McGill.CA / Integrated Quantitative Biology Initiative / Research Output

Publications

These findings are published either by members of the IQBI or using equipment that is affiliated with the initiative. Publications are sorted by year.
 

2021

  1. Abhi Ghosh, Snchari Biswas, Tiffany Turner, Anne-Marie Kietzig, Mathieu Brochu. Surface, microstructure, and tensile deformation characterization of LPBF SS316L microstruts micro-machined with femtosecond laser. Materials & Design, https://doi.org/10.1016/j.matdes.2021.110045
  2. Sara Matthews, Elvis Genbo Xu, Eva Roubeau Dumont, Victoria Meola, Oluwadamilola Pikuda, Rachel S. Cheong, Mingrui Guo, Rui Tahara, Hans C. E. Larsson and Nathalie Tufenkji. Polystyrene micro- and nanoplastics affect locomotion and daily activity of Drosophila melanogaster. Journal of Environmental Science, Nano. https://doi.org/10.1039/D0EN00942C
  3. Demers-Potvin, A., H. C. E. Larsson, M. Cournoyer, and O. Béthoux. Wing morphology of a new Cretaceous praying mantis solves the phylogenetic jigsaw of early‐diverging extant lineages. Systematic Entomology, DOI: 10.1111/syen.12457
  4. Khan N, Pelletier D, McAlear TS, Croteau N, Veyron S, Bayne AN, Black C, Ichikawa M, Khalifa AAZ, Chaaban S, Kurinov I, Brouhard G, Bechstedt S, Bui KH, Trempe JF. Crystal structure of human PACRG in complex with MEIG1 reveals roles in axoneme formation and tubulin binding. Structure, doi: 10.1016/j.str.2021.01.001
  5. Alekseev, V. I., J. Mitchell, R. C. McKellar, M. Barbi, H. C. E. Larsson, and A. Bukejs. The first described turtle beetles from Eocene Baltic amber, with notes on fossil Chelonariidae. Foss.Rec, https://doi.org/10.5194/fr-24-19-2021
  6. Meziane, M. R. Genthial and J. Vogel. Kar9 symmetry breaking alone is insufficient to ensure spindle alignment. Sci. Reports 11, DOI: 10.1038/s41598-021-83136-w
  7. Knüppel R, Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax T, Albers SV, Oeffinger M and Ferreira-Cerca S. Insights into molecular adaptation of KsgA/Dim1-dependent rRNA modifications in archaea. Nucl. Acids Res, https://doi.org/10.1093/nar/gkaa1268
  8. Oikonomopoulos S, Bayega A, Fahiminiya S, Djambazian H, Berube P, Ragoussis J. Methodologies for Transcript Profiling Using Long-Read Technologies. BMC Genomics, DOI: 10.1186/s12864-020-6672-3
  9. A.T. Molines, J. Lemière, C.H. Edrington, C.T. Hsu, I.E. Steinmark, K. Suhling, G. Goshima, L.J. Holt, G. J. Brouhard, F Chang. Physical properties of the cytoplasm modulate the rates of microtubule growth and shrinkage. BioRxiv, doi: https://doi.org/10.1101/2020.10.27.352716
  10. Louis-Philippe Bergeron-Sandoval, Sandeep Kumar, Hossein Khadivi Heris, Catherine L. A. Chang, Caitlin E. Cornell, Sarah L. Keller, Paul François, Adam G. Hendricks, Allen J. Ehrlicher, Rohit V. Pappu, Stephen W.Michnick. Proteins with prion-like domains can form viscoelastic condensates that enable membrane remodeling and endocytosis. BioRxiv, doi: https://doi.org/10.1101/145664
  11. Kapadia N, El-Hajj ZW, Reyes-Lamothe R. Bound2Learn: a machine learning approach for classification of DNA-bound proteins from single-molecule tracking experiments. Nucleic Acid Res,  doi:10.1093/nar/gkab186.
  12. Bensidoun P, Zenklusen D and Oeffinger M. Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export. WIREs RNA, https://doi.org/10.1002/wrna.1660
  13. Mérot C, Berdan E, Cayuela H, Djambazian H, Ferchaud AL, Laporte M, Normandeau E, Ragoussis J, Wellenreuther M, Bernatchez L. Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly. Mol Biol Evol, DOI: 10.1093/molbev/msab143
  14. Paulina-Carabajal, A., P. J. Currie, T. W. Dudgeon, H. C. E. Larsson, T. Miyashita. Two braincases of Daspletosaurus (Theropoda: Tyrannosauridae) from the Late Cretaceous of southern Alberta: anatomy and comparison. Canadian Journal of Earth Sciences, https://doi.org/10.1139/cjes-2020-0185

2020

  1. Reznikov N, Buss, DJ, Provencher B, McKee MD, Piché N. Deep learning for 3D imaging and image analysis in biomineralization research. Journal of Structural Biology 212 (2020). https://doi.org/10.1016/j.jsb.2020.107598
  2. Demers-Potvin A, Szwedo J, Paragnani C, Larsson H. 2020. First North American occurrence of hairy cicadas discovered in a Late Cretaceous (Cenomanian) exposure from Labrador, Canada. Acta Palaeontologica Polonica 65 (1): 85-98 doi:https://doi.org/10.4202/app.00669.2019
  3. LeBlanc ARH, Apesteguía S, Larsson HCE, Caldwell MW. 2020. Unique tooth morphology and prismatic enamel in Late Cretaceous sphenodontians from Argentina. Current Biology 30: 1755-1761.e2. https://doi.org/10.1016/j.cub.2020.02.071
  4. Bui H-N, Larsson HCE. 2020. Development and evolution of regionalization within the avian axial column. Zoological Journal of the Linnean Society, zlaa038, https://doi.org/10.1093/zoolinnean/zlaa038
  5. Oikonomopoulos S, Bayega A, Fahiminiya S, Djambazian H, Berube P and Ragoussis J (2020). Methodologies for Transcript Profiling Using Long-Read Technologies. Front. Genet. 11:606.
  6. Bayega A, Djambazian H, Tsoumani KT, Gregoriou ME, Sagri E, Drosopoulou E, Mavragani-Tsipidou P, Giorda K, Tsiamis G, Bourtzis K, Oikonomopoulos S, Dewar K, Church DM, Papanicolaou A, Mathiopoulos KD, Ragoussis J. De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly. BMC Genomics, March 2020. https://doi.org/10.1186/s12864-020-6672-3
  7. Kamila R. Mustafina, Yukiko Sato, John W. Hanrahan, Paul W. Wiseman: STED Superresolution Imaging of DUOX1 and CEN2 Reveals Substructure of Membrane Macromolecular Complexes in Human Bronchial Epithelial Cells. Biophysical Journal, Feb 2020, https://doi.org/10.1016/j.bpj.2019.11.928
  8. Laprade H, Querido E, Smith MJ, Guérit D, Crimmins H, Conomos D, Pourret E, Chartrand P, Sfeir A. Single-Molecule Imaging of Telomerase RNA Reveals a Recruitment-Retention Model for Telomere Elongation. Mol Cell. doi: 10.1016/j.molcel.2020.05.005

2019

  1. Soubry N, Wang A and Reyes-Lamothe R. Replisome activity slowdown after exposure to ultraviolet light in Escherichia coli. PNAS in press
  2. Hemery, M. & Francois, P. In Silico Evolution of Biochemical Log-Response. J Phys Chem B (2019). doi:10.1021/acs.jpcb.8b10974
  3. Kazarine, A. et al. Multimodal virtual histology of rabbit vocal folds by nonlinear microscopy and nano computed tomography. Biomedical Optics Express 10, 1151 (2019).
  4. Laflamme G., Sim S., Leary A., Pascariu M., Vogel J and D'amours D. Interphase microtubules safeguard mitotic progression by suppressing an aurora B-dependent arrest induced by DNA replication stress. Cell Reports 26, 2875, (2019)
  5. Fernando F. Garberoglio,, Sebastián Apesteguía, Tiago R. Simões, Alessandro Palci, Raúl O. Gómez, Randall L. Nydam, Hans C. E. Larsson, Michael S. Y. Lee and Michael W. Caldwell: New skulls and skeletons of the Cretaceous legged snake Najash, and the evolution of the modern snake body plan. Science Advances, 20 Nov 2019: Vol. 5, no. 11, eaax5833; DOI: 10.1126/sciadv.aax5833
  6. Laura M. HernandezElvis Genbo XuHans C. E. LarssonRui TaharaVimal B. MaisuriaNathalie Tufenkji: Plastic Teabags Release Billions of Microparticles and Nanoparticles into Tea; Environmental Science & Technology 2019 53 (21), 12300-12310, DOI: 10.1021/acs.est.9b02540
  7. Elvis Genbo Xu, Nicholas Lin, Rachel S. Cheong, Charlotte Ridsdale, Rui Tahara, Trina Y. Du, Dharani Das, Jiping Zhu, Laura Peña Silva, Agil Azimzada, Hans C. E. Larsson, and Nathalie Tufenkji: Artificial turf infill associated with systematic toxicity in an amniote vertebrate; PNAS December 10, 2019 116 (50) 25156-25161; https://doi.org/10.1073/pnas.1909886116
  8. Allen Leary, Shannon Sim, Elena Nazarova, Kristian Shulist, Rachel Genthial, Shun KaiYang, Khanh HuyBui, Paul Francois and Jackie Vogel: Successive Kinesin-5 Microtubule Crosslinking and Sliding Promote Fast, Irreversible Formation of a Stereotyped Bipolar Spindle; Curr Biol. 2019 Nov 18;29(22):3825-3837.e3. doi: 10.1016/j.cub.2019.09.030.
  9. Foret, M. K. et al. Effect of antioxidant supplements on lipid peroxidation levels in primary cortical neuron cultures. Free Radical Biology and Medicine 130, 471–477 (2019).
  10. Rosenbaum, B., Raatz, M., Weithoff, G., Fussmann, G. F. & Gaedke, U. Estimating parameters from multiple time series of population dynamics using Bayesian inference. Front. Ecol. Evol., 22 January 2019. https://doi.org/10.3389/fevo.2018.00234
  11. Tahara, R. & Larsson, H. C. E. Head pneumatic sinuses in Japanese quail and zebra finch. Jul 2019,  Zool J Linn Soc doi:10.1093/zoolinnean/zly089
  12. Razi, A. et al. Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit. bioRxiv 525360 (2019). doi:10.1101/525360
  13. Fowler DA, Larsson HCE. 2019. The benefits differential equations bring to limb development. WIREs Developmental Biology e364: 1–11. https://doi.org/10.1002/wdev.364
  14. Suzuki H, Kumar SA, Shuai S, Diaz-Navarro A, Gutierrez-Fernandez A, De Antonellis P, Cavalli FMG, Juraschka K, Farooq H, Shibahara I, Vladoiu MC, Zhang J, Abeysundara N, Przelicki D, Skowron P, Gauer N, Luu B, Daniels C, Wu X, Forget A, Momin A, Wang J, Dong W, Kim SK, Grajkowska WA, Jouvet A, Fevre-Montange M, Garre ML, Nageswara Rao AA, Giannini C, Kros JM, French PJ, Jabado N, Ng HK, Poon WS, Eberhart CG, Pollack IF, Olson JM, Weiss WA, Kumabe T, Lopez-Aguilar E, Lach B, Massimino M, Van Meir EG, Rubin JB, Vibhakar R, Chambless LB, Kijima N, Klekner A, Bognar L, Chan JA, Faria CC, Ragoussis J, Pfister SM, Goldenberg A, Wechsler-Reya RJ, Bailey SD, Garzia L, Morrissy AS, Marra MA, Huang X, Malkin D, Ayrault O, Ramaswamy V, Puente XS, Calarco JA, Stein L, Taylor MD. 2019. Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. Nature. https://doi.org/10.1038/s41586-019-1650-0
  15. Tahara R, Larsson HCE. 2019. Development of the paratympanic pneumatic system of Japanese quail. Journal of Morphology: 1-38. Doi: 10.1002/jmor.21045
  16. Lari A, Farzam F, Bensidoun P, Oeffinger M, Zenklusen D, Grunwald D, Montpetit B. Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast. Methods Mol Biol. doi: 10.1007/978-1-4939-9674-2_9

 

2018

  1. Bernier, F., Tahara, R. & Gendron, M. Additive manufacturing powder feedstock characterization using X-ray tomography. Metal Powder Report 73, 158–162 (2018).
  2. Rademaker, T. J., Bengio, E. & François, P. Attack and defence in cellular decision-making: lessons from machine learning. arXiv:1807.04270 [physics, q-bio, stat] (2018).
  3. Di Trani, J. M., Moitessier, N. & Mittermaier, A. K. Complete Kinetic Characterization of Enzyme Inhibition in a Single Isothermal Titration Calorimetric Experiment. Anal. Chem. 90, 8430–8435 (2018).
  4. Harrison, P. M. Compositionally Biased Dark Matter in the Protein Universe. PROTEOMICS 18, 1800069 (2018).
  5. Lee, S.-J., Kong, M., Harrison, P. & Hijri, M. Conserved Proteins of the RNA Interference System in the Arbuscular Mycorrhizal Fungus Rhizoglomus irregulare Provide New Insight into the Evolutionary History of Glomeromycota. Genome Biol Evol 10, 328–343 (2018).
  6. Bayega, A., Fahiminiya, S., Oikonomopoulos, S. & Ragoussis, J. Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing. Methods Mol. Biol. 1783, 209–241 (2018).
  7. Djambazian, H. et al. De novo genome assembly of the olive fruit fly (Bactrocera oleae) developed through a combination of linked-reads and long-read technologies. bioRxiv 505040 (2018). doi:10.1101/505040
  8. Narasumani, M. & Harrison, P. M. Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins. PLoS Comput. Biol. 14, e1006349 (2018).
  9. Pleše, P. et al. Dynamic observations of vesiculation reveal the role of silicate crystals in bubble nucleation and growth in andesitic magmas. Lithos 296, 532–546 (2018).
  10. Fowler, D. A., Filla, M. B., Little, C. D., Rongish, B. J. & Larsson, H. C. E. Live tissue antibody injection: A novel method for imaging ECM in limb buds and other tissues. Methods Cell Biol. 143, 41–56 (2018).
  11. Trcek, T., Rahman, S. & Zenklusen, D. Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH. Methods Mol. Biol. 1720, 35–54 (2018).
  12. Athanasiadou, D. et al. Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell. Science Advances 4, eaar3219 (2018).
  13. Hsu, C.-T., Brouhard, G. J. & Francois, P. Numerical parameter space compression and its application to microtubule dynamic instability. bioRxiv 475772 (2018). doi:10.1101/475772
  14. Trani, J. M. D. et al. Rapid measurement of inhibitor binding kinetics by isothermal titration calorimetry. Nature Communications 9, 893 (2018).
  15. Chaudhary, A. R., Berger, F., Berger, C. L. & Hendricks, A. G. Tau directs intracellular trafficking by regulating the forces exerted by kinesin and dynein teams. Traffic 19, 111–121 (2018).
  16. Chaaban, S. et al. The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth. Dev. Cell 47, 191-204.e8 (2018).
  17. Bayega, A. et al. Transcript Profiling Using Long-Read Sequencing Technologies. Methods Mol. Biol. 1783, 121–147 (2018).
  18. Hendricks, A. G. Viewpoint: Low Efficiency Spotted in a Molecular Motor. Physics 11, (2018).
  19. Lessard, F. et al. Senescence-associated ribosome biogenesis defects contributes to cell cycle arrest through the Rb pathway. Nature Cell Biology 20, 789 (2018).
  20. Adivarahan, S. et al. Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway. Mol. Cell 72, 727-738.e5 (2018).
  21. Lengefeld J. et al. Spatial cues and not spindle pole maturation drive the asymmetry of astral microtubules between new and preexisting spindle poles. Molecular Biology of the Cell 29, No. 1, 10-28 (2018)
  22. Leary, A, E Nazarova, S Sim, K Shulist, P Francois and J Vogel. Kinesin-5 forms a stable bipolar spindle in a fast, irreversible snap. doi: https://doi.org/10.1101/452821
  23. Portalier, S. M. J., Fussmann, G. F., Loreau, M. & Cherif, M. The mechanics of predator–prey interactions: First principles of physics predict predator–prey size ratios. Functional Ecology 33, 323–334 (2019).
  24. Greene, L. E., Lincoln, R. & Cosa, G. Tuning Photoinduced Electron Transfer Efficiency of Fluorogenic BODIPY-α-Tocopherol Analogues. Photochemistry and Photobiology 95, 192–201 (2018).
  25. Perez-Romero CA, Lalonde M, Chartrand P, Cusanelli E. Induction and relocalization of telomeric repeat-containing RNAs during diauxic shift in budding yeast. Curr Genet, Oct 18. doi: 10.1007/s00294-018-0829-5
  26. Avogaro L, Querido E, Dalachi M, Jantsch MF, Chartrand P, Cusanelli E. Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells. RNA Biol. doi: 10.1080/15476286.2018.1456300
  27. Louis-Philippe Bergeron-Sandoval, Hossein Khadivi Heris, Catherine Chang, Caitlin E. Cornell, Sarah L. Keller,  View ORCID ProfilePaul François, Adam G. Hendricks, Allen J. Ehrlicher, Rohit V. Pappu, Stephen W. Michnick. Endocytosis caused by liquid-liquid phase separation of proteins. BioRxiv. doi: https://doi.org/10.1101/145664 

 

2017

  1. King, B. R. et al. Visualization of the lymphocytic choriomeningitis mammarenavirus (LCMV) genome reveals the early endosome as a possible site for genome replication and viral particle pre-assembly. J. Gen. Virol. (2017). doi:10.1099/jgv.0.000930
  2. Vakiloroayaei, A., Shah, N. S., Oeffinger, M. & Bayfield, M. A. The RNA chaperone La promotes pre-tRNA maturation via indiscriminate binding of both native and misfolded targets. Nucleic Acids Res. 45, 11341–11355 (2017).
  3. Reimer, K. A. et al. The sole LSm complex in Cyanidioschyzon merolae associates with pre-mRNA splicing and mRNA degradation factors. RNA 23, 952–967 (2017).
  4. Scott, D. D. et al. Nol12 is a multifunctional RNA binding protein at the nexus of RNA and DNA metabolism. Nucleic Acids Res. 45, 12509–12528 (2017).
  5. Burlacu, E. et al. High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast. Nat Commun 8, 714 (2017).
  6. Harrison, P. M. fLPS: Fast discovery of compositional biases for the protein universe. BMC Bioinformatics 18, 476 (2017).
  7. Beattie, T. R. et al. Frequent exchange of the DNA polymerase during bacterial chromosome replication. eLife 6, e21763 (2017).
  8. Bergeron-Sandoval, L.-P. et al. Endocytosis caused by liquid-liquid phase separation of proteins. bioRxiv 145664 (2017). doi:10.1101/145664
  9. Joly-Lopez, Z. et al. Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements. Front Plant Sci 8, 2027 (2017).
  10. Shulist K. et al. Interrogation of ɣ-tubulin alleles using high-resolution fitness measurements reveals a distinct cytoplasmic function in spindle alignment. Scientific Reports 7:11398 (2017)
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