GBCB Faculty

For more information about the program Admission process and fellowships Graduate School GBCB Liason
Dr. David Bevan
Program Chair
Department of Biochemistry
201 Fralin Hall
Blacksburg, VA 24061
540/ 231-5040, drbevan@vt.edu
Dr. T. M. Murali
Admissions Committee Chair & Associate Professor
Department of Computer Science
2160B Torgerson Hall
Blacksburg, VA 24061
540/ 231-8534, murali@vt.edu
Dennie Munson
Graduate Program Assistant
Office of the Dean of the Graduate School
Virginia Tech and VBI
Washington Street, Phase I (0477)
Blacksburg, VA 24061
540/ 231-1968, dennie@vt.edu

 

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Faculty Name Department Affiliation Accepting Students Research Focus Area Research Summary

Sandu Adrian Sandu
Professor
sandu@vt.edu
web site
  • Department of Computer Science and Applications
Yes
  • Computational Biology
  • High Performance Computing
  • Math
  • Modeling and Simulation
In the Computational Science Laboratory we do fundamental research in numerical methods and develop novel algorithms for the adaptive solution of ordinary and partial differential equations, linear algebra, optimization, methods to model systems with uncertainty, etc. We develop high performance software for large scale-parallel platforms. We apply our new technologies to many important fields. Examples include modeling of atmospheric pollution for better environmental policies; simulation of the stochastic chemical processes inside living cells and understanding the complex biological regulation networks; design of optimal trajectories for the future generation of satellites at Jet Propulsion Laboratory; assimilation of real data streams into atmospheric models for improved forecasts of extreme events like hurricanes; etc. Computational platforms range from multicore workstations and accelerated architectures (e.g., GPUs, IBM cell) to large scale parallel supercomputers.

li song li

songli@vt.edu
web site
Yes
  • Microbiology, including microbe host interactions
Current Research: >Identifying conserved alternative splicing variants and antisense transcripts in diverse plant species. >Developing a computational framework to systematically define best parameters and pipeline for mapping and assembly of next generation sequencing reads in crop species. > Developing machine learning methods that identify active regulatory networks controlling cell type- or condition-specific gene expression. >Improving Hidden Markov Model (HMM) based gene prediction method. Our new method will incorporate diverse genomic evidence such as PEAT-seq, Ribo-seq and evolutionary conservation to improve splicing variant discovery and annotation in both model species and crop species.
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Kim Inyoung Kim
Associate Professor
inyoungk@vt.edu
web site
Yes
  • Biological Data Mining and Statistics
* Semiparametric/Nonparametric Model and Method using Regression Splines or Gaussian Process * Nonlinear Mixed Effect Model for Correlated/Clustered Data * Semi/Nonparametric Bayesian Modeling and Computing in High Dimensional Data Analysis (p>>n) * Statistical Kernel Machine Learning * Nonparametric Functional Analysis * Measurement Error in Nonlinear/Nonparametric Model Analysis * Biostatistics (Environmental Health, Epidemiology, Public Health, Equine Medicine, and Various Cancer Metastasis) * Bioinformatics (Functional Genomics, System Biology: Protein-Protein Interaction, Proteomics) My research interests focus on developing semi/nonparametric statistical methods and theory using regression splines or Gaussian/Dirichlet process to address issues in several areas (epidemiology, medicine, genomics, proteomics, and system biology) for high and low dimensional analysis. Both Frequentist and Bayesian methods have been developed.

Kojima Shihoko Kojima
Biocomplexity Institute Fellow and Assistant Professor
skojima@vt.edu
web site
  • Biological Sciences
  • Health Sciences
Yes
  • Animal Sciences
  • Biomedicine
  • Cell Biology
  • Genetics and Molecular Biology
  • Genomics
  • Systems Biology
Why do you wake up everyday in the morning and go to sleep at night? What controls this behavior? How is it controlled? We are interested in deciphering genetic codes of biological rhythms to understand how the molecular clock machinery controls circadian biochemistry, physiology, and ultimately behavior.
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Lewis Bryan Lewis
Research Associate Professor
blewis75@vt.edu
web site
  • Biocomplexity Institute at Virginia Tech
Yes
  • Biological Data Mining and Statistics
  • High Performance Computing
  • Infectious Diseases
  • Modeling and Simulation
  • Public Health
My research has focused on understanding the transmission dynamics of infectious diseases within specific populations through both analysis and simulation. I am a computational epidemiologist with over 10 years of experience in crafting, analyzing, and interpreting the results of models in the context of real public health problems. While pursuing my PhD as a computational epidemiologist, I acted as a liaison between the computer scientists and mathematicians building simulation software and decision makers who wanted answers to pressing public policy questions. Throughout the past 7 years I have been heavily involved in a series of projects modeling potential response to an influenza pandemic that supported planning and response activities at the federal-level

Senger Ryan Senger
Associate Professor
senger@vt.edu
web site
  • Department of Biological Systems Engineering
Yes
Metabolic Engineering and Systems Biology
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Abbas Kaja Abbas
Assisstant Professor
kaja.abbas@vt.edu
web site
  • Department of Population Health Sciences at the Virginia-Maryland College of Veterinary Medicine.
  • Biocomplexity Institute, NDSSL
Yes
  • Computational Biology
  • Modeling and Simulation
  • Systems Biology
My research focus is on epidemiological and economic modeling of infectious diseases at the interface of infectious disease system dynamics and public health systems research. I welcome collaborations in related research projects to improve health policy and practice; feel free to contact me.
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Chen Jing Chen
Assisstant Professor
chenjing@vt.edu
web site
  • Department of Biological Sciences
Yes
  • Computational Biology
  • Math
  • Microbiology, including microbe host interactions
  • Modeling and Simulation
  • Systems Biology
We build mathematical models to study cell biology, especially how spatial, temporal and mechanical regulations couple with biochemical signals to control cellular functions. We typically work in close collaboration with experimental groups. Current research projects in the lab include: *Circadian gene expression. *Cell division mechanism. *Bacterial motility. *Phage-bacteria interactions
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Williams Mark Williams
Associate Professor
markhw@vt.edu
web site
  • Department of Horticulture
Yes
  • Biological Data Mining and Statistics
Research areas are: Biological Data Mining and Statistics, Plant-environment Microbiomics, Soil metagenomics, Plant-microbial ecology
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Holliday Jason Holliday
Associate Professor
jah1@vt.edu
web site
  • Department of Forest Resources and Environmental Conservation (FREC)
Yes
Research Synopsis: Utilizing genotype-phenotype association studies and landscape genomics, we elucidate the genetic determinants of complex adaptive traits, using the black cottonwood tree (commonly known as ‘poplar’) as a model.
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Cimini Daniela Cimini
Associate Professor
cimini@vt.edu
web site
  • Department of Biological Sciences
  • Biocomplexity Institute Research Fellow
Yes
  • Genetics and Molecular Biology
  • Systems Biology
Research in the Cimini lab focuses in two major areas: (i)role of mechanics and dynamics of mitotic apparatus components in ensuring accurate chromosome segregation during cell division; (ii) causes and consequences of aneuploidy (abnormal chromosome numbers) in normal and cancer cells.
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Hauf Silke Hauf
Assistant Professor
silke.hauf@vt.edu
web site
  • Department of Biological Sciences
  • Biocomplexity Institute Research Fellow
Yes
  • Computational Biology
  • Cyberinfrastructure and Bioinformatics
  • Genetics and Molecular Biology
  • Systems Biology
We want to understand the mechanisms behind the extremely reliable and robust execution of cellular processes. To this end we study cell division, a highly complex process that – despite its complexity – is typically completed flawlessly, even when external or internal conditions vary. Our methods include yeast molecular genetics, quantitative live cell imaging, computational modeling and bioinformatics. Research Interests: > Robustness in cell cycle progression > Chromosome segregation fidelity > Quantitative fluorescence microscopy
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Li Liwu Li
Professor
lwli@vt.edu
web site
  • Biological Sciences
Yes
  • Biomedicine
  • Computational Biology
  • Genetics and Molecular Biology
  • Modeling and Simulation
  • Systems Biology
Major Field of Interest: Molecular and Cellular Mechanism of Human Inflammatory Diseases Current Research: Molecular pathways controlling innate immunity and inflammation, Dynamic programming of innate immune leukocytes, and Pathogenesis of acute and chronic inflammatory diseases such as sepsis and atherosclerosis
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Maroof Saghai Maroof
Professor
smaroof@vt.edu
web site
  • Department of Crop and Soil Environmental Sciences
Yes
  • Genetics and Molecular Biology
  • Genomics
  • Microbiology, including microbe host interactions
  • Plant Sciences
  • Systems Biology
Our research projects have been funded by NSF, USDA/NRI, USDA/NIFA, industrial sector and various commodity boards. These projects provide opportunities for training undergraduate and graduate students and postdoctoral fellows. My graduate students conduct original and independent research involving laboratory, field and greenhouse experiments using the tools of genomics and bioinformatics. They interact with project collaborators via conference calls and work group meetings, prepare reports and publish their experimental results in scientific journals. They also actively participate in teaching by serving as teaching assistants for various courses and by training of undergraduate students.
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Zhu Jinsong Zhu
Associate Professor
zhujin@vt.edu
web site
  • Department of Biochemistry
Yes
  • Genetics and Molecular Biology
Signal transduction and gene regulation in insects; genetic control of the mosquito defense reactions against malaria parasites

Tu Zhijian (Jake) Tu
Professor
jaketu@vt.edu
web site
  • Biochemistry
Yes
  • Computational Biology
  • Genetics and Molecular Biology
  • Genomics
  • Systems Biology
We employ systems biology and bioinformatic approaches to 1) develop a synthetic gene drive in mosquitoes for the control of malaria and dengue, and 2) investigate mosquito sex determination, which may offer novel control strategies based on genetic manipulations of sex ratio and male fertility.

Murali T. M. Murali
Associate Professor
tmurali@vt.edu
web site
  • Computer Science
  • School of Biomedical Sciences and Engineering
  • Computational Tissue Engineering interdisciplinary graduate education program
Yes
  • Biological Data Mining and Statistics
  • Computational Biology
  • Microbiology, including microbe host interactions
  • Systems Biology
Phenomenological and predictive models of molecular interaction networks. Fusing top-down and bottom-up approaches in systems biology. Computational tissue engineering. Host-pathogen molecular interaction networks. Hypergraph representations of molecular interactions.

Eubank Stephen Eubank
Professor
eubank@vt.edu
web site
  • Biocomplexity Institute at Virginia Tech
  • Department of Physics
  • Public Health Program
Yes
  • Computational Biology
  • High Performance Computing
  • Math
  • Modeling and Simulation
  • Systems Biology
Research in simulating large socio-technical systems; computational epidemiology; scaling in complex systems; network structure / graph theory.
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Grene Ruth Grene
Professor
grene@vt.edu
web site
  • Department of Plant Pathology, Physiology, & Weed Science (PPWS)
Yes
  • Biological Data Mining and Statistics
  • Genetics and Molecular Biology
  • Genomics
  • Plant Sciences
  • Systems Biology
Functional genomics: global effects of stress imposition on gene expression and regulatory pathways. Relationships between environmental signaling and stress resistance: mechanisms in plants. Bioinformatics and visualization tools for analysis and depiction
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Veilleux Richard Veilleux
Professor
potato@vt.edu
web site
  • Horticulture
Yes
  • Genetics and Molecular Biology
  • Genomics
  • Plant Sciences
We are working on two major projects, one centered on genes for micronutrient (Fe and Zn) acquisition in potato and the other on sequencing monoploid potato with just a single allele per locus to understand copy number variation and genomic complexities of the heterozygous tetraploid crop.

Helm Richard Helm
Associate Professor
helmrf@vt.edu
web site
  • Department of Biochemistry
Yes
Program Focus: The laboratory works collaboratively with numerous groups on campus using mass spectrometry to help answer biological questions in all kingdoms of life. Key areas of expertise are in the proteomics and metabolomics, or the analysis, identification and quantification of proteins and metabolites. Liquid chromatography-mass spectrometry is the main tool that we use to analyze samples for detecting and measuring levels of proteins and small molecules.
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Ramakrishnan Naren Ramakrishnan
Professor
naren@vt.edu
web site
  • Computer Science
Yes
  • Computational Biology
  • Cyberinfrastructure and Bioinformatics
Mining scientific datasets in domains such as systems biology, neuroscience, sustainability, and intelligence analysis.

Marathe Madhav Marathe
Professor
marathe@vt.edu
web site
  • Director of Network Dynamics and Simulation Science Lab, Biocomplexity Institute
  • Department of Computer Science and Applications
  • Courtesy Appointment in Electrical and Computer Engineering
Yes
  • Biological Data Mining and Statistics
  • Computational Biology
  • Cyberinfrastructure and Bioinformatics
  • Genetics and Molecular Biology
  • Genomics
  • High Performance Computing
  • Math
  • Microbiology, including microbe host interactions
  • Modeling and Simulation
  • Systems Biology
Research in interaction-based modeling and simulation of complex systems; design and analysis of algorithms and computational complexity; wireless and next generation communication networks; HPC and grid computing; computational epidemiology and economics.
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Zhang Liqing Zhang
Associate professor
lqzhang@vt.edu
web site
  • Computer Science
Yes
  • Biological Data Mining and Statistics
  • Computational Biology
  • Cyberinfrastructure and Bioinformatics
  • Genomics
  • High Performance Computing
  • Systems Biology
My research interest includes computational prediction of the effect of genetic variants on human diseases and phenotypes, designing programs for analyzing and mining of large-scale biological data including NGS data, microarray data, proteomics data, and cancer genomics.
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Heath Lenwood Heath
Professor
heath@vt.edu
web site
  • Department of Computer Science
Yes
  • Biological Data Mining and Statistics
  • Computational Biology
  • Cyberinfrastructure and Bioinformatics
  • Genomics
  • Plant Sciences
I work in computational biology and bioinformatics, concentrating on algorithms, databases, and bioinformatics tools. I enjoy sequence analysis from the nucleotide to the genome levels and analyzing and modeling biological data, especially omics data. Looking for students with a CS background.
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Watson Layne Watson
Professor
ltw@vt.edu
web site
  • Computer Science
  • Mathematics
Yes
  • Biological Data Mining and Statistics
  • Computational Biology
  • Cyberinfrastructure and Bioinformatics
  • High Performance Computing
  • Math
  • Modeling and Simulation
  • Systems Biology
Dr. Watson's current research interests include numerical analysis, nonlinear programming, mathematical software, solid mechanics, fluid mechanics, image processing, scientific computation, and bioinformatics. His work is at the interface of mathematics, computer science, and science and engineering disciplines (including biology).

Bassaganya-Riera Josep Bassaganya-Riera
Professor, Director
jbassaga@vt.edu
web site
  • Biocomplexity Institute at Virginia Tech
  • Wake Forest University School of Biomedical Engineering and Sciences
  • Department of Biomedical Sciences and Pathobiology
Yes
  • Biomedicine
  • Cyberinfrastructure and Bioinformatics
  • High Performance Computing
  • Microbiology, including microbe host interactions
  • Modeling and Simulation
  • Systems Biology
Josep Bassaganya-Riera is the Director of the Nutritional Immunology and Molecular Medicine Laboratory (NIMML, www.nimml.org) and a Professor of Immunology at VBI. He leads large-scale research programs on infectious diseases, gastrointestinal health, and obesity-related inflammatory complication
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Tyson John Tyson
University Distinguished Professor
tyson@vt.edu
web site
  • Biological Sciences
  • VBI Faculty Fellow
Yes
  • Computational Biology
  • Modeling and Simulation
  • Systems Biology
Temporal and spatial organization in cellular regulatory systems. Cell cycle, DNA damage and cell signaling. Apoptosis, autophagy and unfolded protein response. T cell differentiation. Circadian rhythms. Nonlinear dynamical systems. Stochastic modeling.

Jelesko John Jelesko
Associate Professor
jelesko@vt.edu
web site
  • Department of Plant Pathology, Physiology, & Weed Science
Yes
  • Biomedicine
  • Computational Biology
  • Cyberinfrastructure and Bioinformatics
  • Genetics and Molecular Biology
  • High Performance Computing
  • Modeling and Simulation
The Jelesko laboratory investigates the molecular evolutionary processes responsible for plant chemical diversity. Our studies range from the deep evolutionary origins of plant specialized metabolism, to the molecular evolutionary patterns responsible for recent enzyme neo-functionalization. Current Projects: “Identification of Poison Ivy Urushiol Biosynthetic Genes Using RNAseq” – this project is funded by the Virginia Bioinformatics Institute & Fralin Life Science Institute Small Grants Program and is aimed at developing informatic resources enabling the identification and cloning of urushiol biosynthetic genes.
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Lazar Iuliana M. Lazar
Associate Professor
malazar@vt.edu
web site
  • Department of Biological Sciences
Yes
  • Systems Biology
Major Fields of Interest: Oncoproteomics, breast cancer cell cycle, signaling, biomarker discovery, development of advanced mass spectrometry and microfluidic technologies for the interrogation of biological systems.
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Hoeschele Ina Hoeschele
Professor
inah@vt.edu
web site
  • Department of Statistics
  • Biocomplexity Institute and Adjunct Professor VT Carilion School of Medicine
  • Member, Comprehensive Cancer Ctr., Wake Forest Univ School of Medicine
Yes
  • Biological Data Mining and Statistics
  • Biomedicine
  • Computational Biology
  • Cyberinfrastructure and Bioinformatics
  • Genetics and Molecular Biology
  • Genomics
  • Modeling and Simulation
  • Systems Biology
Statistical genetics/genomics, applied statistics & statistical bioinformatics; QTL linkage and association mapping in human populations and inbred line crosses; statistical design and analysis of (multi) omics experiments and genetical systems biology studies; large human population studies.
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Sharakhov Igor Sharakhov
Associate Professor
igor@vt.edu
web site
  • Entomology
  • Public Health Program at Virginia Tech
  • Fralin Life Science Institute
Yes
  • Genetics and Molecular Biology
  • Genomics
Dr. Sharakhov seeks to understand how mosquito genomes are organized and evolve as mosquitoes adapt to diverse environments and change their ability to transmit malaria parasites.
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Mortveit Henning Mortveit
Associate Professor
Henning.Mortveit@vt.edu
web site
  • VBI
  • Department of Mathematics
  • NDSSL
Yes
  • High Performance Computing
  • Math
  • Modeling and Simulation
Research in discrete, finite dynamical systems (sequential dynamical systems, generalized cellular automata); graph dynamics and the interplay between graph structure and dynamical properties; mathematical modeling of discrete dynamical systems. See: http://www.math.vt.edu/people/hmortvei/research/
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Schubot Florian Schubot

fschubot@vt.edu
web site
  • Biological Sciences
Yes

Smith Ed Smith
Professor
esmith@vt.edu
web site
  • Animal and Poultry Sciences
Yes
  • Animal Sciences
  • Computational Biology
  • Genetics and Molecular Biology
  • Genomics
Using genomic tools, especially those that can reliably define genome variation, to identify genes that influence traits important to poultry, livestock, and humans.
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Bevan David Bevan
Associate Professor
drbevan@vt.edu
web site
  • Department of Biochemistry
Yes
  • Biomedicine
  • Computational Biology
  • Modeling and Simulation
Research involves the application of computational molecular modeling to the study of protein structure, function, and dynamics. Current projects are related to Alzheimer's disease, diabetes, obesity, and inflammation. In addition, we are designing enzymes with desired substrate specificity.

Shaffer Cliff Shaffer
Professor
shaffer@vt.edu
web site
  • Computer Science
Yes
  • Computational Biology
  • Modeling and Simulation
  • Systems Biology
My focus is on modeling and simulation tools for systems biology. Model representation is the biggest bottleneck for Systems Biology today. Improved tools can support the creative process, enabling development of more complex models that are needed to advance the science.

Lawrence Christopher Lawrence
Associate Professor
cblawren@vt.edu
web site
  • Department of Biological Sciences
Yes
  • Biomedicine
  • Computational Biology
  • Genomics
  • Microbiology, including microbe host interactions
Major Field of Interest: Fungal pathogenesis and human respiratory disease. Current Research: (1) The role of fungi in invasive and chronic respiratory disorders including asthma, allergic rhinitis, and chronic rhinosinusitis (CRS); (2) Molecular immunobiology of allergens and other proinflammatory proteins from fungi; (3) Alternaria genome sequencing, annotation, and development of database platforms; (4) Hormone-protein interactions including human and plant systems with a particular emphasis on NSAID allergy; (5) Fungal Biotechnology.
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Barrett Christopher Barrett
Professor, Director NDSSL and NCR
cbarre04@vt.edu
web site
  • Biocomplexity Institute at Virginia Tech
  • Department of Computer Science
Yes
  • Cyberinfrastructure and Bioinformatics
  • High Performance Computing
  • Math
  • Modeling and Simulation
Research in integrated high-performance simulation and data service architectures; human population dynamics and associated social networks; epidemiology and spread of infectious diseases; computational and behavioral economics and systems biology.
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North Chris North

north@vt.edu
web site
  • Computer Science
Yes

Vinatzer Boris Vinatzer
Associate Professor
vinatzer@vt.edu
web site
  • Plant Pathology,
  • Physiology & Weed Science
Yes
  • Biological Data Mining and Statistics
  • Genetics and Molecular Biology
  • Genomics
  • Microbiology, including microbe host interactions
  • Plant Sciences
Dr. Vinatzer uses the latest technological advances in genomics in combination with population genetics and microbial genetics to better understand the emergence, spread, and virulence mechanisms of bacterial crop pathogens in order to develop new avenues to control crop diseases.
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Mukhopadhyay Biswarup Mukhopadhyay
Associate Professor
bmukhopa@vt.edu
web site
  • Department of Biochemistry
  • Adjunct Associate Professor Biological Sciences
  • Adjunct Associate Professor, Dept. of Internal Medicine, VT Carilion School of Medicine
Yes
  • Biological Data Mining and Statistics
  • Biomedicine
  • Computational Biology
  • Genetics and Molecular Biology
  • Genomics
  • Microbiology, including microbe host interactions
  • Systems Biology
Research in methanogenic archaea; remnants or precursors of sulfate reduction pathway genes; redox regulation of energy metabolism; structure-function relationships in archaeal-type PEPC; coal bed microbiology; role of coenzyme F420 in cell material biosynthesis and biodegradation.
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Onufriev Alexey Onufriev
Associate professor
alexey@vt.edu
web site
  • Computer Science and Physics
Yes
  • High Performance Computing
  • Modeling and Simulation
We use theoretical and computational methods to understand dynamics and function of biomolecular systems such as proteins, DNA, and their complexes. In particular, we seek to uncover major principles that govern DNA compaction in living cells at several scales, from nucleosome to chromosomes.

Cao Yang Cao
Associate Professor
ycao@vt.edu
web site
  • Department of Computer Science
Yes
  • Computational Biology
  • High Performance Computing
  • Math
  • Modeling and Simulation
  • Systems Biology
Our group focuses on the development of multiscale, multiphysics modeling and simulation methods and tools that help biologists build, simulate and analyze complex biological systems, simulate their dynamics and analyze their functions.
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Yes - I am presently accepting student applications
No - I am not presently accepting student applications
Maybe - I would consider accepting an application from the right student