平特五不中

平特五不中.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.
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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,听
  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.
  3. Demers-Potvin, A., H. C. E. Larsson, M. Cournoyer, and O. B茅thoux.听Wing morphology of a new Cretaceous praying mantis solves the phylogenetic jigsaw of early鈥恉iverging extant lineages.听Systematic Entomology,听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.听Crystal structure of human PACRG in complex with MEIG1 reveals roles in axoneme formation and tubulin binding.听Structure,听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.听The first described turtle beetles from Eocene Baltic amber, with notes on fossil Chelonariidae. Foss.Rec,听
  6. Meziane, M. R. Genthial and J. Vogel.听Kar9 symmetry breaking alone is insufficient to ensure spindle alignment.听Sci. Reports 11,听DOI: 10.1038/s41598-021-83136-w
  7. Kn眉ppel R, Trahan C, Kern M, Wagner A, Gr眉nberger F, Hausner W, Quax T, Albers SV, Oeffinger M and Ferreira-Cerca S.听Insights into molecular adaptation of KsgA/Dim1-dependent rRNA modifications in archaea.听Nucl. Acids Res,听
  8. Oikonomopoulos S, Bayega A, Fahiminiya S, Djambazian H, Berube P, Ragoussis J.听Methodologies for Transcript Profiling Using Long-Read Technologies.听BMC Genomics,听DOI: 10.1186/s12864-020-6672-3
  9. A.T. Molines, J. Lemi猫re, C.H. Edrington, C.T. Hsu, I.E. Steinmark, K. Suhling, G. Goshima, L.J. Holt, G. J. Brouhard, F Chang.听Physical properties of the cytoplasm modulate the rates of microtubule growth and shrinkage. BioRxiv,听doi:
  10. Louis-Philippe Bergeron-Sandoval, Sandeep Kumar, Hossein Khadivi Heris, Catherine L. A. Chang, Caitlin E. Cornell, Sarah L. Keller, Paul Fran莽ois, Adam G. Hendricks, Allen J. Ehrlicher, Rohit V. Pappu, Stephen W.Michnick.听Proteins with prion-like domains can form viscoelastic condensates that enable membrane remodeling and endocytosis.听BioRxiv,听doi:
  11. Kapadia N, El-Hajj ZW, Reyes-Lamothe R.听Bound2Learn: a machine learning approach for classification of DNA-bound proteins from single-molecule tracking experiments.听Nucleic Acid Res, 听doi:10.1093/nar/gkab186.
  12. Bensidoun P, Zenklusen D听and Oeffinger M.听Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export.听WIREs RNA,听
  13. M茅rot C, Berdan E, Cayuela H, Djambazian H, Ferchaud AL, Laporte M, Normandeau E, Ragoussis J, Wellenreuther M, Bernatchez L.听Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly.听Mol Biol Evol,听DOI: 10.1093/molbev/msab143
  14. Paulina-Carabajal, A., P. J. Currie, T. W. Dudgeon, H. C. E. Larsson, T. Miyashita.听Two braincases of Daspletosaurus (Theropoda: Tyrannosauridae) from the Late Cretaceous of southern Alberta: anatomy and comparison.听Canadian Journal of Earth Sciences,听

2020

  1. Reznikov N, Buss, DJ, Provencher B, McKee MD, Pich茅 N.听Deep learning for 3D imaging and image analysis in biomineralization research.听Journal of Structural Biology 212 (2020).听
  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:
  3. LeBlanc ARH, Apestegu铆a S, Larsson HCE, Caldwell MW. 2020. Unique tooth morphology and prismatic enamel in Late Cretaceous sphenodontians from Argentina. Current Biology 30: 1755-1761.e2.
  4. Bui H-N, Larsson HCE. 2020. Development and evolution of regionalization within the avian axial column. Zoological Journal of the Linnean Society, zlaa038,
  5. Oikonomopoulos S, Bayega A, Fahiminiya S, Djambazian H, Berube P and Ragoussis J (2020).听Methodologies for Transcript Profiling Using Long-Read Technologies.听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.听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.听BMC Genomics, March 2020.听
  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.听Biophysical Journal, Feb 2020,听
  8. Laprade H, Querido E, Smith MJ, Gu茅rit D, Crimmins H, Conomos D, Pourret E,听Chartrand P, Sfeir A.听Single-Molecule Imaging of Telomerase RNA Reveals a Recruitment-Retention Model for Telomere Elongation.听Mol Cell.听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,, Sebasti谩n Apestegu铆a, Tiago R. Sim玫es, Alessandro Palci, Ra煤l O. G贸mez, 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 Pe帽a 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;
  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鈥�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.
  11. Tahara, R. & Larsson, H. C. E. Head pneumatic sinuses in Japanese quail and zebra finch. Jul 2019, 听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鈥�11.
  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.听Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma.听Nature.听
  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,听Zenklusen D, Grunwald D, Montpetit B.听Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast.听Methods Mol Biol.听doi: 10.1007/978-1-4939-9674-2_9

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2018

  1. Bernier, F., Tahara, R. & Gendron, M. Additive manufacturing powder feedstock characterization using X-ray tomography. Metal Powder Report 73, 158鈥�162 (2018).
  2. Rademaker, T. J., Bengio, E. & Fran莽ois, 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鈥�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鈥�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鈥�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. Ple拧e, P. et al. Dynamic observations of vesiculation reveal the role of silicate crystals in bubble nucleation and growth in andesitic magmas. Lithos 296, 532鈥�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鈥�56 (2018).
  11. Trcek, T., Rahman, S. & Zenklusen, D. Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH. Methods Mol. Biol. 1720, 35鈥�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鈥�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鈥�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:听
  23. Portalier, S. M. J., Fussmann, G. F., Loreau, M. & Cherif, M. The mechanics of predator鈥損rey interactions: First principles of physics predict predator鈥損rey size ratios. Functional Ecology 33, 323鈥�334 (2019).
  24. Greene, L. E., Lincoln, R. & Cosa, G. Tuning Photoinduced Electron Transfer Efficiency of Fluorogenic BODIPY-伪-Tocopherol Analogues. Photochemistry and Photobiology 95, 192鈥�201 (2018).
  25. Perez-Romero CA, Lalonde M, Chartrand P, Cusanelli E.听Induction and relocalization of telomeric repeat-containing RNAs during diauxic shift in budding yeast. Curr Genet, Oct 18.听doi: 10.1007/s00294-018-0829-5
  26. Avogaro L, Querido E, Dalachi M, Jantsch MF, Chartrand P, Cusanelli E.听Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells.听RNA Biol.听doi: 10.1080/15476286.2018.1456300
  27. Louis-Philippe听Bergeron-Sandoval,听Hossein Khadivi听Heris,听Catherine听Chang,听Caitlin E.听Cornell,听Sarah L.听Keller,听听View ORCID ProfilePaul听Fran莽ois,听Adam G.听Hendricks,听Allen J.听Ehrlicher,听Rohit V.听Pappu,听Stephen W.听Michnick.听Endocytosis caused by liquid-liquid phase separation of proteins.听BioRxiv.听doi:听听

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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鈥�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鈥�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鈥�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 桑-tubulin alleles using high-resolution fitness measurements reveals a distinct cytoplasmic function in spindle alignment. Scientific Reports 7:11398 (2017)
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