The People – Genotypes to Phenotypes

Our interdisciplinary team stretches across the entire United States, spanning three jurisdictions – Idaho, Rhode Island, and Vermont. The researchers are equipped with expertise in computational protein modeling, diverse biological systems, measurement of protein biophysical properties, and mathematical modeling. The group is comprised of talented faculty, postdoctoral fellows, graduate students, undergraduate students and staff.

Meet the team

The RII Track-2 FEC research team consists of researchers and scientists from across the country.

Nearly 35 researchers and scientists gathered for the first time in May of 2018.

Brian Cleveley

University of Idaho
Senior Instructor
Virtual Technology & Design

Protein

Model Systems

Employing Augmented Reality to explore proteins through the interplay of interactive 3D virtual and physical models.

Techniques

Jean-Marc Gauthier

University of Idaho
Associate Professor
Virtual Technology & Design

Dynamic virtual protein: visualization, interaction patterns, collaboration with virtual agents, evaluation of user experience.

Model Systems

Mixed reality, virtual reality, augmented reality, visualization, interaction design, user interaction, user experience, usability, evaluation, vrtual protein structures, amino-acid.

Techniques

Brent Lockwood

Co-PI

University of Vermont
Assistant Professor
Department of Biology

Adaptation to temperature in the eurkaryotic origin recognition complexprotein and alcohol dehydrogenase of the fruit fly Drosophila melanogaster.

Model Systems

Enzyme assays, fluorescence anisotropy, confocal fluorescence microscopy, reverse genetics.

Techniques

Chris Marx

University of Idaho
Professor
Department of Biological Sciences

Craig Miller

Co-PI

University of Idaho
Assistant Professor
Department of Biological Sciences

phiX174 and related bacteriophage, their capsid proteins, and their interactions with host bacteria.

Model Systems

Deep mutational scanning, one-pot mutagenesis, golden gate genome assembly, epistasis, statistical modeling.

Techniques

Tanya Miura

University of Idaho
Associate Professor
Department of Biological Sciences

Respiratory Syncytial Virus (RSV) Fusion (F) glycoprotein.

Model Systems

Reverse genetics/recombinant virus production, virus inhibition assays, virus evolution experiments, flow cytometry, antibody production and purification, mammalian cell culture and transfection, microscopy, cell fusion assays, mutant library design and expression cloning.

Techniques

Mandar T Naik

Brown University
Assistant Professor
Molecular Pharmacology, Physiology and Biotechnology

TEM-1 ß-lactamase, Sea Urchin carbonic anhydrase.

Model Systems

Structure-function relationship, Structural biology and biophysics.

Techniques

Brandon Ogbunu

Co-PI

Brown University
Assistant Professor
Department of Ecology and Evolutionary Biology

Dihydrofolate reductase (DHFR), lytic phage, E.coli, in silico fitness landscapes, in silico networks.

Model Systems

Reverse genetics, experimental evolution, chimeric protein engineering, individual-based computer simulations, genetic algorithms, network modeling, analytic modeling

Techniques

Jagdish Patel

University of Idaho
Research Assistant Professor
Molecular Modeling

Protein, protein-protein, protein-ligand, antibody-antigen, membrane protein, virus.

Model Systems

Molecular modeling, molecular dynamics, enhanced sampling techniques, folding stability calculation, binding affinity calculation, homology modeling, structure-based drug design.

Techniques

Melissa Pespeni

University of Vermont
Assistant Professor
Department of Biology

Alpha carbonic anhydrase, the purple sea urchin Strongylocentrotus purpuratus.

Model Systems

Select and sequence, experimental evolution, next-generation sequencing, bioinformatics and data visualization.

Techniques

Paul Rowley

University of Idaho
Assistant Professor
Department of Biological Sciences

Virus-host interactions using HIV and viruses of Brewer’s yeast. Killer toxins produced by fungi.

Model Systems

Molecular biology, biochemistry, microbiology, and virology.

Techniques

Brenda Rubenstein

Brown University
Assistant Professor
Department of Chemistry

Beta-lactamase, PhiX, a range of metalloenzymes

Model Systems

Molecular Dynamics, Monte Carlo, empirical potentials for determining folding free energies such as FoldX and Pyrosetta, docking software such as GLIDE and Autodock Vina.

Techniques

Andreas Vasdekis

University of Idaho
Assistant Professor
Department of Physics

TEM-1 β-lactamase, population heterogeneity response to point mutations, antibiotics, and temperature.

Model Systems

Bioimaging, microfluidics, stochastic models.

Techniques

Daniel Weinreich

Co-PI

Brown University
Associate Professor
Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology

The bacterial drug-resistance enzyme TEM-1 ß-lactamase, lytic phage, the brewer’s yeast Saccharomyces cerevisiae.

Model Systems

Reverse genetics, deep mutational scanning, long-term microbial experimental evolution, individual-based computer simulations, analytic modeling.

Techniques

Holly Wichman

University of Idaho
Professor
Department of Biological Sciences

Marty Ytreberg

University of Idaho
Professor
Department of Physics

Protein, protein-protein, protein-substrate, antibody-antigen, virus.

Model Systems

Molecular modeling, molecular dynamics, folding stability calculation, binding affinity calculation, homology modeling.

Techniques