featured publications

COMBINATORIAL AND ALGEBRAIC ENUMERATION: A SURVEY OF THE WORK OF IAN P. GOULDEN AND DAVID M. JACKSON

Foley, Angèle M.a; Morales, Alejandro H.bRattan, Amarpreetc; Yeats, Karend

a Department of Physics and Computer Science, Wilfrid Laurier University, 75 University Avenue West, Waterloo, N2L 3C5, ON, Canada
b Department of Mathematics and Statistics, University of Massachusetts Amherst, 710 N. Pleasant Street, Amherst, 01003, MA, United States
c Department of Mathematics, Simon Fraser University, 8888 University Dr, Burnaby, V5A 1S6, BC, Canada
d Department of Combinatorics and Optimization, University of Waterloo, 200 University Ave W, Waterloo, N2L 3G1, ON, Canada

Algebraic Combinatorics, Volume 5, Issue 6, Pages 1205-1226 2022, DOI: 10.5802/alco.269

TROPICAL TANGENTS FOR COMPLETE INTERSECTION CURVES

Ilten, Nathan1, Len, Yoav2

Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, V5A1S6, BC, Canada
2 Mathematical Institute, University of St Andrews, St Andrews, KY16 9SS, United Kingdom

Mathematics of Computation, Volume 92, Issue 340, Pages 931-979 March 2023, DOI: 10.1090/mcom/3782

CLIC-01: MANUFACTURE AND DISTRIBUTION OF NON-CRYOPRESERVED CAR-T CELLS FOR PATIENTS WITH CD19 POSITIVE HEMATOLOGIC MALIGNANCIES

Kekere, Natasha1,2 ... Holt, Robert A.3,4,5

1 Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
2 Division of Hematology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
3 Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
4 Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
5 Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada

Frontiers in Immunology, Volume 13, 19 December 2022, DOI: 10.3389/fimmu.2022.1074740

ANCESTRAL RECONSTRUCTION REVEALS CATALYTIC INACTIVATION OF ACTIVATION-INDUCED CYTIDINE DEAMINASE CONCOMITANT WITH COLD WATER ADAPTATION IN THE GADIFORMES BONY FISH

Atefeh Ghorbani1,2, S. Javad Khataeipour3, Monica H. Solbakken4, David N. G. Huebert1,2, Minasadat Khoddami1, Khalil Eslamloo5, Cassandra Collins1, Tiago Hori5, Sissel Jentoft4, Matthew L. Rise5 and Mani Larijani1,2

1 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada, 2 Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada, 3 Department of Computer Science, Faculty of Science, Memorial University of Newfoundland, St. John’s, Canada, 4 Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway, 5 Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada

BMC Biology, Volume 20, Issue 1, December 2022, DOI: 10.1186/s12915-022-01489-8

Potent De Novo Macrocyclic Peptides That Inhibit O-GlcNAc Transferase through an Allosteric Mechanism

Alteen, Matthew G.a; Peacock, Haydenb; Meek, Richard W.c; Busmann, Jil A.d; Zhu, Shaa; Davies, Gideon J.c; Suga, Hiroakib; Vocadlo, David J.a, d

a Department of Chemistry, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada; b Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo, 113-0033, Japan; c York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom; d Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada

Angewandte Chemie - International Edition, Volume 135, Issue 3, 16 January 2023, https://doi.org/10.1002/anie.202215671

GLYCOSIDE HYDROLASE CATALYSIS: DO SUBSTRATES AND MECHANISM-BASED COVALENT INHIBITORS REACT VIA MATCHING TRANSITION STATES?

Akintola, Oa, Farren-Dai, M.a, Ren, W.a, Bhosale, S.a, Britton, R.a, Świderek, K.b, Moliner, V.b, Bennet, Andrew J.a

aDepartment of Chemistry, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada; bBioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, 12071, Spain

ACS Catalysis, Volume 12, Issue 23, Pages 14667 - 14678, 2 December 2022, DOI: https://doi.org/10.1021/acscatal.2c04027

PROBING THE EFFECT OF IONOMER SWELLING ON THE STABILITY OF ANION EXCHANGE MEMBRANE WATER ELECTROLYZERS

Chen, B.a, Mardle, P.a, Holdcroft, S.a

aDepartment of Chemistry, Simon Fraser University

Journal of Power Sources, Volume 550, 1 December 2022, Article number: 232134, https://doi.org/10.1016/j.jpowsour.2022.232134

BAYESIAN INFORMATION ENGINE THAT OPTIMALLY EXPLOITS NOISY MEASUREMENTS

Saha, T. K.a, Lucero, J. N. E.a, Ehrich, J.a, Sivak, D. A.a, Bechhoefer, J.a

aDepartment of Physics, Simon Fraser University

Physical Review Letters, Open Access, Volume 129, Issue 33, 23 September 2022, Article number: 130601, DOI: https://doi.org/10.1103/PhysRevLett.129.130601

 

THE CALCULATION OF PLAYER SPEED FROM TRACKING DATA

Wu, L. Y.a, Swartz, T. B.a

aDepartment of Statistics and Actuarial Science, Simon Fraser University

International Journal of Sports Science and Coaching, Open Access, 2022, DOI: https://doi.org/10.1177/1747954122112

X-RAY CRYSTALLOGRAPHIC CHARACTERIZATION OF THE SARS-COV-2 MAIN PROTEASE POLYPROTEIN CLEAVAGE SITES ESSENTIAL FOR VIRAL PROCESSING AND MATURATION

Lee, J.a,b, Kenward, C.a, Worrall, L.J.a, Vuckovic, M.a, Gentile, F.c, Ton, A.T.c, Ng, M.a, Cherkasov, A.c, Strynadka, N.C.J.a, Paetzel, Mb

aDepartment of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, BC; bDepartment of Molecular Biology and Biochemistry, Simon Fraser University; cVancouver Prostate Centre, The University of British Columbia, Vancouver, BC

Nature Communications 13, Article number: 5196, September 2022, DOI: https://doi.org/10.1038/s41467-022-32854-4

General Variability Leads to Specific Adaptation Toward Optimal Movement Policies

Abram, S.J.a, Poggensee, K.L.b, Sánchez, N.c, ..., Donelan, J.M.d

aSchool of Engineering Science, Simon Fraser University; bDepartment of Mechanical Engineering, Stanford University, Stanford, CA, USA; cDivision of Biokinesiology and Physical Therapy, University of Southern California, Los Angeles, CA, USA; dDepartment of Biomedical Physiology and Kinesiology, Simon Fraser University

Current Biology, Volume 32, Issue 10, 23 May 2022, pages 2222-2232.e5, https://doi.org/10.1016/j.cub.2022.04.015

Self-Assembly of PBTTT-C14 Thin Films in Supercritical Fluids

Yousefi, N.a, Pettipas, R.D.b, Kelly, T.L.b, Kaake, L.G.a

aDepartment of Chemistry, Simon Fraser University; bDepartment of Chemistry, University of Saskatchewan, Saskatoon, SK

Materials Advances, Volume 3, Issue 5, 4 February 2022, pages 2515-2523, DOI:10.1039/d1ma00847a

Sparse Functional Partial Least Squares Regression with a Locally Sparse Slope Function

Guan, T.a, Lin, Z.b, Groves, K.c, Cao, J.d

aDepartment of Mathematics and Statistics, Brock University, St. Catherines, Ontario; bDepartment of Statistics and Data Science, National University of Singapore, Singapore; cEngineered Wood Products Manufacturing, FPInnovations, Vancouver, BC; dDepartment of Statistics and Actuarial Science, Simon Fraser University

Statistics and Computing, Volume 32, Issue 2, 9 March 2022, DOI:10.1007/s11222-021-10066-y

Thermal Proteome Profiling Reveals the O-GlcNAc-Dependent Meltome

King, D.T.a,b, Serrano-Negrón, J.E.a, Zhu, Y.a,b, Moore, C.L.c, Shoulders, M.D.c, Foster, L.J.d,e, Vocadlo, D.J.a,b

aDepartment of Molecular Biology and Biochemistry, Simon Fraser University; bDepartment of Chemistry, Simon Fraser University; cDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; dMichael Smith Laboratories, University of British Columbia, Vancouver, BC; eDepartment of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC

Journal of the American Chemical Society, Volume 144, Issue 9, 1 March 2022, Pages 3833-3842. DOI:10.1021/jacs.1c10621

Chloroquine Treatment Induces Secretion of Autophagy-Related Proteins and Inclusion of Atg8-Family Proteins in Distinct Extracellular Vesicle Populations

Xu, J.a,b, Yang, K.C.a,b, Go, N.E.a,b, Colborne, S.a, Ho, C.J.a,b, ..., Morin, G.B.,a,c, Gorski, S.M.a,b,c,d

aCanada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC; bDepartment of Molecular Biology and Biochemistry, Simon Fraser University; cDepartment of Medical Genetics, University of British Columbia, Vancouver, BC; dCentre for Cell Biology, Development and Disease, Simon Fraser University

Autophagy, 28 Feb 2022, DOI:10.1080/15548627.2022.2039535

Phylogeography and Transmission of M. tuberculosis in Moldova: A Perspective Genomic Analysis

Yang, C.a,b, Sobkowiak, B.c, Naidu, V.c, ..., Colijn, C.c, Cohen, T.b

aSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China; bDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; cDepartment of Mathematics, Simon Fraser University

PLOS Medicine, Volume 19, Issue 2, 22 Feb 2022, Article number e1003933, DOI:10.1371/journal.pmed.1003933

Anomalous Heating in a Colloidal System

Kumar, A.a , Chétrite, R.b, Bechhoefer, J.a

aDepartment of Physics, Simon Fraser University; bLaboratoire J. A. Dieudonné, Université de Nice Sophia Antipolis, Nice, France

Proceedings of the National Academy of Sciences of the United States of America, Volume 119, Issue 5, 1 Feb 2022, e2118484119, doi: 10.1073/pnas.2118484119

 

The Natural Products Atlas 2.0: A Database of Microbially-Derived Natural Products

van Santen, J.A.a, Poynton, E.F.a, Iskakova, D.a, McMann, E.a, Alsup, T.A.b, Clark, T.N.a, Fergusson, C.H.a, Fewer, D.P.c, Hughes, A.H.d, McCadden, C.A.b, Parra, J.d, Soldatou, S.e, Rudolf, J.D.b, Janssen, E.M.-L.f, Duncan, K.R.d, Linington, R.G.a

aDepartment of Chemistry, Simon Fraser University; bDepartment of Chemistry, University of Florida, Gainesville, USA; cDepartment of Microbiology, University of Helsinki, Helsinki, Finland; dStrathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow, UK; eMarine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen, UK; fDepartment of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Duebendorf, Switzerland

Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D1317–D1323, doi: 10.1093/nar/gkab941  

Seismic Reflections from a Lithospheric Suture Zone below the Archaean Yilgarn Craton

Calvert, A.J.a , Doublier, M.P.b,c, Sellars, S.E.a

aDepartment of Earth Sciences, Simon Fraser University; bMineral Systems Branch, Geoscience Australia; cCentre for Exploration Targeting, School of Earth and Environment, The University of Western Australia

Nature Communications, Volume 12, 13 December 2021, https://doi.org/10.1038/s41467-021-27516-w

Mouse Organ-Specific Proteins and Functions

Sun, B.a,b, Lorang, C.c, Qin, S.c, Zhang, Y.a, Liu, K.a, Li, G.c, Sun, Z.c, Francke, A.d, Utleg, A.G.c, Hu, Z.c, Wang, K.c, Moritz, R.L.c, Hood, L.c

aDepartment of Chemistry, Simon Fraser University; bDepartment of Molecular Biology and Biochemistry, Simon Fraser University; cInstitute for Systems Biology, Seattle, USA; dDepartment of Computing Science, Simon Fraser University

Cells, Volume 10, 8 December 2021, https://doi.org/10.3390/cells10123449

A Functional Proportional Hazard Cure Rate Model for Interval-Censored Data

Shi, H.a, Ma, D.b, Beg, M.F.b, Cao, J.a

aDepartment of Statistics and Acturial Science, Simon Fraser University; bSchool of Engineering, Simon Fraser University

Statistical Methods in Medical Research, Volume 31, 22 November 2021, Pages 154-168, DOI: 10.1177/09622802211052972

Processive RNA polymerization and promoter recognition in an RNA World

Cojocaru, R.a, Unrau, P.J.a

aDepartment of Molecular Biology and Biochemistry, Simon Fraser University

Science, Volume 371, 19 March 2021, Pages 1225-1232, DOI: 10.1126/science.abd9191

Half a century of global decline in oceanic sharks and rays

Pacoureau, N.a, Rigby, C.L., Kyne, P.M., Sherley, R.B., Winker, H., Carlson, J.K., Fordham, S.V., Barreto, R., Fernando, D., Francis, M.P., Jabado, R.W., Herman, K.B., Liu, K.-M., Marshall, A.D., Pollom, R.A.a, Romanov, E.V., Simpfendorfe, C.A., Yin, J.S.a, Kindsvater, H.K., Dulvy, N.K.a

aDepartment of Biological Sciences, Simon Fraser University

Nature, Volume 589, 27 January 2021, Pages 567-571, https://doi.org/10.1038/s41586-020-03173-9

PSORTdb 4.0: expanded and redesigned bacterial and archaeal protein subcellular localization database incorporating new secondary localizations

Lau, W.Y.V., Hoad, G.R., Jin, V., Winsor, G.L., Madyan, A., Gray, K.L., Laird, M.R., Lo, R., Brinkman, F.S.L.

Department of Moleculary Biology and Biochemistry, Simon Fraser University

Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D803–D808, https://doi.org/10.1093/nar/gkaa1095