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) |
| 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)
| Vibudh Agrawal | Algorithmic discovery of genetic regulatory elements |
| Si Chen | Statistical mechanics of graphs and emergent manifolds, quantum gravity |
| John Dupuis | Saponsin-like protein-membrane interactions (Supervised jointly with Rickey Yada) |
| Miguel Garcia | Magnetic sensing proteins |
| William Guest | Misfolding and aggregation in prion protein and SOD1 (M.D./Ph.D. Program) (Supervised jointly 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) |
| 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.) |
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 |
| 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 |