 Steven Samuel Plotkin, Associate Professor at UBC |
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Plotkin Research Group |
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Principal Researcher |
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Steve Plotkin | Protein misfolding and neurodegenerative disease; Molecular-genetic basis of multicellularity |
Graduate Researchers |
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Aina Adekunle | PhD student, Computational protein misfolding |
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Charlotte Barclay | MSc student, Models of cell differentiation and development in ctenophores |
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Gabriel Dall'Alba | MSc student, Models of cell differentiation and development in ctenophores |
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Pranav Garg | PhD student, Models of cell differentiation and development in ctenophores |
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Shawn Hsueh | PhD student, Computational protein misfolding |
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Jason Nguyen | PhD student, Evolution of Multicellularity |
Neil Cashman |
Protein misfolding and propagation in neurodegenerative disease |
Eric Jan |
Viral evolution of SARS-CoV-2 |
| Nobu Tokuriki Department of Biochemistry and Molecular Biology, UBC |
Viral evolution of SARS-CoV-2 1 Shared PDF |
| Joerg Rottler Soft Condensed Matter and Computational Material Physics, UBC |
Computational force spectroscopy |
| Andriy Kovalenko Department of Mechanical Engineering, University of Alberta |
Protein misfolding in Amyotropic lateral sclerosis (ALS) |
| Cecilia Clementi Computational Biophysics, Free University of Berlin |
Protein folding mechanism |
Alumni of The Plotkin Research Group |
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Post-Doctoral Researchers |
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| Luke McAlary | Molecular interplay of liquid-liquid phase separation and pathogenic aggregation of TDP43 in ALS. Dr. McAlary is currently the Bill Gole MND Australia Post Doctoral Research Fellow at the University of Wollongong. |
| Xubiao Peng | Energy landscape theory for protein misfolding: applications to ALS and cancer. Dr Peng is currently an Associate Professor at the Beijing Institute of Technology. |
| Erik Abrahamsson | Dr. Abrahamsson received his Ph.D. in Chemistry from Göteborg University in Sweden. He is a co-author of our BioVEC molecular visualization software. |
| Atanu Das | Dr. Das is interested in Protein folding, misfolding and aggregation, as well as DNA modification and repair. Dr. Das completed a postdoctoral fellowship in the group of Dmitrii E. Makarov at UT Austin, Department of Chemistry and is currently at the CSIR-National Chemical Laboratory. |
| Reza Ejtehadi | Dr. Ejtehadi is interested in soft condensed matter physics, biological macromolecules, complex systems, and simulations and computational physics. He is currently a Professor at Sharif University. |
| Mahdi Ghelichi | Protein misfolding and dysregulation in cancer. Dr. Ghelichi is currently a Data Scientist at Globalive Technology. |
| Yuri Gusev | Dr. Gusev received his Ph.D. in Mathematical Physics from the University of Manitoba; his current research at Perimeter Institute involves quantum gravity. |
| Mona Habibi | Simulation of mechanically-induced protein unfolding and monomerization for misfolding-prone proteins,
mhabibi(at)phas.ubc.ca Dr. Habibi is currently a Data Scientist at Data Scientist, Finning International. |
| Daniel Luesebrink | Dimer binding affinity calculations for SOD1; approach to equilibrium |
| Eric Mills | Density functional theory of solvation; protein unfolding thermodynamics. Dr. Mills is currently the Managing Editor, Journal of the American Chem. Society, Chem. Reviews, and Accounts of Chem. Reviews millsea(at)phas.ubc.ca |
| Corina Stewart | SARS-Cov-2 Evolution |
Sabbatical Visitors |
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Peter Lenz |
Protein science; Molecular mechanisms in cancer (February - August 2017) |
Prof. Hector Dominguez |
Metal-protein interactions (August 2015 - July 2016) |
Apichart Linhananta |
Osmolyte-Induced Protein Stability (January - July 2009) |
Visiting Researchers |
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| Kyra Boulding | Quest University exchange student, Ctenophore transgenic system (October - November 2018) |
| Benjamin Hilton | Imperial College London, Protein-protein interactions (July - August 2018) |
| Matthias Huber |
Mechanisms of protein folding (June 2004 - April 2005) |
| Mark Nijland | Wageningen University Netherlands, First-principles dimer binding calculations for SOD1 and other proteins (June - December 2019) |
Graduate Researchers |
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| Vibudh Agrawal | Algorithmic discovery of genetic regulatory elements |
| Si Chen | Statistical mechanics of graphs and emergent manifolds, quantum gravity. sichen(at)phas.ubc.ca |
| John Dupuis | Saponsin-like protein-membrane interactions |
| Miguel Garcia | Magnetic sensing proteins. miguel(at)phas.ubc.ca |
| William Guest |
Misfolding and aggregation in prion protein and SOD1 (M.D./Ph.D. Program) |
| Shirin Hadizadeh | Osmolyte effects on protein stability shirin(at)physics.ubc.ca |
| Tiam Heydari | Theory of liquid-liquid phase separation, Mechanisms of germ cell specification in early metazoans |
| Rawnak Hoque | Bioinformatics of cancer expression data |
| Todd Kilstrom | Computational Protein misfolding; Protein stability and instability |
| Ali Mohazab |
High-dimensional distance metrics, applications to protein folding (Ph.D. Program) alirm(at)phas.ubc.ca |
| Alex Morriss-Andrews |
Rigid body simulations of coarse-grained DNA |
| Baris Oztop | Protein folding rates and mechanisms boztop(at)fen.bilkent.edu.tr |
| Alena Shmygelska | Energy parameters and search algorithms for protein structure prediction (Co-supervised, with Holger Hoos, Comp. Sci.) |
Graduate Rotation Students - GSAT Program |
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| Matthew Bundala | Molecular dynamics techniques |
| Hannah-Ruth Engelbrecht | Maintenance and Aquaculture of Ctenophore lab system; Ctenophore genome sequencing |
| Min Feng | Molecular dynamics simulation and visualization |
| Kathryn Lande | Ctenophore transgenic system |
| Megan Wolf | Maintenance and Aquaculture of Ctenophore lab system; Ctenophore genome sequencing |
Undergraduate Researchers |
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| Stefan Avall | Large- scale simulations of protein folding with implicit many-body Hamiltonians |
| Gurbir Bhangu | Genetics of differentiation in ctenophores |
| Kyle Bower | Steiner minimal networks in high-dimension |
| Christopher Chang | Genetics of stem cell niches in C-elegans |
| Alvin Cheung |
Osmolytes and protein stability |
| Sebastian Cogswell | Many-variable analysis of determinants of protein folding rates |
| Philip Edgcumbe | Structure and Chirality in computational models of DNA |
| John Flores | Dimer stability of superoxide dismutase and ALS |
| Zach Hamilton | Disordered protein ensembles; membrane bound proteins |
| Johanna Hansen | Single molecule gene sequencing by nano-pore translocation |
| Johnathan Hoggarth | TDP-43 liquid-liquid phase separation and stress granule formation in ALS |
| Justin Hsu | Simulation tests of protein folding mechanisms |
| Derek Inman | Molecular dynamics simulations of superoxide dismutase misfolding |
| Lana Kashino | Ctenophore transgenic system, transcription factor binding |
| Benjamin Lindner | Interaction potentials for protein structure prediction |
| Sebastian Ohse | Effects of confinement and osmolyte concentration on protein stability |
| Gene Polovy | Energetic analysis of alpha-spectrin repeat proteins |
| David Rudko | Protein-DNA binding; Gene finding |
| Mine Sher | Experimental protein misfolding, Ctenophore transgenic system (UBC Co-op student) |
| Brian Sin | Unfolded protein ensembles; protein folding kinetics |
| Kwinten Van Gassen | Protein energetics and loop entropy |
| Brittany Welsh | Molecular genetics; evolution |
Jim Xu |
Protein Dimer Binding Free Energy Calculations |
| Christopher Yearwood | Simulations of coarse-grained DNA with rigid-body molecular dynamics |
| Rachel Zhao | Novel therapeutic targets for intrinsically-disordered, prion-like proteins involved in Alzheimer’s and ALS |
| Jacqueline Zheng-Lin | Animal husbandry of ctenophores, rotifers, and copepods (UBC Co-op student) |
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