UBC Logo Steven Samuel Plotkin, Associate Professor at UBC
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Plotkin Research Group

Principal Researcher

Steve Plotkin Protein misfolding and neurodegenerative disease; Molecular-genetic basis of multicellularity

Graduate Researchers

Aina Adekunle PhD student, Computational protein misfolding
Charlotte Barclay MSc student, Models of cell differentiation and development in ctenophores
Gabriel Dall'Alba MSc student, Models of cell differentiation and development in ctenophores
Pranav Garg PhD student, Models of cell differentiation and development in ctenophores
Shawn Hsueh PhD student, Computational protein misfolding
Jason Nguyen PhD student, Evolution of Multicellularity 

Neil Cashman
Department of Medicine, Division of Neurology, UBC

Protein misfolding and propagation in neurodegenerative disease
18 Publications and 14 Patents: full list of publications here
PI on 2 joint project grants
1 shared PDF, 1 shared MD/PhD student

Eric Jan
Department of Biochemistry and Molecular Biology, UBC

Viral evolution of SARS-CoV-2
1 Shared PDF

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
4 Publications: full list of publications here
1 shared PDF, 1 shared MSc student

Andriy Kovalenko
Department of Mechanical Engineering, University of Alberta

Protein misfolding in Amyotropic lateral sclerosis (ALS)
PI on 2 joint project grants

Cecilia Clementi
Computational Biophysics, Free University of Berlin

Protein folding mechanism
1 Publication: full list of publications here

Alumni of The Plotkin Research Group

Post-Doctoral Researchers

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
(Supervised jointly with Prof. Joerg Rottler)

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
Corina Stewart SARS-Cov-2 Evolution

Sabbatical Visitors

Peter Lenz
Center for Synthetic Microbiology,
University of Marburg, Germany

Protein science; Molecular mechanisms in cancer (February - August 2017)

Prof. Hector Dominguez
Materials Science Institute,
Universidad Nacional Autónoma de México

Metal-protein interactions (August 2015 - July 2016)

Apichart Linhananta
Lakehead University, Canada

Osmolyte-Induced Protein Stability (January - July 2009)

Visiting Researchers

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

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
johndupuis1 (at) hotmail (dot) com
(Supervised jointly with Rickey Yada)

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)
(Shared with Faculty of Medicine, Neil Cashman

Shirin Hadizadeh Osmolyte effects on protein stability
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
(Supervised jointly with Neil Cashman)

Ali Mohazab
High-dimensional distance metrics, applications to protein folding (Ph.D. Program)
Alex Morriss-Andrews

Rigid body simulations of coarse-grained DNA
(Co-supervised, with Joerg Rottler, Physics)

Baris Oztop Protein folding rates and mechanisms
Alena Shmygelska Energy parameters and search algorithms for protein structure prediction
(Co-supervised, with Holger Hoos, Comp. Sci.)

Graduate Rotation Students - GSAT Program

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

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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