Chen built mathematical models for a wide range of biological mechanisms, including the spatiotemporal regulation of spindle assembly checkpoint mechanism, mechano-chemistry of bacterial motility mechanisms, skeletomuscular biomechanics, functioning neuronal networks, etc.

Dr. Chen's current interests lie in coordinated motility in bacterial colony, spatiotemporal signaling and noise regulation in mitosis, and gene expression regulation in circadian rhythm.

Contact: 

Phone: (540) 231-1359

Email: chenjing@vt.edu    

Research Groups: 

The Chen Research Group

Dr. Chung's research interests concern various forms of inverse problems. Driven by its application, he develops and analyzes efficient numerical methods for inverse problems.

Applications of interest are, but not limited to, systems biology, medical imaging, and dynamical systems. Estimating parameter for dynamical systems (ODE constraint optimization) are prototype inverse problems, which can be particular challenging. With his broad background in computational methods for parameter estimation and experimental design, Dr. Chung has gathered key expertise in parameter estimation and experimental design for systems biology. Currently, he am leading an NIH R21 project on identifying interactions of microbial communities.

In his research Dr. Chung addresses and investigates computational and statistical methods, prediction models, and estimation methods to analyze and predict biological behaviors and medical concerns. An interdisciplinary approach towards research can be found throughout his scientific work.

Contact: 

Phone: (540) 231-3446

Email: mcchung@vt.edu    

Research Groups: 

Dr. Chung's Homepage

Dr. Cimini's research focuses on two major areas: (i) investigating how the mechanics and dynamics of mitotic apparatus components ensure accurate chromosome segregation during mitosis; (ii) how aneuploidy affects cell division and cell proliferation. Her experience in systems biology is mainly linked to the first area of investigation, for which her lab has established fruitful collaborations with mathematical modelers. For their research, they use live-cell and high-resolution light microscopy data to build mathematical models that describe the forces acting within the mitotic apparatus at different stages of mitosis. Using these models, they make new predictions that they then test designing new experiments. 

Contact: 

Phone: (540) 231-8241

Email: cimini@vt.edu   

Research Groups: 

Cimini Research Group

Dr. Ciupe's research focuses on development, analysis and validation of mathematical models that describe immune system responses to viral diseases such as human immunodeficiency virus, hepatitis B virus, dengue virus and equine infectious anemia virus. Besides modeling virus-host interactions, she is investigating possible homeostatic mechanisms that regulate lymphocyte population size and T cell receptor diversity, the immune deficiencies that lead to diabetes, and the use of dynamical systems to model archeological data.

The mathematical questions associated with Dr. Ciupe's research range from the study of existence and positivity of solutions of systems of ordinary and delayed differential equations, to conducting local and global stability analysis of steady state solutions, to determining conditions for the emergence of bi-stable solutions, to optimization techniques involved in data fitting, to analysis of the sensitivity of models to changes in parameters and errors in data measurements, and finally, to questions regarding model validation. Biologically, she aims to determine the individual and combined contributions of cellular and antibody immune responses in protection against viral infections, the host-virus mechanisms responsible for transitions from acute to chronic disease, and the determination of the values of unknown parameters.

Contact: 

Phone: (540) 231-3190

Email: stanca@vt.edu    

Research Groups: 

Dr. Ciupe's Homepage

Stephen Eubank is deputy director, Network Dynamics and Simulation Science Laboratory, tenured professor, Department of Population Health Sciences, and adjunct professor, Department of Physics. His past research includes fluid turbulence; nonlinear dynamics and chaos; time series analysis of markets (as a founder of Prediction Company); natural language processing (as Visiting Scientist at ATR in Kyoto, Japan); and simulations of large interaction-based systems.>

As a staff member at Los Alamos National Laboratory, he played a leading role in the development of the traffic microsimulation component of the Transportation Analysis and Simulation System (TRANSIMS), developed the Epidemiological Simulation System(EpiSims) project, and served as team leader for the Urban Infrastructure Suite (UIS), of which both TRANSIMS and EpiSims are parts. UIS is a collection of interoperable simulations of interacting infrastructures, each of which simulates the behavior of every individual in a large urban region. The goal of UIS is to model the dynamics of systems including both physical and social components. Since arriving at the Biocomplexity Institute of Virginia Tech in January, 2005, he has pursued interests both in developing advanced technology for the study of realistic socio-technical systems and also in understanding how the dynamics of diffusive processes on networks, e.g. disease transmission, are related to the structure of the underlying networks. He is the PI on one of the research groups making up the NIH's MIDAS (Modeling Infectious Disease Agent Study) network.

Contact: 

Phone: (540) 231-2504

Email: seubank@vbi.vt.edu
    

Dr. Feng was trained in microbiology, computational biology and biomolecular engineering and has always been interested in interdisciplinary tools at the interfaces of these areas and what they can do for biological studies.  He became interested in cell metabolism during his Ph.D. training. Dr. Feng's independent research has been focused on developing new tools and technologies for rigorous and holistic investigation of microbial metabolism. His group developed a series of web-based databases and modeling tools (e.g., MicrobesFlux and iTAP database) for metabolism analysis. His research was featured in numerous public media highlights. Currently, Dr. Feng's interests are developing computational approaches to integrate multi-omics data with cell phenotype analysis.

Contact: 

Phone: (540) 231-2974

Email: xueyang@vt.edu
    

Research Groups: 

Biomolecular Engineering Lab

Dr. Finkielstein is Associate Professor of Cell and Molecular Biology in the Department of Biological Sciences at Virginia Tech, Director of the Integrated Cellular Responses Laboratory, and Member of the Board of Directors of the Virginia Breast Cancer Foundation.

She has more than fifteen years experience as an accomplished scholar, teacher, and researcher. She founded the Integrated Cellular Responses Laboratory (ICRL) at Virginia Tech where her group works to understand the contribution of environmental factors on breast cancer initiation and progression.

Dr. Finkielstein's laboratory has produced over 50 publications and book chapters in the field, including articles in top journals such as Nature and Cell. In addition, She has filled and commercialized patents, trained over 120 undergraduate students that continued their graduate education in top and Ivy League Universities, and graduated numerous MSc and PhDs in the last years. Furthermore, Dr. Finkielstein has been running an international high school exchange program that has facilitated a new cultural and scientific experience to many Virginia and Argentinean students.

Contact: 

Phone: (540) 231-1159

Email: finkielc@vt.edu

    

As a general rule, the more complex a machine is, the more likely it is to break - simply because there are more potential breaking points. Yet, cells are highly complex entities and are extremely robust, i.e. they perform their functions reliably even in variable intra- and extracellular milieus. We want to understand the underlying basis: what makes biological systems robust?

To study this question, we look at cell division, a process that is essential for life and whose deregulation is common in cancer. When cells divide, a multitude of changes need to happen in a very short time, and any error can be fatal. Hence, reliability and robustness are crucial. To understand the underlying principles, we combine perturbations with high-end, quantitative microscopy, which allows us to obtain single-cell, time-resolved and spatial information.

Computational modeling, for which we collaborate with experts in this field, helps us to interpret these experiments and to develop new hypotheses. We work with fission yeast, which is an excellent model for eukaryotic cells, and where we can easily introduce perturbations using CRISPR/Cas9 and other state-of-the-art technologies.

Contact: 

Phone: (540) 231-7318

Email: silke@vbi.vt.edu
    

Research Groups: 

Hauf Research Group

Hauf Lab

Lenwood S. Heath is a professor in the Department of Computer Science at Virginia Tech.  His research interests include theoretical computer science, algorithms, graph theory, computational biology, and bioinformatics.  Dr. Heath completed a Ph.D. in computer science at the University of North Carolina, Chapel Hill, an M.S. in mathematics at the University of Chicago, and a B.S. in mathematics at the University of North Carolina, Chapel Hill.  Before joining the faculty at Virginia Tech in 1987, he was an instructor of applied mathematics and member of the Laboratory of Computer Science at MIT.

Dr. Heath is a member of SIAM, a member of the International Society for Computational Biology (ISCB), and a senior member of the Institute of Electrical and Electronics Engineers (IEEE).  He is an editor of the Journal of Interconnection Networks (JOIN).

Contact: 

Phone: (540) 231-4352

Email: heath@vt.edu

    

Research Groups: 

Dr. Heath's Homepage

Professor, Statistics

Professor, Biocomplexity Institute

Dr. Hoeschele has been a Professor at Biocomplexity Institute of Virginia Tech and in the Department of Statistics at Virginia Tech since 2002. Prior to this appointment, she was Assistant and Associate Professor and Professor of Statistical Genetics in the Department of Dairy Science at Virginia Tech. Dr. Hoeschele was a Visiting Professor at the University of New England (Australia) in 1993, at Wageningen Agricultural University (The Netherlands) in 1995, and in the Statistics Department at North Carolina State University in 1999.

Dr. Hoeschele has served and continues to serve as the Principal Investigator on smaller statistical methodology grants and as statistics/statistical genetics co-Investigator on large, collaborative grants in genomics and Genetical Systems Biology. Her current collaborative research focuses on the genetical genomics and genetical epigenomics of common and complex human diseases such as cardiovascular disease, diabetes and obesity, via collaborations with investigators at Wake Forest University Medical School. Dr. Hoeschele's current statistical methodology research focuses on multivariate statistical methods for genome-wide asssociation (and linkage) analyses of high-dimensional phenotypes such as genome-wide gene expression, and the utilization of the SNP-phenotype associations for causal inference.

Contact: 

Phone: (540) 231-3135

Email: inah@vbi.vt.edu

Stefan Hoops is a senior project associate at Biocomplexity Institute of Virginia Tech. He earned his Ph.D. in Mathematical Physics from the Norwegian Institute of Technology in 1993.  Before joining Biocomplexity Institute in 2000, Hoops served as a software designer/developer for Schumann Consulting Corporation in Germany from 1995-2000.  He was elected in 2006 as one of the 5 editors of the Systems Biology Markup Language (SBML), serving for the years 2007-2009.

At Biocomplexity Institute, Hoops works with Dr. Pedro Mendes in the Biochemical Networks Modeling Group. The research group is interested in understanding how cells work at the biochemical level. Their approach can be labeled as Systems Biology, as they derive quantitative dynamic models from integrative functional genomic data. They have ongoing projects in development of methodologies and software for the complete process of going from functional genomic data to computational models: biochemical simulators (Gepasi and COPASI), database design (DOME and B-Net), data analysis, network inference, parameter estimation for nonlinear models, and theoretical aspects of biochemical regulation (such as Metabolic Control Analysis).

The rotation of the earth creates a daily fluctuation of environmental cues, and organisms have evolved internal timing systems, called circadian clocks, to coordinate their daily activities to anticipate and prepare for these environmental changes. Because circadian rhythmicity is a fundamental aspect of temporal organization in essentially every cell in the body, and governs many biological processes ranging from molecular and biochemical pathways to physiological and behavioral rhythms, disruption of the circadian clock can have a severe influence on human health, ranging from psychiatric disorders, obesity, cardiovascular diseases, to certain types of cancer. 

The mission of the Kojima laboratory is to understand how the molecular clock machinery in each cell controls circadian biochemistry, physiology and ultimately behavior at a molecular level. We specifically focus on rhythmic gene expression in various mouse tissues, with a special emphasis on transcription-independent gene regulatory mechanisms. We use various approaches such as neuroscience, molecular/cellular biology, genomics, bioinformatics and computational biology to open up an exciting new avenue and address unforeseen questions.

Contact: 

Phone: (540) 231-4614
Email: rvjensen@vt.edu

The rotation of the earth creates a daily fluctuation of environmental cues, and organisms have evolved internal timing systems, called circadian clocks, to coordinate their daily activities to anticipate and prepare for these environmental changes. Because circadian rhythmicity is a fundamental aspect of temporal organization in essentially every cell in the body, and governs many biological processes ranging from molecular and biochemical pathways to physiological and behavioral rhythms, disruption of the circadian clock can have a severe influence on human health, ranging from psychiatric disorders, obesity, cardiovascular diseases, to certain types of cancer.

The mission of the Kojima laboratory is to understand how the molecular clock machinery in each cell controls circadian biochemistry, physiology and ultimately behavior at a molecular level. We specifically focus on rhythmic gene expression in various mouse tissues, with a special emphasis on transcription-independent gene regulatory mechanisms. We use various approaches such as neuroscience, molecular/cellular biology, genomics, bioinformatics and computational biology to open up an exciting new avenue and address unforeseen questions.

Contact: 

Phone: (540) 231-5196

Email: skojima@vt.edu

Research Groups: 

Kojima Research Group

Cancer is a disease of the cell cycle that results in uncontrolled proliferation of cells. In our laboratory, we explore the molecular mechanisms of breast cancer cell cycle regulation by using holistic, mass spectrometry-based systems biology approaches.

We develop proteomic technologies for investigating the pathways that enable cancer cells to bypass tightly regulated molecular checkpoints, proliferate in an unrestrained manner, metastasize and hijack normal biological function. Further, we capitalize on the power of our proteomic data to identify novel therapeutic drug-targets, and to develop microfluidic architectures for targeted detection of biomarkers indicative of disease.

Contact: 

Phone: (540) 231-5077

Email: malazar@vt.edu

Research Groups: 

Lazar Lab

Professor, Biological Sciences

Dr. Li studies innate immune memory underlying both acute and chronic inflammation. His group has defined mechanisms governing the novel paradigms such as differential polarization and skewing of immune environment as well as priming and tolerance of macrophages. These dynamic paradigms play key roles during both the pathogenesis and resolution of human inflammatory diseases such as atherosclerosis, sepsis, wound healing, and cancer.

Contact: 

Phone: (540) 231-1992

Email: lwli@vt.edu

Research Groups: 

Li Laboratory

Dr. Marathe is an expert in interaction-based modeling and the simulation of large, complex biological, information, social, and technical systems. As the Director of the Network Dynamics and Simulation Science Laboratory, he leads the basic and applied research program where researchers are advancing the science and engineering of co-evolving complex networks and developing innovative computational tools based on these advances to support policy informatics.

Marathe is an ACM Fellow for his contributions to high-performance computing algorithms and software environments for simulating and analyzing socio-technical systems. Marathe is also named a Fellow of IEEE for his contributions to the development of formal models and software tools for understanding socio-technical networks.

Contact: 

Phone: (540) 231-8832

Email: marathe@vt.edu

I am broadly interested in the dynamics of biological systems, with an emphasis on synthetic gene networks in bacteria. My research is characterized by the experimental and theoretical investigation of synthetic gene oscillators, proteolytic degradation pathways, and (more recently) bacterial persistence. Experimental tools include fluorescence microscopy, molecular biology techniques, and microfluidics. Theoretical tools include nonlinear dynamics, queueing theory, stochastic chemical reaction networks, and machine learning.

Contact: 

Phone: (540) 231-3332

Email: wmather@vt.edu

Research Groups: 

Dr. Mather's webpage

Dr. Mukhopadhyay's group studies the biochemical mechanisms used by microorganisms to survive under extreme conditions with specific focus on the methanogenic archaea, natural gas production and tuberculosis. They also examine the structure-function relationships of two CO2-fixing enzymes (PEPCK and PEPC) with relevance in type 2 diabetes and production of chemicals and food crop.

Contact: 

Phone: (540) 231-1219

Email: biswarup@vt.edu

Research Groups: 

Biocomplexity Institute

The overall goal of Murali's research in computational systems biology is to build phenomenological and predictive models of the intricate interaction networks that govern the functioning of a living cell. He designs algorithms and computational tools based on graph theory, data mining, and machine learning to obtain networkoriented system-level insights into fundamental questions on cellular phenomena.

Current projects include signaling pathway reconstruction and crosstalk, synthesis of top-down and bottom-up approaches in systems biology, systems biology of bioengineered livers, and host-pathogen protein interactions. 

Contact: 

Phone: (540) 231-1799

Email: shoops@vbi.vt.edu

Dr. Onufriev's research group develops and uses computational methods to understand dynamics and function of large biomolecular systems such as proteins, DNA, and their complexes. 

Contact: 

Phone: (540) 231-4237

Email: alexey@cs.vt.edu

Research Groups: 

Dr. Onufriev's Website

Dr. Rajagopalan's research interests are in hepatic tissue engineering, Self assembly of polyelectrolytes, Cell-matrix interactions, Chemotaxis and mechanotaxis, Corneal tissue engineering, and Nanostructured materials

Contact: 

Phone: (540) 231-4851

Email: padmar@vt.edu

My primary interest in systems biology is in the tools and visualizations that support the process by which modelers develop biochemical reaction models. The principle goal is to support the modeler in the process of developing larger scale models. This includes visualizations and automated optimization tools, as well as model design and editing tools. I see many parallels between the process of developing, maintaining, and analyzing a model based on a collection of chemical reaction equations and the software development process.

Contact: 

Phone: (540) 231-4354

Email: shaffer@vt.edu

Research Groups: 

Dr. Shaffer's webpage

I am broadly interested in understanding of how a eukaryotic genome is organized and how it changes over time. More specifically I am looking at if and how the linear and three-dimensional organization of chromosomes affect the function and evolution of insect genomes.

We use light microscopy, molecular techniques, and bioinformatics to delve into the genome at three different levels: the 3D structure of the cell nucleus, epigenetic modifications of chromosomes, and organization of DNA sequence. We investigate the effect of chromosomal attachments to the nuclear envelope on chromosome territories, gene-gene contacts, and genome rearrangements. We found that computational models of a fruit fly nucleus with more numerous attachments form more distinct chromosome territories, the frequency of intra-chromosomal gene-gene contacts increases, but the frequency of inter-chromosomal contacts decreases. By analyzing mapped genome assemblies of Anopheles gambiae, An. stephensi, An. funestus, An. atroparvus, and An. albimanus, we found that rearrangements of the X chromosome occur 3 times faster than autosomal rearrangements pointing to a special role of sex chromosomes in evolution of malaria mosquitoes. We characterized a major epigenetic component of the An. gambiae germ-line – small non-coding Piwi-interacting RNA (piRNA) sequences and their euchromatic and heterochromatic clusters. We also identified a subset of the piRNA-enriched genes that have functions related to reproduction and embryonic development.

Overall, my research helps to understand the mechanisms of mosquito evolution, adaptation, and reproduction. This knowledge can facilitate the development of innovative genome-based approaches for mosquito-borne disease control.

 

Contact: 

Phone: (540) 231-7316

Email: igor@vt.edu

My laboratory employs systems biology or functional genomics approaches to study the basic biology of sex-determination and embryonic development in mosquitoes. On the basis of such fundamental information, we are developing novel genetic applications to control mosquito-borne infectious diseases. Such applications include a synthetic gene drive system for efficient and safe spread of refractory genes in mosquito populations and genetic manipulation of mosquito sex ratios and fertility.

We have experience with transgenic Aedes and Anopheles mosquitoes and next-generation sequencing of RNA and genomic samples. We have recently developed novel genomic and bioinformatics approaches to study Anopheles Y chromosome genes. We have recently discovered a male-determining factor in Aedes aegypti. We have also clearly demonstrated complete dosage compensation in An. stephensi by RNA-seq analysis of genes on different chromosomes of both sexes. Our research has the potential to bridge a major gap in our understanding of mosquito biology and lead to novel control strategies based on manipulation of mosquito sex ratios and fertility.

Contact: 

Phone: (540) 231-8062

Email: jaketu@vt.edu

My expertise is building deterministic and stochastic models of the molecular control systems that underlie various aspects of cell physiology, including the cell cycle control system in yeast, drug sensitivity and resistance in breast cancer cells, circadian rhythms, cell differentiation in the immune system, stem cell dynamics in the shoot apical meristem of plants, and the growth, division and differentiation of alphaproteobacteria.

My group builds comprehensive, accurate, predictive models of these control systems and uses these models to understand the observations and data collected by our experimental colleagues. Deterministic models are formulated in terms of nonlinear differential equations describing the temporal dynamics of the reaction network, and, when appropriate, including spatial transport and diffusion of molecules. Stochastic models are formulated in terms of elementary chemical reactions and transport processes, simulated by Gillespie’s stochastic simulation algorithm, or, for more complex networks, by chemical Langevin equations.

Contact: 

Phone (lab1): (540) 231-5958 
Phone (lab2): (540) 231-5508

Email: tyson@vt.edu

My research interest has been related to systems biology mainly through our analyses of various omics analyses.

The point of systems biology is to consider the system as a whole, rather than isolating them into separate pieces, which has been the traditional approach used in biology. Examples of relevant projects  include understanding the disease relationship through a systems biology approach, integrated analyses of various genomic, transcriptomic, proteomic, exome data in lung cancer, and identification/prediction of protein complex using network properties. Also relevant is the most recent collaboration with colleagues from the dairy science department, crop science department, and Civil Engineering department to understand the dynamics of antibiotic resistance genes/bacteria in a farming system using a systems approach.

Contact: 

Phone: (540) 231-1799

Email: shoops@vbi.vt.edu

Research Groups: 

Dr. Zhang's website