Current Group Members

Collaborators (Past and Present)
Neil Cashman Department of Medicine, Division of Neurology, UBC | Protein misfolding and propagation in neurodegenerative disease, |
Cecilia Clementi Computational Biophysics, Free University of Berlin | Protein folding mechanism |
Eric Jan Department of Biochemistry and Molecular Biology, UBC | Viral evolution of SARS-CoV-2 |
Andriy Kovalenko Department of Mechanical Engineering, University of Alberta | Protein misfolding in Amyotropic lateral sclerosis (ALS) |
Honglin Luo Department of Pathology and Laboratory Medicine, UBC | Pandemic preparedness using mutation resistant vaccines and antibodies |
Joerg Rottler Soft Condensed Matter and Computational Material Physics, UBC | Computational force spectroscopy |
Nobu Tokuriki Department of Biochemistry and Molecular Biology, UBC | Viral evolution of SARS-CoV-2 |
Group Alumni
Post-Doctoral Researchers
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 |
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.Protein science; Molecular mechanisms in cancer (February – August 2017) |
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 |
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. |
Corina Stewart | SARS-Cov-2 Evolution (Supervised jointly with Eric Jan) |
Sabbatical Visitors
Prof. Hector Dominguez Materials Science Institute, Universidad Nacional Autónoma de México | Metal-protein interactions (August 2015 – July 2016) |
Peter Lenz Center for Synthetic Microbiology, University of Marburg, Germany | Protein science; Molecular mechanisms in cancer (February – August 2017) |
Apichart Linhananta Lakehead University, Canada | Osmolyte-Induced Protein Stability (January – July 2009) |
Visiting Research Students
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 | Eidgenössische Technische Hochschule Zürich, 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 Students (PhD and MSc)
Aina Adekunle | Computational protein misfolding |
Vibudh Agrawal | Algorithmic discovery of genetic regulatory elements |
Charlotte Barclay | Cell differentiation and development in ctenophores |
Si Chen | Statistical mechanics of graphs and emergent manifolds, quantum gravity |
Gabriel Dall’Alba | Cell differentiation and development in ctenophores |
John Dupuis | Saponsin-like protein-membrane interactions (Co-supervised with Rickey Yada) |
Miguel Garcia | Magnetic sensing proteins |
Pranav Garg | Cell differentiation and development in ctenophores |
William Guest | Misfolding and aggregation in prion protein and SOD1 (M.D./Ph.D. Program) (Co-supervised with 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 |
Shawn Hsueh | Computational protein misfolding |
Todd Kilstrom | Computational Protein misfolding; Protein stability and instability (Co-supervised with Neil Cashman) |
Eric Mills | Density functional theory of solvation; protein unfolding thermodynamics. |
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.) |
Kai Xiao | Viral evolution of SARS-CoV-2 (Co-supervised with Nobu Tokuriki) |
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 |
Mariah Lumpa | Annotated Jupyter notebook of genome assembly algorithm |
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 |
Matthew Cooke | SOD1 thermomechanical stability |
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 |
JinYuan Liu | Computational genome annotation |
Connor Meehan | Statistical mechanics of Steiner networks |
Brian Ng | Gene search problems in transciption |
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, Jointly supervised with Neil Cashman) |
Brian Sin | Unfolded protein ensembles; protein folding kinetics |
Kaye Soriano | Co-Op Student- Viral evolution of SARS-CoV-2 |
Kwinten Van Gassen | Protein energetics and loop entropy |
Brent Wathen | Protein structure prediciton |
Brittany Welsh | Molecular genetics; evolution |
Oscan Xia | Computational protein misfolding and aggregation |
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) |
Anna Zhinitsky | Developmental genetic networks in ctenophores |